Starting phenix.real_space_refine on Sat Aug 23 09:26:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rbm_19032/08_2025/8rbm_19032.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rbm_19032/08_2025/8rbm_19032.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rbm_19032/08_2025/8rbm_19032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rbm_19032/08_2025/8rbm_19032.map" model { file = "/net/cci-nas-00/data/ceres_data/8rbm_19032/08_2025/8rbm_19032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rbm_19032/08_2025/8rbm_19032.cif" } resolution = 3.24 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 10 7.16 5 P 4 5.49 5 S 75 5.16 5 C 7287 2.51 5 N 1828 2.21 5 O 2055 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s 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: 11259 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1394 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 179} Chain: "C" Number of atoms: 3289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3289 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 37, 'TRANS': 408} Chain: "D" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2629 Classifications: {'peptide': 349} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 325} Chain: "E" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1585 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 202} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1482 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 6, 'TRANS': 187} Chain: "B" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 174 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "b" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 98 Classifications: {'peptide': 11} Link IDs: {'PTRANS': 1, 'TRANS': 9} Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Unusual residues: {'FES': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'FMN': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 422 Unusual residues: {'FMN': 1, 'LMT': 9, 'PTY': 1, 'RBF': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 184 SG CYS A 25 52.825 59.013 42.509 1.00 81.07 S ATOM 8114 SG CYS E 122 52.424 61.634 39.776 1.00 49.73 S ATOM 844 SG CYS A 113 48.411 58.765 38.075 1.00 85.37 S ATOM 7505 SG CYS E 39 49.017 56.076 40.975 1.00 29.83 S ATOM 4136 SG CYS C 376 49.877 60.379 82.747 1.00 78.97 S ATOM 4451 SG CYS C 419 53.579 57.329 83.727 1.00 62.32 S ATOM 4094 SG CYS C 370 52.104 56.960 77.246 1.00 49.34 S ATOM 4119 SG CYS C 373 48.224 54.481 81.953 1.00 57.45 S ATOM 4382 SG CYS C 409 52.100 71.272 84.978 1.00 46.23 S ATOM 4404 SG CYS C 412 49.293 68.299 90.100 1.00 51.64 S ATOM 4420 SG CYS C 415 51.030 65.041 85.052 1.00 64.78 S ATOM 4162 SG CYS C 380 46.027 67.945 84.876 1.00 60.82 S Time building chain proxies: 3.26, per 1000 atoms: 0.29 Number of scatterers: 11259 At special positions: 0 Unit cell: (91.84, 111.52, 132.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 10 26.01 S 75 16.00 P 4 15.00 O 2055 8.00 N 1828 7.00 C 7287 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 654.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 201 " pdb="FE1 FES A 201 " - pdb=" SG CYS A 25 " pdb="FE1 FES A 201 " - pdb=" SG CYS E 122 " pdb="FE2 FES A 201 " - pdb=" SG CYS E 39 " pdb="FE2 FES A 201 " - pdb=" SG CYS A 113 " pdb=" SF4 C 501 " pdb="FE1 SF4 C 501 " - pdb=" SG CYS C 376 " pdb="FE2 SF4 C 501 " - pdb=" SG CYS C 419 " pdb="FE3 SF4 C 501 " - pdb=" SG CYS C 370 " pdb="FE4 SF4 C 501 " - pdb=" SG CYS C 373 " pdb=" SF4 C 502 " pdb="FE3 SF4 C 502 " - pdb=" SG CYS C 415 " pdb="FE2 SF4 C 502 " - pdb=" SG CYS C 412 " pdb="FE4 SF4 C 502 " - pdb=" SG CYS C 380 " pdb="FE1 SF4 C 502 " - pdb=" SG CYS C 409 " Number of angles added : 30 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2564 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 8 sheets defined 57.9% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 3.746A pdb=" N PHE