Starting phenix.real_space_refine on Sat Aug 23 13:50:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ucs_42139/08_2025/8ucs_42139.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ucs_42139/08_2025/8ucs_42139.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ucs_42139/08_2025/8ucs_42139.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ucs_42139/08_2025/8ucs_42139.map" model { file = "/net/cci-nas-00/data/ceres_data/8ucs_42139/08_2025/8ucs_42139.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ucs_42139/08_2025/8ucs_42139.cif" } resolution = 2.4 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= 0.001 sd= 0.073 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 102 5.16 5 C 8038 2.51 5 N 2087 2.21 5 O 2378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12605 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 362 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 45, 354 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} Conformer: "B" Number of residues, atoms: 45, 354 Classifications: {'peptide': 45} Link IDs: {'TRANS': 44} bond proxies already assigned to first conformer: 351 Chain: "B" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 394 Classifications: {'peptide': 50} Link IDs: {'TRANS': 49} Chain: "C" Number of atoms: 1942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1942 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain: "D" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1978 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "E" Number of atoms: 1942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1942 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain: "F" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1978 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain: "G" Number of atoms: 1943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1943 Classifications: {'peptide': 253} Link IDs: {'PTRANS': 8, 'TRANS': 244} Chain: "H" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 688 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "I" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 688 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "J" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 688 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.74, per 1000 atoms: 0.22 Number of scatterers: 12605 At special positions: 0 Unit cell: (98.406, 114.345, 127.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 102 16.00 O 2378 8.00 N 2087 7.00 C 8038 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 0.91 Conformation dependent library (CDL) restraints added in 474.8 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2996 Finding SS restraints... Secondary structure from input PDB file: 89 helices and 1 sheets defined 86.6% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 19 through 40 removed outlier: 3.799A pdb=" N PHE A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A 34 " --> pdb=" O LEU A 30 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 60 Processing helix chain 'B' and resid 17 through 40 removed outlier: 4.131A pdb=" N ALA B 21 " --> pdb=" O ASP B 17 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N PHE B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 60 Processing helix chain 'C' and resid 8 through 24 removed outlier: 3.608A pdb=" N VAL C 13 " --> pdb=" O PRO C 9 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.571A pdb=" N VAL C 32 " --> pdb=" O ASN C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 54 Processing helix chain 'C' and resid 57 through 72 removed outlier: 3.799A pdb=" N LYS C 71 " --> pdb=" O ARG C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 95 removed outlier: 3.609A pdb=" N ARG C 93 " --> pdb=" O ARG C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 99 through 105 removed outlier: 3.550A pdb=" N ASN C 105 " --> pdb=" O ASP C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 123 through 174 Proline residue: C 157 - end of helix Processing helix chain 'C' and resid 177 through 189 removed outlier: 3.671A pdb=" N GLY C 186 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 202 Processing helix chain 'C' and resid 202 through 233 removed outlier: 4.177A pdb=" N GLY C 227 " --> pdb=" O MET C 223 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ALA C 230 " --> pdb=" O GLU C 226 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN C 232 " --> pdb=" O VAL C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 245 Processing helix chain 'C' and resid 249 through 258 Processing helix chain 'D' and resid 6 through 24 Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 35 through 42 Processing helix chain 'D' and resid 42 through 54 Processing helix chain 'D' and resid 55 through 70 removed outlier: 3.608A pdb=" N PHE D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 95 removed outlier: 3.662A pdb=" N ILE D 81 " --> pdb=" O ASN D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 121 Processing helix chain 'D' and resid 123 through 174 Proline residue: D 157 - end of helix Processing helix chain 'D' and resid 177 through 202 removed outlier: 3.678A pdb=" N THR D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 233 Processing helix chain 'D' and resid 239 through 245 removed outlier: 3.740A pdb=" N VAL D 245 " --> pdb=" O GLU D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 246 through 248 No H-bonds generated for 'chain 'D' and resid 246 through 248' Processing helix chain 'D' and resid 249 through 258 removed outlier: 4.454A pdb=" N GLN D 254 " --> pdb=" O PRO D 250 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ALA D 255 " --> pdb=" O PRO D 251 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LYS D 258 " --> pdb=" O GLN D 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 24 removed outlier: 3.742A pdb=" N VAL E 13 " --> pdb=" O PRO E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 removed outlier: 3.764A