A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 31 removed outlier: 3.644A pdb=" N PHE A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N SER A 31 " --> pdb=" O PHE A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 62 Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 71 through 95 removed outlier: 3.986A pdb=" N ILE A 91 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N LYS A 93 " --> pdb=" O MET A 89 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER A 95 " --> pdb=" O ILE A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 99 Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.995A pdb=" N ILE A 109 " --> pdb=" O TYR A 105 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 105 through 110' Processing helix chain 'A' and resid 113 through 126 Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 128 through 159 removed outlier: 3.777A pdb=" N ILE A 149 " --> pdb=" O LEU A 145 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'C' and resid 119 through 123 removed outlier: 3.998A pdb=" N GLU C 123 " --> pdb=" O PRO C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 134 removed outlier: 3.554A pdb=" N LEU C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.540A pdb=" N LYS C 150 " --> pdb=" O PRO C 146 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 183 Processing helix chain 'C' and resid 183 through 198 Processing helix chain 'C' and resid 211 through 222 Processing helix chain 'C' and resid 236 through 240 removed outlier: 3.570A pdb=" N MET C 239 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N GLY C 240 " --> pdb=" O TYR C 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 236 through 240' Processing helix chain 'C' and resid 241 through 251 Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 270 through 283 Processing helix chain 'C' and resid 311 through 319 Processing helix chain 'C' and resid 385 through 395 Processing helix chain 'C' and resid 397 through 404 removed outlier: 3.567A pdb=" N TYR C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.545A pdb=" N TYR C 417 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 413 through 418' Processing helix chain 'C' and resid 424 through 447 removed outlier: 3.564A pdb=" N ASP C 447 " --> pdb=" O ALA C 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 41 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 41 through 67 Processing helix chain 'D' and resid 69 through 75 removed outlier: 3.737A pdb=" N ASP D 75 " --> pdb=" O ARG D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 88 removed outlier: 3.842A pdb=" N THR D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 106 removed outlier: 3.768A pdb=" N GLY D 98 " --> pdb=" O PRO D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 135 Processing helix chain 'D' and resid 155 through 164 Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 193 through 200 removed outlier: 3.606A pdb=" N PHE D 200 " --> pdb=" O LEU D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 220 through 232 Processing helix chain 'D' and resid 237 through 258 Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 273 through 281 Processing helix chain 'D' and resid 284 through 288 removed outlier: 3.657A pdb=" N SER D 288 " --> pdb=" O PRO D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 313 Processing helix chain 'D' and resid 318 through 337 Proline residue: D 331 - end of helix Processing helix chain 'E' and resid 18 through 25 removed outlier: 3.843A pdb=" N LEU E 25 " --> pdb=" O PHE E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 38 through 44 Processing helix chain 'E' and resid 47 through 72 Processing helix chain 'E' and resid 77 through 79 No H-bonds generated for 'chain 'E' and resid 77 through 79' Processing helix chain 'E' and resid 80 through 104 removed outlier: 3.603A pdb=" N VAL E 84 " --> pdb=" O VAL E 80 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N ALA E 102 " --> pdb=" O