pdb=" N VAL E 32 " --> pdb=" O ASN E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 54 removed outlier: 3.514A pdb=" N PHE E 40 " --> pdb=" O VAL E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 70 removed outlier: 3.603A pdb=" N PHE E 70 " --> pdb=" O ILE E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 94 Processing helix chain 'E' and resid 100 through 105 removed outlier: 3.543A pdb=" N ASN E 104 " --> pdb=" O GLU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 119 Processing helix chain 'E' and resid 123 through 174 Proline residue: E 157 - end of helix removed outlier: 3.521A pdb=" N ASN E 174 " --> pdb=" O GLN E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 180 through 189 Processing helix chain 'E' and resid 189 through 202 Processing helix chain 'E' and resid 202 through 234 Processing helix chain 'E' and resid 236 through 246 removed outlier: 3.649A pdb=" N SER E 246 " --> pdb=" O GLU E 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 258 Processing helix chain 'F' and resid 6 through 24 Processing helix chain 'F' and resid 29 through 34 Processing helix chain 'F' and resid 35 through 54 removed outlier: 3.618A pdb=" N GLY F 44 " --> pdb=" O PHE F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 70 Processing helix chain 'F' and resid 76 through 95 Processing helix chain 'F' and resid 96 through 98 No H-bonds generated for 'chain 'F' and resid 96 through 98' Processing helix chain 'F' and resid 99 through 105 removed outlier: 3.548A pdb=" N ASN F 105 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing helix chain 'F' and resid 108 through 121 Processing helix chain 'F' and resid 123 through 174 Proline residue: F 157 - end of helix removed outlier: 3.580A pdb=" N ASN F 174 " --> pdb=" O GLN F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 202 removed outlier: 3.654A pdb=" N THR F 192 " --> pdb=" O ALA F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 234 Processing helix chain 'F' and resid 238 through 245 removed outlier: 3.611A pdb=" N GLU F 242 " --> pdb=" O ARG F 238 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 248 No H-bonds generated for 'chain 'F' and resid 246 through 248' Processing helix chain 'F' and resid 249 through 254 removed outlier: 4.193A pdb=" N GLN F 254 " --> pdb=" O PRO F 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 26 removed outlier: 3.745A pdb=" N GLY G 26 " --> pdb=" O GLY G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 35 through 54 Processing helix chain 'G' and resid 55 through 72 removed outlier: 3.581A pdb=" N PHE G 70 " --> pdb=" O ILE G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 94 Processing helix chain 'G' and resid 95 through 98 removed outlier: 3.589A pdb=" N SER G 98 " --> pdb=" O GLY G 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 95 through 98' Processing helix chain 'G' and resid 99 through 105 Processing helix chain 'G' and resid 111 through 120 removed outlier: 3.643A pdb=" N VAL G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 174 Proline residue: G 157 - end of helix Processing helix chain 'G' and resid 177 through 179 No H-bonds generated for 'chain 'G' and resid 177 through 179' Processing helix chain 'G' and resid 180 through 189 Processing helix chain 'G' and resid 189 through 202 Processing helix chain 'G' and resid 202 through 233 Processing helix chain 'G' and resid 236 through 246 removed outlier: 3.884A pdb=" N SER G 246 " --> pdb=" O GLU G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 249 through 260 removed outlier: 3.520A pdb=" N GLN G 254 " --> pdb=" O PRO G 250 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL G 259 " --> pdb=" O ALA G 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 255 Processing helix chain 'H' and resid 259 through 266 removed outlier: 3.531A pdb=" N ALA H 264 " --> pdb=" O THR H 260 " (cutoff:3.500A) Processing helix chain 'H' and resid 271 through 280 Processing helix chain 'H' and resid 283 through 295 Processing helix chain 'H' and resid 304 through 320 Processing helix chain 'I' and resid 239 through 244 removed outlier: 4.130A pdb=" N ILE I 244 " --> pdb=" O GLU I 241 " (cutoff:3.500A) Processing helix chain 'I' and resid 247 through 256 removed outlier: 3.539A pdb=" N ARG I 253 " --> pdb=" O VAL I 249 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL I 254 " --> pdb=" O ALA I 250 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ARG I 256 " --> pdb=" O GLN I 252 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 268 removed outlier: 3.835A pdb=" N LYS I 268 " --> pdb=" O ALA I 264 " (cutoff:3.500A) Processing helix chain 'I' and resid 271 through 281 removed outlier: 3.665A pdb=" N ALA I 275 " --> pdb=" O SER I 271 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL I 277 " --> pdb=" O GLU I 273 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN I 281 " --> pdb=" O VAL I 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 296 Processing helix chain 'I' and resid 301 through 319 removed outlier: 3.573A pdb=" N GLN I 310 " --> pdb=" O GLU I 306 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY I 311 " --> pdb=" O LYS I 307 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE I 316 " --> pdb=" O ILE I 312 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG I 317 " --> pdb=" O VAL I 313 " (cutoff:3.500A) Processing helix chain 'J' and resid 247 through 256 removed outlier: 3.787A pdb=" N GLN J 252 " --> pdb=" O ASP J 248 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG J 253 " --> pdb=" O VAL J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 268 removed outlier: 3.562A pdb=" N LYS J 268 " --> pdb=" O ALA J 264 " (cutoff:3.500A) Processing helix chain 'J' and resid 271 through 279 Processing helix chain 'J' and resid 283 through 298 removed outlier: 3.733A pdb=" N SER J 288 " --> pdb=" O LYS J 284 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU J 292 " --> pdb=" O SER J 288 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU J 295 " --> pdb=" O LYS J 291 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLY J 298 " --> pdb=" O ILE J 294 " (cutoff:3.500A) Processing helix chain 'J' and resid 302 through 319 removed outlier: 4.138A pdb=" N GLU J 306 " --> pdb=" O ILE J 302 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS J 307 " --> pdb=" O MET J 303 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE J 316 " --> pdb=" O ILE J 312 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 43 991 hydrogen bonds defined for protein. 2928 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: 1.56 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4116 1.34 - 1.46: 2682 1.46 - 1.58: 5786 1.58 - 1.70: 0 1.70 - 1.81: 199 Bond restraints: 12783 Sorted by residual: bond pdb=" CB GLU I 292 " pdb=" CG GLU I 292 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.14e+00 bond pdb=" CB ASP J 293 " pdb=" CG ASP J 293 " ideal model delta sigma weight residual 1.516 1.541 -0.025 2.50e-02 1.60e+03 9.72e-01 bond pdb=" CB MET H 303 " pdb=" CG MET H 303 " ideal model delta sigma weight residual 1.520 1.549 -0.029 3.00e-02 1.11e+03 9.62e-01 bond pdb=" CB ASP F 86 " pdb=" CG ASP F 86 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.39e-01 bond pdb=" CB ASP I 262 " pdb=" CG ASP I 262 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.26e-01 ... (remaining 12778 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 17026 1.81 - 3.63: 147 3.63 - 5.44: 43 5.44 - 7.25: 6 7.25 - 9.06: 3 Bond angle restraints: 17225 Sorted by residual: angle pdb=" CA MET H 303 " pdb=" CB MET H 303 " pdb=" CG MET H 303 " ideal model delta sigma weight residual 114.10 121.90 -7.80 2.00e+00 2.50e-01 1.52e+01 angle pdb=" CB MET H 303 " pdb=" CG MET H 303 " pdb=" SD MET H 303 " ideal model delta sigma weight residual 112.70 121.76 -9.06 3.00e+00 1.11e-01 9.13e+00 angle pdb=" N ILE F 6 " pdb=" CA ILE F 6 " pdb=" C ILE F 6 " ideal model delta sigma weight residual 113.10 110.36 2.74 9.70e-01 1.06e+00 7.98e+00 angle pdb=" CA GLU J 273 " pdb=" CB GLU J 273 " pdb=" CG GLU J 273 " ideal model delta sigma weight residual 114.10 119.62 -5.52 2.00e+00 2.50e-01 7.62e+00 angle pdb=" C ASP E 108 " pdb=" N ASP E 109 " pdb=" CA ASP E 109 " ideal model delta sigma weight residual 121.54 126.71 -5.17 1.91e+00 2.74e-01 7.33e+00 ... (remaining 17220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 6588 17.83 - 35.66: 852 35.66 - 53.48: 260 53.48 - 71.31: 55 71.31 - 89.14: 19 Dihedral angle restraints: 7774 sinusoidal: 3122 harmonic: 4652 Sorted by residual: dihedral pdb=" CA GLY C 227 " pdb=" C GLY C 227 " pdb=" N VAL C 228 " pdb=" CA VAL C 228 " ideal model delta harmonic sigma weight residual 180.00 161.09 18.91 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA VAL D 202 " pdb=" C VAL D 202 " pdb=" N PHE D 203 " pdb=" CA PHE D 203 " ideal model delta harmonic sigma weight residual -180.00 -161.48 -18.52 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA VAL F 202 " pdb=" C VAL F 202 " pdb=" N PHE F 203 " pdb=" CA PHE F 203 " ideal model delta harmonic sigma weight residual -180.00 -161.56 -18.44 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 7771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1473 0.037 - 0.074: 450 0.074 - 0.111: 81 0.111 - 0.148: 7 0.148 - 0.185: 1 Chirality restraints: 2012 Sorted by residual: chirality pdb=" CA THR F 8 " pdb=" N THR F 8 " pdb=" C THR F 8 " pdb=" CB THR F 8 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.56e-01 chirality pdb=" CG LEU E 172 " pdb=" CB LEU E 172 " pdb=" CD1 LEU E 172 " pdb=" CD2 LEU E 172 " both_signs ideal model delta sigma weight residual False -2.59 -2.72 0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE C 122 " pdb=" N ILE C 122 " pdb=" C ILE C 122 " pdb=" CB ILE C 122 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 2009 not shown) Planarity restraints: 2184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET H 303 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" C MET H 303 " -0.040 2.00e-02 2.50e+03 pdb=" O MET H 303 " 0.015 2.00e-02 2.50e+03 pdb=" N ASP H 304 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN E 236 " -0.034 5.00e-02 4.00e+02 5.13e-02 4.21e+00 pdb=" N PRO E 237 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO E 237 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 237 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 250 " 0.028 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO C 251 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 251 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO C 251 " 0.024 5.00e-02 4.00e+02 ... (remaining 2181 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2490 2.77 - 3.30: 12723 3.30 - 3.83: 22411 3.83 - 4.37: 26233 4.37 - 4.90: 43397 Nonbonded interactions: 107254 Sorted by model distance: nonbonded pdb=" NH2 ARG C 238 " pdb=" OD2 ASP D 120 " model vdw 2.235 3.120 nonbonded pdb=" O GLY G 95 " pdb=" OG SER G 98 " model vdw 2.260 3.040 nonbonded pdb=" O GLY F 95 " pdb=" OG SER F 98 " model vdw 2.271 3.040 nonbonded pdb=" O ARG H 253 " pdb=" NH1 ARG H 253 " model vdw 2.274 3.120 nonbonded pdb=" O GLY D 22 " pdb=" OG SER D 25 " model vdw 2.281 3.040 ... (remaining 107249 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 16 through 32 or resid 34 through 60)) selection = (chain 'B' and (resid 16 through 32 or resid 34 through 60)) } ncs_group { reference = (chain 'C' and resid 8 through 259) selection = (chain 'D' and resid 8 through 259) selection = (chain 'E' and resid 8 through 259) selection = (chain 'F' and resid 8 through 259) selection = (chain 'G' and resid 8 through 259) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } 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=0.37 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: 5.670 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: 0.000 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 10.420 Find NCS groups from input model: 0.150 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:8.