MET E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.930A pdb=" N VAL E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'E' and resid 132 through 135 removed outlier: 3.907A pdb=" N ASN E 135 " --> pdb=" O CYS E 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 132 through 135' Processing helix chain 'E' and resid 136 through 168 removed outlier: 3.715A pdb=" N LEU E 165 " --> pdb=" O ILE E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 178 Processing helix chain 'E' and resid 179 through 186 removed outlier: 4.600A pdb=" N TRP E 184 " --> pdb=" O HIS E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 201 removed outlier: 3.668A pdb=" N ALA E 199 " --> pdb=" O ILE E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 227 removed outlier: 3.830A pdb=" N PHE E 206 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ILE E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL E 208 " --> pdb=" O GLY E 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 79 removed outlier: 4.316A pdb=" N LEU G 43 " --> pdb=" O GLN G 39 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET G 60 " --> pdb=" O THR G 56 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N GLY G 63 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N THR G 64 " --> pdb=" O MET G 60 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLU G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 93 removed outlier: 3.886A pdb=" N ASP G 93 " --> pdb=" O PRO G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 172 Processing helix chain 'G' and resid 188 through 192 Processing helix chain 'G' and resid 202 through 222 Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.898A pdb=" N ALA B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 27 through 28 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 38 removed outlier: 6.525A pdb=" N VAL C 102 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 38 Processing sheet with id=AA4, first strand: chain 'C' and resid 48 through 49 Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 165 Processing sheet with id=AA6, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AA7, first strand: chain 'C' and resid 328 through 329 Processing sheet with id=AA8, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.545A pdb=" N ALA G 118 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N GLU G 133 " --> pdb=" O LEU G 150 " (cutoff:3.500A) 583 hydrogen bonds defined for protein. 1671 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.42: 4558 1.42 - 1.63: 6819 1.63 - 1.85: 108 1.85 - 2.07: 0 2.07 - 2.28: 28 Bond restraints: 11513 Sorted by residual: bond pdb=" O5' FMN C 500 " pdb=" P FMN C 500 " ideal model delta sigma weight residual 1.676 1.819 -0.143 2.00e-02 2.50e+03 5.13e+01 bond pdb=" O5' FMN D 411 " pdb=" P FMN D 411 " ideal model delta sigma weight residual 1.676 1.591 0.085 2.00e-02 2.50e+03 1.79e+01 bond pdb=" O5' FMN G 301 " pdb=" P FMN G 301 " ideal model delta sigma weight residual 1.676 1.595 0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C5' FMN C 500 " pdb=" O5' FMN C 500 " ideal model delta sigma weight residual 1.418 1.341 0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" O1P FMN G 301 " pdb=" P FMN G 301 " ideal model delta sigma weight residual 1.542 1.481 0.061 2.00e-02 2.50e+03 9.17e+00 ... (remaining 11508 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 15151 2.05 - 4.09: 369 4.09 - 6.14: 105 6.14 - 8.19: 18 8.19 - 10.24: 34 Bond angle restraints: 15677 Sorted by residual: angle pdb=" C ASN A 112 " pdb=" N CYS A 113 " pdb=" CA CYS A 113 " ideal model delta sigma weight residual 121.54 129.62 -8.08 1.91e+00 2.74e-01 1.79e+01 angle pdb=" C2 LMT D 405 " pdb=" C3 LMT D 405 " pdb=" C4 LMT D 405 " ideal model delta sigma weight residual 117.09 106.85 10.24 3.00e+00 1.11e-01 1.16e+01 angle pdb=" C2 LMT D 402 " pdb=" C3 LMT D 402 " pdb=" C4 LMT D 402 " ideal model delta sigma weight