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12783 Z= 0.105 Angle : 0.485 9.064 17225 Z= 0.253 Chirality : 0.036 0.185 2012 Planarity : 0.004 0.051 2184 Dihedral : 18.156 89.141 4778 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.36 % Allowed : 28.89 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.20), residues: 1613 helix: 0.70 (0.14), residues: 1354 sheet: None (None), residues: 0 loop : -0.95 (0.39), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 317 TYR 0.006 0.001 TYR F 256 PHE 0.016 0.001 PHE C 59 TRP 0.017 0.001 TRP E 21 HIS 0.001 0.000 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00252 (12783) covalent geometry : angle 0.48520 (17225) hydrogen bonds : bond 0.21686 ( 991) hydrogen bonds : angle 7.31428 ( 2928) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 250 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: D 223 MET cc_start: 0.8604 (ptm) cc_final: 0.8391 (ptt) REVERT: F 104 ASN cc_start: 0.7700 (m-40) cc_final: 0.7267 (m110) REVERT: F 108 ASP cc_start: 0.7627 (t70) cc_final: 0.7171 (t70) outliers start: 4 outliers final: 4 residues processed: 253 average time/residue: 0.6073 time to fit residues: 165.7169 Evaluate side-chains 237 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 233 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain F residue 14 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.3980 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 29 ASN D 29 ASN J 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.198669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.129264 restraints weight = 12309.071| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.78 r_work: 0.3179 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3001 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12783 Z= 0.148 Angle : 0.548 7.566 17225 Z= 0.299 Chirality : 0.040 0.167 2012 Planarity : 0.005 0.049 2184 Dihedral : 4.804 52.718 1743 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.37 % Allowed : 25.04 % Favored : 70.60 % 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 aren not related in a simple way. whole: 1.65 (0.21), residues: 1613 helix: 1.48 (0.14), residues: 1378 sheet: None (None), residues: 0 loop : -0.96 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 238 TYR 0.009 0.001 TYR F 110 PHE 0.023 0.002 PHE B 48 TRP 0.009 0.001 TRP B 19 HIS 0.001 0.001 HIS G 142 Details of bonding type rmsd covalent geometry : bond 0.00317 (12783) covalent geometry : angle 0.54793 (17225) hydrogen bonds : bond 0.05148 ( 991) hydrogen bonds : angle 4.53180 ( 2928) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 258 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 47 LYS cc_start: 0.7677 (tmtt) cc_final: 0.7000 (mttm) REVERT: B 56 GLN cc_start: 0.7384 (mt0) cc_final: 0.7180 (mm-40) REVERT: C 68 GLN cc_start: 0.7081 (tm-30) cc_final: 0.6566 (tm-30) REVERT: C 72 ASP cc_start: 0.5765 (OUTLIER) cc_final: 0.4993 (p0) REVERT: C 187 LYS cc_start: 0.8388 (mppt) cc_final: 0.7516 (mmtt) REVERT: D 35 ASP cc_start: 0.9091 (t70) cc_final: 0.8891 (t70) REVERT: F 14 LEU cc_start: 0.8352 (mt) cc_final: 0.7995 (tp) REVERT: F 108 ASP cc_start: 0.7515 (t70) cc_final: 0.7089 (t70) REVERT: F 129 GLU cc_start: 0.7491 (tm-30) cc_final: 0.7247 (pt0) REVERT: G 56 MET cc_start: 0.7604 (tpt) cc_final: 0.7365 (mmp) REVERT: G 141 ARG cc_start: 0.8109 (mtm-85) cc_final: 0.7702 (mtm110) outliers start: 59 outliers final: 17 residues processed: 288 average time/residue: 0.5352 time to fit residues: 166.5509 Evaluate side-chains 262 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 244 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain C residue 36 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain I residue 318 ARG Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 64 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 146 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN D 29 ASN F 254 GLN G 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.196536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.127447 restraints weight = 12116.189| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.81 r_work: 0.3147 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12783 Z= 0.182 Angle : 0.566 8.467 17225 Z= 0.306 Chirality : 0.041 0.168 2012 Planarity : 0.005 0.050 2184 Dihedral : 4.671 56.298 1737 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.73 % Allowed : 24.53 % Favored : 70.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.21), residues: 1613 helix: 1.51 (0.14), residues: 1383 sheet: None (None), residues: 0 loop : -1.09 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 61 TYR 0.008 0.002 TYR E 110 PHE 0.025 0.002 PHE B 48 TRP 0.011 0.001 TRP B 19 HIS 0.002 0.001 HIS G 142 Details of bonding type rmsd covalent geometry : bond 0.00417 (12783) covalent geometry : angle 0.56558 (17225) hydrogen bonds : bond 0.05280 ( 991) hydrogen bonds : angle 4.45984 ( 2928) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 240 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7572 (tp40) REVERT: B 47 LYS cc_start: 0.7716 (tmtt) cc_final: 0.7000 (mttm) REVERT: B 56 GLN cc_start: 0.7468 (mm-40) cc_final: 0.7215 (mm-40) REVERT: C 68 GLN cc_start: 0.7058 (tm-30) cc_final: 0.6561 (tm-30) REVERT: C 72 ASP cc_start: 0.5523 (OUTLIER) cc_final: 0.4742 (p0) REVERT: C 185 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.8045 (mpt) REVERT: C 187 LYS cc_start: 0.8435 (mppt) cc_final: 0.7548 (mmtm) REVERT: E 112 LYS cc_start: 0.7389 (OUTLIER) cc_final: 0.7097 (mtpt) REVERT: F 14 LEU cc_start: 0.8373 (mt) cc_final: 0.8032 (tp) REVERT: F 108 ASP cc_start: 0.7542 (t70) cc_final: 0.7106 (t70) REVERT: G 129 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6655 (mp0) REVERT: G 141 ARG cc_start: 0.8088 (mtm-85) cc_final: 0.7720 (mtm110) REVERT: J 303 MET cc_start: 0.6362 (ttt) cc_final: 0.6087 (mpt) outliers start: 64 outliers final: 28 residues processed: 283 average time/residue: 0.6964 time to fit residues: 212.1476 Evaluate side-chains 271 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 MET Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 185 MET Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 112 LYS Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain I residue 318 ARG Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain J residue 288 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 5 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 53 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN F 254 GLN G 68 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.198704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.128890 restraints weight = 16003.353| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.20 r_work: 0.3139 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12783 Z= 0.136 Angle : 0.518 7.601 17225 Z= 0.279 Chirality : 0.039 0.160 2012 Planarity : 0.005 0.049 2184 Dihedral : 4.508 52.884 1737 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.29 % Allowed : 25.04 % Favored : 70.67 % 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 aren not related in a simple way. whole: 1.97 (0.21), residues: 1613 helix: 1.72 (0.14), residues: 1381 sheet: None (None), residues: 0 loop : -1.16 (0.41), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 61 TYR 0.009 0.001 TYR F 110 PHE 0.022 0.002 PHE B 48 TRP 0.010 0.001 TRP B 19 HIS 0.001 0.000 HIS G 142 Details of bonding type rmsd covalent geometry : bond 0.00295 (12783) covalent geometry : angle 0.51759 (17225) hydrogen bonds : bond 0.04456 ( 991) hydrogen bonds : angle 4.18739 ( 2928) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 251 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7944 (OUTLIER) cc_final: 0.7592 (tp40) REVERT: B 47 LYS cc_start: 0.7637 (tmtt) cc_final: 0.6933 (mttm) REVERT: B 55 MET cc_start: 0.8017 (OUTLIER) cc_final: 0.7766 (ttm) REVERT: B 56 GLN cc_start: 0.7414 (mm-40) cc_final: 0.7118 (mm-40) REVERT: C 68 GLN cc_start: 0.6969 (tm-30) cc_final: 0.6489 (tm-30) REVERT: C 72 ASP cc_start: 0.5295 (OUTLIER) cc_final: 0.4569 (p0) REVERT: C 187 LYS cc_start: 0.8450 (mppt) cc_final: 0.7550 (mmtm) REVERT: D 35 ASP cc_start: 0.9125 (t70) cc_final: 0.8902 (t70) REVERT: D 177 ASP cc_start: 0.7725 (t0) cc_final: 0.7337 (t0) REVERT: F 14 LEU cc_start: 0.8383 (mt) cc_final: 0.8017 (tp) REVERT: G 56 MET cc_start: 0.7630 (tpt) cc_final: 0.7408 (mmp) REVERT: G 129 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.6614 (mp0) REVERT: G 141 ARG cc_start: 0.8078 (mtm-85) cc_final: 0.7726 (mtm110) REVERT: J 303 MET cc_start: 0.6407 (ttt) cc_final: 0.6067 (mpt) outliers start: 58 outliers final: 23 residues processed: 290 average time/residue: 0.7020 time to fit residues: 219.2964 Evaluate side-chains 266 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 239 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain J residue 249 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 67 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 129 optimal weight: 1.9990 chunk 121 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 111 optimal weight: 0.0980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN F 254 GLN G 68 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.198589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.129045 restraints weight = 12499.340| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.91 r_work: 0.3194 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12783 Z= 0.131 Angle : 0.510 7.560 17225 Z= 0.275 Chirality : 0.038 0.162 2012 Planarity : 0.004 0.050 2184 Dihedral : 4.461 53.632 1737 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 4.44 % Allowed : 25.04 % Favored : 70.52 % 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 aren not related in a simple way. whole: 2.12 (0.21), residues: 1613 helix: 1.81 (0.14), residues: 1385 sheet: None (None), residues: 0 loop : -1.06 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 61 TYR 0.009 0.001 TYR F 110 PHE 0.022 0.002 PHE B 48 TRP 0.010 0.001 TRP B 19 HIS 0.001 0.000 HIS G 142 Details of bonding type rmsd covalent geometry : bond 0.00283 (12783) covalent geometry : angle 0.50965 (17225) hydrogen bonds : bond 0.04318 ( 991) hydrogen bonds : angle 4.11475 ( 2928) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 239 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7929 (OUTLIER) cc_final: 0.7558 (tp40) REVERT: B 47 LYS cc_start: 0.7681 (tmtt) cc_final: 0.7036 (mttm) REVERT: B 55 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7715 (ttm) REVERT: B 56 GLN cc_start: 0.7419 (mm-40) cc_final: 0.7106 (mm-40) REVERT: C 68 GLN cc_start: 0.6928 (tm-30) cc_final: 0.6515 (tm-30) REVERT: C 72 ASP cc_start: 0.5266 (OUTLIER) cc_final: 0.4543 (p0) REVERT: C 187 LYS cc_start: 0.8435 (mppt) cc_final: 0.7548 (mmtm) REVERT: D 35 ASP cc_start: 0.9116 (t70) cc_final: 0.8898 (t70) REVERT: D 177 ASP cc_start: 0.7718 (t0) cc_final: 0.7356 (t0) REVERT: F 14 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8011 (tp) REVERT: F 108 ASP cc_start: 0.7585 (t70) cc_final: 0.7130 (t70) REVERT: G 129 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6614 (mp0) REVERT: G 141 ARG cc_start: 0.8063 (mtm-85) cc_final: 0.7703 (mtm110) REVERT: J 303 MET cc_start: 0.6437 (ttt) cc_final: 0.6095 (mpt) outliers start: 60 outliers final: 30 residues processed: 280 average time/residue: 0.6877 time to fit residues: 207.4176 Evaluate side-chains 272 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 237 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 318 ARG Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain J residue 271 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 51 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 154 optimal weight: 0.2980 chunk 136 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN F 254 GLN G 68 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.197769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.128915 restraints weight = 12830.199| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 2.02 r_work: 0.3155 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2991 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2991 r_free = 0.2991 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2991 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12783 Z= 0.144 Angle : 0.526 8.157 17225 Z= 0.283 Chirality : 0.039 0.166 2012 Planarity : 0.005 0.051 2184 Dihedral : 4.528 55.865 1737 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.44 % Allowed : 25.25 % Favored : 70.31 % 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 aren not related in a simple way. whole: 2.09 (0.21), residues: 1613 helix: 1.79 (0.14), residues: 1387 sheet: None (None), residues: 0 loop : -1.02 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 61 TYR 0.009 0.001 TYR F 110 PHE 0.023 0.002 PHE B 48 TRP 0.010 0.001 TRP B 19 HIS 0.002 0.001 HIS G 142 Details of bonding type rmsd covalent geometry : bond 0.00320 (12783) covalent geometry : angle 0.52550 (17225) hydrogen bonds : bond 0.04503 ( 991) hydrogen bonds : angle 4.15612 ( 2928) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 237 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7543 (tp40) REVERT: B 47 LYS cc_start: 0.7692 (tmtt) cc_final: 0.7002 (mttm) REVERT: B 55 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7685 (mtt) REVERT: B 56 GLN cc_start: 0.7433 (mm-40) cc_final: 0.7112 (mm-40) REVERT: C 61 ARG cc_start: 0.7404 (ttp80) cc_final: 0.7042 (ttt180) REVERT: C 68 GLN cc_start: 0.6881 (tm-30) cc_final: 0.6436 (tm-30) REVERT: C 72 ASP cc_start: 0.5203 (OUTLIER) cc_final: 0.4463 (p0) REVERT: C 92 ARG cc_start: 0.7742 (mtp85) cc_final: 0.7349 (mtt-85) REVERT: C 187 LYS cc_start: 0.8456 (mppt) cc_final: 0.7543 (mmtm) REVERT: D 35 ASP cc_start: 0.9136 (t70) cc_final: 0.8893 (t70) REVERT: D 177 ASP cc_start: 0.7724 (t0) cc_final: 0.7464 (t0) REVERT: F 14 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8006 (tp) REVERT: F 59 PHE cc_start: 0.8480 (t80) cc_final: 0.8266 (t80) REVERT: F 108 ASP cc_start: 0.7584 (t70) cc_final: 0.7116 (t70) REVERT: G 129 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: G 141 ARG cc_start: 0.8092 (mtm-85) cc_final: 0.7679 (mtm110) REVERT: J 303 MET cc_start: 0.6428 (ttt) cc_final: 0.6099 (mpt) outliers start: 60 outliers final: 34 residues processed: 276 average time/residue: 0.6938 time to fit residues: 206.4041 Evaluate side-chains 268 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 229 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 243 ILE Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain J residue 271 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 88 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 141 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN F 254 GLN G 68 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.197085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.126883 restraints weight = 12296.250| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.58 r_work: 0.3190 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12783 Z= 0.159 Angle : 0.544 8.514 17225 Z= 0.292 Chirality : 0.040 0.170 2012 Planarity : 0.005 0.052 2184 Dihedral : 4.585 56.118 1737 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.44 % Allowed : 25.18 % Favored : 70.38 % 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 aren not related in a simple way. whole: 2.02 (0.21), residues: 1613 helix: 1.73 (0.14), residues: 1387 sheet: None (None), residues: 0 loop : -1.01 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 61 TYR 0.009 0.001 TYR F 110 PHE 0.023 0.002 PHE B 48 TRP 0.010 0.001 TRP B 19 HIS 0.002 0.001 HIS G 142 Details of bonding type rmsd covalent geometry : bond 0.00358 (12783) covalent geometry : angle 0.54373 (17225) hydrogen bonds : bond 0.04669 ( 991) hydrogen bonds : angle 4.21546 ( 2928) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 230 time to evaluate : 0.547 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7540 (tp40) REVERT: B 47 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7084 (mttm) REVERT: B 55 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7761 (ttm) REVERT: B 56 GLN cc_start: 0.7489 (mm-40) cc_final: 0.7186 (mm-40) REVERT: C 61 ARG cc_start: 0.7457 (ttp80) cc_final: 0.7081 (ttt180) REVERT: C 68 GLN cc_start: 0.6977 (tm-30) cc_final: 0.6562 (tm-30) REVERT: C 72 ASP cc_start: 0.5351 (OUTLIER) cc_final: 0.4593 (p0) REVERT: C 92 ARG cc_start: 0.7746 (mtp85) cc_final: 0.7357 (mtt-85) REVERT: C 187 LYS cc_start: 0.8423 (mppt) cc_final: 0.7524 (mmtt) REVERT: F 14 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.8056 (tp) REVERT: F 92 ARG cc_start: 0.7217 (mtp85) cc_final: 0.6920 (mtt-85) REVERT: F 108 ASP cc_start: 0.7607 (t70) cc_final: 0.7154 (t70) REVERT: F 129 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7700 (pp20) REVERT: G 129 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6644 (mp0) REVERT: G 141 ARG cc_start: 0.8069 (mtm-85) cc_final: 0.7676 (mtm110) REVERT: J 303 MET cc_start: 0.6447 (ttt) cc_final: 0.6129 (mpt) outliers start: 60 outliers final: 39 residues processed: 271 average time/residue: 0.6884 time to fit residues: 201.1371 Evaluate side-chains 275 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 229 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 243 ILE Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 268 LYS Chi-restraints excluded: chain I residue 284 LYS Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain J residue 271 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 23 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN ** G 236 