residual 117.09 107.07 10.02 3.00e+00 1.11e-01 1.12e+01 angle pdb=" C2 LMT A 202 " pdb=" C3 LMT A 202 " pdb=" C4 LMT A 202 " ideal model delta sigma weight residual 117.09 107.42 9.67 3.00e+00 1.11e-01 1.04e+01 angle pdb=" C2 LMT D 408 " pdb=" C3 LMT D 408 " pdb=" C4 LMT D 408 " ideal model delta sigma weight residual 117.09 107.47 9.62 3.00e+00 1.11e-01 1.03e+01 ... (remaining 15672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.32: 6786 24.32 - 48.63: 330 48.63 - 72.95: 80 72.95 - 97.27: 30 97.27 - 121.59: 48 Dihedral angle restraints: 7274 sinusoidal: 3262 harmonic: 4012 Sorted by residual: dihedral pdb=" CA ILE D 106 " pdb=" C ILE D 106 " pdb=" N GLY D 107 " pdb=" CA GLY D 107 " ideal model delta harmonic sigma weight residual -180.00 -154.85 -25.15 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ILE C 85 " pdb=" C ILE C 85 " pdb=" N GLY C 86 " pdb=" CA GLY C 86 " ideal model delta harmonic sigma weight residual 180.00 -158.66 -21.34 0 5.00e+00 4.00e-02 1.82e+01 dihedral pdb=" C5B LMT D 409 " pdb=" C1B LMT D 409 " pdb=" O5B LMT D 409 " pdb=" O1B LMT D 409 " ideal model delta sinusoidal sigma weight residual 295.61 174.02 121.59 1 3.00e+01 1.11e-03 1.63e+01 ... (remaining 7271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.014: 1905 1.014 - 2.028: 0 2.028 - 3.042: 0 3.042 - 4.056: 0 4.056 - 5.070: 4 Chirality restraints: 1909 Sorted by residual: chirality pdb=" C2' FMN G 301 " pdb=" C1' FMN G 301 " pdb=" C3' FMN G 301 " pdb=" O2' FMN G 301 " both_signs ideal model delta sigma weight residual False -2.52 2.55 -5.07 2.00e-01 2.50e+01 6.43e+02 chirality pdb=" CB THR G 202 " pdb=" CA THR G 202 " pdb=" OG1 THR G 202 " pdb=" CG2 THR G 202 " both_signs ideal model delta sigma weight residual False 2.55 -2.46 5.01 2.00e-01 2.50e+01 6.27e+02 chirality pdb=" C4' FMN G 301 " pdb=" C3' FMN G 301 " pdb=" C5' FMN G 301 " pdb=" O4' FMN G 301 " both_signs ideal model delta sigma weight residual False -2.50 2.43 -4.93 2.00e-01 2.50e+01 6.07e+02 ... (remaining 1906 not shown) Planarity restraints: 1884 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G 301 " 0.115 2.00e-02 2.50e+03 3.31e-02 4.94e+01 pdb=" C10 FMN G 301 " -0.011 2.00e-02 2.50e+03 pdb=" C2 FMN G 301 " -0.020 2.00e-02 2.50e+03 pdb=" C4 FMN G 301 " 0.019 2.00e-02 2.50e+03 pdb=" C4A FMN G 301 " 0.008 2.00e-02 2.50e+03 pdb=" C5A FMN G 301 " 0.008 2.00e-02 2.50e+03 pdb=" C6 FMN G 301 " 0.014 2.00e-02 2.50e+03 pdb=" C7 FMN G 301 " 0.002 2.00e-02 2.50e+03 pdb=" C7M FMN G 301 " 0.013 2.00e-02 2.50e+03 pdb=" C8 FMN G 301 " -0.017 2.00e-02 2.50e+03 pdb=" C8M FMN G 301 " -0.044 2.00e-02 2.50e+03 pdb=" C9 FMN G 301 " -0.024 2.00e-02 2.50e+03 pdb=" C9A FMN G 301 " -0.010 2.00e-02 2.50e+03 pdb=" N1 FMN G 301 " -0.027 2.00e-02 2.50e+03 pdb=" N10 FMN G 301 " -0.006 2.00e-02 2.50e+03 pdb=" N3 FMN G 301 " 0.003 2.00e-02 2.50e+03 pdb=" N5 FMN G 301 " 0.013 2.00e-02 2.50e+03 pdb=" O2 FMN G 301 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN D 411 " 0.012 2.00e-02 2.50e+03 1.13e-02 5.79e+00 pdb=" C10 FMN D 411 " 0.000 2.00e-02 2.50e+03 pdb=" C2 FMN D 411 " -0.011 2.00e-02 2.50e+03 pdb=" C4 FMN D 411 " 0.008 2.00e-02 2.50e+03 pdb=" C4A FMN D 411 " 0.007 2.00e-02 2.50e+03 pdb=" C5A FMN D 411 " 0.013 2.00e-02 2.50e+03 pdb=" C6 FMN D 411 " 0.006 2.00e-02 2.50e+03 pdb=" C7 FMN D 411 " -0.002 2.00e-02 2.50e+03 pdb=" C7M FMN D 411 " -0.030 2.00e-02 2.50e+03 pdb=" C8 FMN D 411 " -0.001 2.00e-02 2.50e+03 pdb=" C8M FMN D 411 " -0.006 2.00e-02 2.50e+03 pdb=" C9 FMN D 411 " 0.006 2.00e-02 2.50e+03 pdb=" C9A FMN D 411 " 0.012 2.00e-02 2.50e+03 pdb=" N1 FMN D 411 " -0.010 2.00e-02 2.50e+03 pdb=" N10 FMN D 411 " 0.005 2.00e-02 2.50e+03 pdb=" N3 FMN D 411 " -0.003 2.00e-02 2.50e+03 pdb=" N5 FMN D 411 " 0.013 2.00e-02 2.50e+03 pdb=" O2 FMN D 411 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 105 " -0.011 2.00e-02 2.50e+03 2.19e-02 4.81e+00 pdb=" C ALA D 105 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA D 105 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE D 106 " -0.013 2.00e-02 2.50e+03 ... (remaining 1881 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1506 2.75 - 3.29: 11057 3.29 - 3.83: 18357 3.83 - 4.36: 20873 4.36 - 4.90: 37299 Nonbonded interactions: 89092 Sorted by model distance: nonbonded pdb=" OG SER C 202 " pdb=" O ALA C 227 " model vdw 2.218 3.040 nonbonded pdb=" O2B LMT D 410 " pdb=" O6' LMT D 410 " model vdw 2.221 3.040 nonbonded pdb=" O SER D 88 " pdb=" NH1 ARG D 128 " model vdw 2.240 3.120 nonbonded pdb=" O THR E 41 " pdb=" OG1 THR E 45 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR C 237 " pdb=" O CYS C 412 " model vdw 2.258 3.040 ... (remaining 89087 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.420 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.143 11528 Z= 0.334 Angle : 1.009 30.251 15707 Z= 0.378 Chirality : 0.234 5.070 1909 Planarity : 0.005 0.044 1884 Dihedral : 18.915 121.587 4710 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.19 % Favored : 96.53 % Rotamer: Outliers : 2.06 % Allowed : 5.63 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.31 (0.24), residues: 1411 helix: 1.12 (0.20), residues: 742 sheet: -0.32 (0.70), residues: 79 loop : -0.86 (0.27), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 128 TYR 0.010 0.001 TYR C 237 PHE 0.013 0.001 PHE E 171 TRP 0.009 0.001 TRP D 83 HIS 0.001 0.000 HIS C 268 Details of bonding type rmsd covalent geometry : bond 0.00639 (11513) covalent geometry : angle 0.88388 (15677) hydrogen bonds : bond 0.14313 ( 579) hydrogen bonds : angle 6.74671 ( 1671) metal coordination : bond 0.01140 ( 12) metal coordination : angle 11.19042 ( 30) Misc. bond : bond 0.05914 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 164 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: C 19 ASP cc_start: 0.7647 (p0) cc_final: 0.7174 (p0) REVERT: C 179 ILE cc_start: 0.9477 (tp) cc_final: 0.9261 (tp) REVERT: C 354 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8692 (tt) REVERT: E 212 LEU cc_start: 0.8017 (OUTLIER) cc_final: 0.7779 (mm) REVERT: G 95 PHE cc_start: 0.7645 (m-10) cc_final: 0.7218 (m-10) outliers start: 23 outliers final: 5 residues processed: 182 average time/residue: 0.1336 time to fit residues: 33.4531 Evaluate side-chains 130 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 122 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain E residue 194 GLN Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain G residue 202 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 0.0870 overall best weight: 0.8358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN C 430 GLN C 435 GLN D 189 ASN E 50 ASN E 173 GLN E 194 GLN G 125 ASN G 225 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.093105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.068668 restraints weight = 27740.736| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.96 r_work: 0.2971 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11528 Z= 0.125 Angle : 0.845 33.041 15707 Z= 0.311 Chirality : 0.045 0.353 1909 Planarity : 0.005 0.039 1884 Dihedral : 16.011 90.213 2353 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.39 % Favored : 94.33 % Rotamer: Outliers : 2.59 % Allowed : 10.37 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 0.88 (0.24), residues: 1411 helix: 1.69 (0.20), residues: 752 sheet: 0.13 (0.73), residues: 73 loop : -0.83 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 156 TYR 0.016 0.001 TYR C 237 PHE 0.010 0.001 PHE G 218 TRP 0.008 0.001 TRP D 96 HIS 0.002 0.001 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00272 (11513) covalent geometry : angle 0.68224 (15677) hydrogen bonds : bond 0.03734 ( 579) hydrogen bonds : angle 4.73653 ( 1671) metal coordination : bond 0.01221 ( 12) metal coordination : angle 11.41379 ( 30) Misc. bond : bond 0.00093 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 142 time to