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.196718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.129539 restraints weight = 10747.325| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 1.87 r_work: 0.3125 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12783 Z= 0.166 Angle : 0.566 13.531 17225 Z= 0.301 Chirality : 0.040 0.171 2012 Planarity : 0.005 0.054 2184 Dihedral : 4.621 56.549 1737 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 4.37 % Allowed : 25.18 % Favored : 70.45 % 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 aren not related in a simple way. whole: 1.97 (0.21), residues: 1613 helix: 1.69 (0.14), residues: 1387 sheet: None (None), residues: 0 loop : -1.02 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 61 TYR 0.009 0.001 TYR F 110 PHE 0.026 0.002 PHE F 70 TRP 0.011 0.001 TRP B 19 HIS 0.002 0.001 HIS G 142 Details of bonding type rmsd covalent geometry : bond 0.00377 (12783) covalent geometry : angle 0.56602 (17225) hydrogen bonds : bond 0.04740 ( 991) hydrogen bonds : angle 4.23719 ( 2928) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 230 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7955 (OUTLIER) cc_final: 0.7588 (tp40) REVERT: B 47 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.7055 (mttm) REVERT: B 55 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7816 (ttm) REVERT: B 56 GLN cc_start: 0.7490 (mm-40) cc_final: 0.7181 (mm-40) REVERT: C 68 GLN cc_start: 0.6927 (tm-30) cc_final: 0.6500 (tm-30) REVERT: C 72 ASP cc_start: 0.5325 (OUTLIER) cc_final: 0.4570 (p0) REVERT: C 92 ARG cc_start: 0.7750 (mtp85) cc_final: 0.7356 (mtt-85) REVERT: C 187 LYS cc_start: 0.8468 (mppt) cc_final: 0.7558 (mmtt) REVERT: D 35 ASP cc_start: 0.9133 (t70) cc_final: 0.8872 (t70) REVERT: F 14 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8024 (tp) REVERT: F 108 ASP cc_start: 0.7624 (t70) cc_final: 0.7146 (t70) REVERT: F 129 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7752 (pp20) REVERT: G 129 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.6693 (mp0) REVERT: G 141 ARG cc_start: 0.8146 (mtm-85) cc_final: 0.7743 (mtm110) REVERT: H 303 MET cc_start: 0.5900 (tmm) cc_final: 0.5470 (tmm) REVERT: J 303 MET cc_start: 0.6439 (ttt) cc_final: 0.6115 (mpt) outliers start: 59 outliers final: 41 residues processed: 272 average time/residue: 0.6356 time to fit residues: 186.5187 Evaluate side-chains 275 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 227 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain F residue 259 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 243 ILE Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 268 LYS Chi-restraints excluded: chain I residue 284 LYS Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain J residue 271 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 147 optimal weight: 9.9990 chunk 110 optimal weight: 3.9990 chunk 97 optimal weight: 0.0980 chunk 104 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 63 optimal weight: 0.1980 chunk 155 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 157 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN F 254 GLN G 68 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.197042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.126925 restraints weight = 12191.795| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 1.82 r_work: 0.3162 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12783 Z= 0.161 Angle : 0.568 12.629 17225 Z= 0.301 Chirality : 0.040 0.169 2012 Planarity : 0.005 0.058 2184 Dihedral : 4.614 56.736 1737 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.37 % Allowed : 25.33 % Favored : 70.31 % 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 aren not related in a simple way. whole: 1.97 (0.21), residues: 1613 helix: 1.70 (0.14), residues: 1387 sheet: None (None), residues: 0 loop : -1.01 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 61 TYR 0.009 0.001 TYR F 110 PHE 0.023 0.002 PHE B 48 TRP 0.011 0.001 TRP B 19 HIS 0.002 0.001 HIS G 142 Details of bonding type rmsd covalent geometry : bond 0.00365 (12783) covalent geometry : angle 0.56797 (17225) hydrogen bonds : bond 0.04671 ( 991) hydrogen bonds : angle 4.22146 ( 2928) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 231 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7932 (OUTLIER) cc_final: 0.7561 (tp40) REVERT: B 47 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7060 (mttm) REVERT: B 55 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7780 (ttm) REVERT: B 56 GLN cc_start: 0.7483 (mm-40) cc_final: 0.7173 (mm-40) REVERT: C 68 GLN cc_start: 0.6923 (tm-30) cc_final: 0.6501 (tm-30) REVERT: C 72 ASP cc_start: 0.5331 (OUTLIER) cc_final: 0.4584 (p0) REVERT: C 92 ARG cc_start: 0.7736 (mtp85) cc_final: 0.7341 (mtt-85) REVERT: C 187 LYS cc_start: 0.8438 (mppt) cc_final: 0.7531 (mmtt) REVERT: D 35 ASP cc_start: 0.9112 (t70) cc_final: 0.8873 (t70) REVERT: E 137 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7170 (tp30) REVERT: F 14 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8044 (tp) REVERT: F 108 ASP cc_start: 0.7605 (t70) cc_final: 0.7147 (t70) REVERT: F 125 GLU cc_start: 0.7296 (pm20) cc_final: 0.6940 (pm20) REVERT: F 129 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7720 (pp20) REVERT: G 129 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6642 (mp0) REVERT: G 141 ARG cc_start: 0.8102 (mtm-85) cc_final: 0.7772 (mtm-85) REVERT: H 303 MET cc_start: 0.5861 (tmm) cc_final: 0.5431 (tmm) REVERT: J 303 MET cc_start: 0.6444 (ttt) cc_final: 0.6146 (mpt) outliers start: 59 outliers final: 39 residues processed: 272 average time/residue: 0.6847 time to fit residues: 200.6194 Evaluate side-chains 273 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 226 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 171 MET Chi-restraints excluded: chain C residue 175 LEU Chi-restraints excluded: chain C residue 179 SER Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 232 GLN Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 137 GLU Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 88 SER Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 69 THR Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 243 ILE Chi-restraints excluded: chain I residue 249 VAL Chi-restraints excluded: chain I residue 284 LYS Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain J residue 271 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 56 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 99 optimal weight: 0.7980 chunk 96 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 80 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN G 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.198793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.130083 restraints weight = 12522.070| |-----------------------------------------------------------------------------| r_work (start): 0.3392 rms_B_bonded: 1.93 r_work: 0.3191 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3030 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3030 r_free = 0.3030 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3030 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12783 Z= 0.132 Angle : 0.542 12.369 17225 Z= 0.287 Chirality : 0.039 0.161 2012 Planarity : 0.005 0.063 2184 Dihedral : 4.477 53.913 1737 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.28 % Allowed : 26.27 % Favored : 70.45 % 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 aren not related in a simple way. whole: 2.18 (0.21), residues: 1613 helix: 1.84 (0.14), residues: 1387 sheet: None (None), residues: 0 loop : -0.99 (0.41), residues: 226 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 238 TYR 0.009 0.001 TYR F 110 PHE 0.023 0.002 PHE F 70 TRP 0.010 0.001 TRP B 19 HIS 0.001 0.001 HIS D 142 Details of bonding type rmsd covalent geometry : bond 0.00289 (12783) covalent geometry : angle 0.54229 (17225) hydrogen bonds : bond 0.04215 ( 991) hydrogen bonds : angle 4.08247 ( 2928) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3226 Ramachandran restraints generated. 1613 Oldfield, 0 Emsley, 1613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 237 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7910 (OUTLIER) cc_final: 0.7551 (tp40) REVERT: B 47 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7073 (mttm) REVERT: B 55 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.7649 (mtt) REVERT: B 56 GLN cc_start: 0.7435 (mm-40) cc_final: 0.7117 (mm-40) REVERT: C 68 GLN cc_start: 0.6931 (tm-30) cc_final: 0.6514 (tm-30) REVERT: C 72 ASP cc_start: 0.5279 (OUTLIER) cc_final: 0.4543 (p0) REVERT: C 92 ARG cc_start: 0.7771 (mtp85) cc_final: 0.7376 (mtt-85) REVERT: C 187 LYS cc_start: 0.8463 (mppt) cc_final: 0.7578 (mmtm) REVERT: D 35 ASP cc_start: 0.9120 (t70) cc_final: 0.8906 (t70) REVERT: F 14 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8012 (tp) REVERT: F 125 GLU cc_start: 0.7268 (pm20) cc_final: 0.6890 (pm20) REVERT: F 129 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7760 (pp20) REVERT: H 303 MET cc_start: 0.5872 (tmm) cc_final: 0.5464 (tmm) REVERT: J 303 MET cc_start: 0.6433 (ttt) cc_final: 0.6137 (mpt) outliers start: 44 outliers final: 28 residues processed: 269 average time/residue: 0.6813 time to fit residues: 197.4739 Evaluate side-chains 263 residues out of total 1372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 229 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LEU Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 249 SER Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain E residue 10 ILE Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 136 ASP Chi-restraints excluded: chain E residue 191 THR Chi-restraints excluded: chain E residue 245 VAL Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 14 LEU Chi-restraints excluded: chain F residue 57 ASP Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain F residue 129 GLU Chi-restraints excluded: chain F residue 231 ILE Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 56 MET Chi-restraints excluded: chain G residue 183 SER Chi-restraints excluded: chain G residue 231 ILE Chi-restraints excluded: chain G residue 245 VAL Chi-restraints excluded: chain H residue 300 VAL Chi-restraints excluded: chain I residue 243 ILE Chi-restraints excluded: chain I residue 284 LYS Chi-restraints excluded: chain I residue 316 ILE Chi-restraints excluded: chain J residue 239 VAL Chi-restraints excluded: chain J residue 249 VAL Chi-restraints excluded: chain J residue 271 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 22 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 0.4980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN C 105 ASN D 29 ASN D 174 ASN ** F 254 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.197379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.128470 restraints weight = 12507.275| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.95 r_work: 0.3171 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12783 Z= 0.156 Angle : 0.567 12.016 17225 Z= 0.300 Chirality : 0.040 0.169 2012 Planarity : 0.005 0.062 2184 Dihedral : 4.561 56.107 1737 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.49 % Allowed : 25.47 % Favored : 71.03 % 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 aren not related in a simple way. whole: 2.06 (0.21), residues: 1613 helix: 1.75 (0.14), residues: 1389 sheet: None (None), residues: 0 loop : -1.00 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 238 TYR 0.009 0.001 TYR F 110 PHE 0.023 0.002 PHE B 48 TRP 0.014 0.001 TRP C 21 HIS 0.002 0.001 HIS G 142 Details of bonding type rmsd covalent geometry : bond 0.00354 (12783) covalent geometry : angle 0.56672 (17225) hydrogen bonds : bond 0.04553 ( 991) hydrogen bonds : angle 4.18186 ( 2928) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7707.05 seconds wall clock time: 131 minutes 41.51 seconds (7901.51 seconds total)