evaluate : 0.425 Fit side-chains revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8399 (mmm-85) cc_final: 0.7885 (mmm-85) REVERT: A 100 ARG cc_start: 0.8576 (mmt180) cc_final: 0.8363 (mmt180) REVERT: A 125 GLU cc_start: 0.8663 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: C 19 ASP cc_start: 0.8280 (p0) cc_final: 0.7905 (p0) REVERT: C 225 PHE cc_start: 0.6978 (m-10) cc_final: 0.6751 (m-10) REVERT: C 354 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8923 (tt) REVERT: D 68 GLN cc_start: 0.9012 (mp10) cc_final: 0.8616 (mp10) REVERT: E 109 LYS cc_start: 0.9356 (mtmm) cc_final: 0.9073 (mtmm) REVERT: E 212 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8309 (mm) REVERT: G 67 GLU cc_start: 0.9326 (tp30) cc_final: 0.8829 (tp30) REVERT: G 106 GLU cc_start: 0.7986 (tp30) cc_final: 0.7765 (tp30) outliers start: 29 outliers final: 13 residues processed: 159 average time/residue: 0.1220 time to fit residues: 27.2790 Evaluate side-chains 142 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 277 CYS Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain B residue 19 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 63 optimal weight: 1.9990 chunk 96 optimal weight: 0.2980 chunk 27 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 chunk 2 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 82 optimal weight: 0.1980 chunk 130 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 189 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.090596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.067629 restraints weight = 27893.450| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.71 r_work: 0.2969 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11528 Z= 0.130 Angle : 0.837 33.311 15707 Z= 0.304 Chirality : 0.044 0.374 1909 Planarity : 0.004 0.040 1884 Dihedral : 13.123 82.371 2347 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.96 % Favored : 94.76 % Rotamer: Outliers : 2.95 % Allowed : 11.17 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1.04 (0.24), residues: 1411 helix: 1.89 (0.19), residues: 751 sheet: 0.22 (0.73), residues: 71 loop : -0.85 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 156 TYR 0.015 0.001 TYR C 237 PHE 0.011 0.001 PHE C 121 TRP 0.007 0.001 TRP D 96 HIS 0.002 0.000 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00295 (11513) covalent geometry : angle 0.66545 (15677) hydrogen bonds : bond 0.03604 ( 579) hydrogen bonds : angle 4.56187 ( 1671) metal coordination : bond 0.01441 ( 12) metal coordination : angle 11.64449 ( 30) Misc. bond : bond 0.00055 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 134 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 89 MET cc_start: 0.8392 (tmm) cc_final: 0.8169 (tmm) REVERT: A 92 ARG cc_start: 0.8363 (mmm-85) cc_final: 0.8034 (mmm-85) REVERT: A 125 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: C 19 ASP cc_start: 0.8119 (p0) cc_final: 0.7736 (p0) REVERT: C 50 MET cc_start: 0.7691 (ppp) cc_final: 0.7355 (ppp) REVERT: C 354 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8880 (tt) REVERT: D 68 GLN cc_start: 0.9031 (mp10) cc_final: 0.8549 (mp10) REVERT: E 109 LYS cc_start: 0.9370 (mtmm) cc_final: 0.9149 (mtmm) REVERT: E 131 PHE cc_start: 0.8639 (t80) cc_final: 0.8397 (t80) REVERT: E 212 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8412 (mm) REVERT: G 106 GLU cc_start: 0.8053 (tp30) cc_final: 0.7846 (tp30) REVERT: G 133 GLU cc_start: 0.8569 (tp30) cc_final: 0.8220 (tp30) outliers start: 33 outliers final: 17 residues processed: 151 average time/residue: 0.1124 time to fit residues: 24.2723 Evaluate side-chains 147 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 326 MET Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 19 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 87 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 65 optimal weight: 0.7980 chunk 97 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 8.9990 chunk 138 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.089244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.064598 restraints weight = 28344.348| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 2.96 r_work: 0.2873 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11528 Z= 0.187 Angle : 0.864 35.136 15707 Z= 0.315 Chirality : 0.045 0.357 1909 Planarity : 0.004 0.039 1884 Dihedral : 11.489 83.396 2347 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.67 % Favored : 94.05 % Rotamer: Outliers : 2.59 % Allowed : 13.05 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1.14 (0.24), residues: 1411 helix: 1.94 (0.19), residues: 757 sheet: 0.20 (0.73), residues: 71 loop : -0.79 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 134 TYR 0.014 0.001 TYR C 237 PHE 0.015 0.001 PHE B 26 TRP 0.008 0.001 TRP D 96 HIS 0.003 0.001 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00439 (11513) covalent geometry : angle 0.67822 (15677) hydrogen bonds : bond 0.03953 ( 579) hydrogen bonds : angle 4.53666 ( 1671) metal coordination : bond 0.02293 ( 12) metal coordination : angle 12.27507 ( 30) Misc. bond : bond 0.00087 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 129 time to evaluate : 0.391 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.8409 (tmm) cc_final: 0.8164 (tmm) REVERT: A 92 ARG cc_start: 0.8399 (mmm-85) cc_final: 0.8097 (mmm-85) REVERT: A 125 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.7680 (mp0) REVERT: A 161 ASN cc_start: 0.9124 (t0) cc_final: 0.8627 (t0) REVERT: C 19 ASP cc_start: 0.8191 (p0) cc_final: 0.7840 (p0) REVERT: C 354 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8942 (tt) REVERT: D 68 GLN cc_start: 0.9092 (mp10) cc_final: 0.8564 (mp10) REVERT: E 109 LYS cc_start: 0.9376 (mtmm) cc_final: 0.9150 (mtmm) REVERT: E 131 PHE cc_start: 0.8612 (t80) cc_final: 0.8145 (t80) REVERT: E 147 MET cc_start: 0.8595 (mmt) cc_final: 0.8369 (tpt) REVERT: G 95 PHE cc_start: 0.7530 (m-10) cc_final: 0.7113 (m-10) outliers start: 29 outliers final: 17 residues processed: 143 average time/residue: 0.1161 time to fit residues: 23.3728 Evaluate side-chains 144 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 189 ASN Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 19 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 chunk 63 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 128 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 28 optimal weight: 20.0000 chunk 92 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 43 optimal weight: 0.0470 chunk 10 optimal weight: 2.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 189 ASN E 66 ASN E 105 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.088438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.064985 restraints weight = 27413.370| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.84 r_work: 0.2882 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11528 Z= 0.129 Angle : 0.825 35.493 15707 Z= 0.294 Chirality : 0.042 0.335 1909 Planarity : 0.004 0.040 1884 Dihedral : 10.608 82.477 2344 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.17 % Favored : 94.61 % Rotamer: Outliers : 2.41 % Allowed : 13.32 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1.24 (0.24), residues: 1411 helix: 2.02 (0.20), residues: 762 sheet: 0.25 (0.73), residues: 71 loop : -0.76 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 134 TYR 0.017 0.001 TYR C 237 PHE 0.013 0.001 PHE B 26 TRP 0.008 0.001 TRP D 96 HIS 0.002 0.000 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00296 (11513) covalent geometry : angle 0.62752 (15677) hydrogen bonds : bond 0.03539 ( 579) hydrogen bonds : angle 4.41377 ( 1671) metal coordination : bond 0.01434 ( 12) metal coordination : angle 12.27482 ( 30) Misc. bond : bond 0.00039 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.8291 (tmm) cc_final: 0.8028 (tmm) REVERT: A 124 ARG cc_start: 0.9176 (tpp80) cc_final: 0.8944 (ttm170) REVERT: A 125 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: A 161 ASN cc_start: 0.9056 (t0) cc_final: 0.8568 (t0) REVERT: C 19 ASP cc_start: 0.8122 (p0) cc_final: 0.7767 (p0) REVERT: C 354 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8905 (tt) REVERT: D 68 GLN cc_start: 0.9131 (mp10) cc_final: 0.8620 (mp10) REVERT: E 109 LYS cc_start: 0.9367 (mtmm) cc_final: 0.9095 (mtmm) REVERT: E 131 PHE cc_start: 0.8589 (t80) cc_final: 0.8283 (t80) REVERT: G 35 MET cc_start: 0.2981 (ttt) cc_final: 0.2725 (tpt) REVERT: B 25 LYS cc_start: 0.6566 (ttpt) cc_final: 0.6333 (mmtp) outliers start: 27 outliers final: 18 residues processed: 146 average time/residue: 0.1065 time to fit residues: 22.0731 Evaluate side-chains 144 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 66 ASN Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 19 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 24 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 110 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 chunk 137 optimal weight: 5.9990 chunk 38 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.086833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.062800 restraints weight = 27941.255| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.81 r_work: 0.2832 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 11528 Z= 0.208 Angle : 0.889 36.423 15707 Z= 0.323 Chirality : 0.044 0.330 1909 Planarity : 0.004 0.040 1884 Dihedral : 10.408 83.348 2344 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.60 % Favored : 94.19 % Rotamer: Outliers : 2.95 % Allowed : 13.49 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1.20 (0.24), residues: 1411 helix: 1.98 (0.19), residues: 763 sheet: 0.07 (0.71), residues: 73 loop : -0.74 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 227 TYR 0.015 0.001 TYR C 237 PHE 0.013 0.002 PHE B 26 TRP 0.007 0.001 TRP D 96 HIS 0.003 0.001 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00492 (11513) covalent geometry : angle 0.69319 (15677) hydrogen bonds : bond 0.04042 ( 579) hydrogen bonds : angle 4.48176 ( 1671) metal coordination : bond 0.02513 ( 12) metal coordination : angle 12.76489 ( 30) Misc. bond : bond 0.00110 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ARG cc_start: 0.9187 (tpp80) cc_final: 0.8929 (ttm170) REVERT: A 125 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.7659 (mp0) REVERT: A 161 ASN cc_start: 0.9117 (t0) cc_final: 0.8629 (t0) REVERT: C 19 ASP cc_start: 0.8205 (p0) cc_final: 0.7876 (p0) REVERT: C 354 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8954 (tt) REVERT: D 68 GLN cc_start: 0.9150 (mp10) cc_final: 0.8585 (mp10) REVERT: E 85 MET cc_start: 0.8686 (mmm) cc_final: 0.8238 (mmm) REVERT: E 109 LYS cc_start: 0.9343 (mtmm) cc_final: 0.9039 (mtmm) REVERT: E 131 PHE cc_start: 0.8661 (t80) cc_final: 0.8282 (t80) REVERT: E 185 MET cc_start: 0.9047 (mtm) cc_final: 0.8807 (mtm) REVERT: E 186 GLU cc_start: 0.8484 (tp30) cc_final: 0.8206 (tp30) REVERT: G 95 PHE cc_start: 0.7550 (m-10) cc_final: 0.7223 (m-10) REVERT: B 25 LYS cc_start: 0.6451 (ttpt) cc_final: 0.6186 (mmmt) outliers start: 33 outliers final: 23 residues processed: 150 average time/residue: 0.0963 time to fit residues: 20.7970 Evaluate side-chains 150 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 125 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 146 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 19 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 131 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 108 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 124 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN G 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.087539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.064106 restraints weight = 27706.013| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 2.80 r_work: 0.2884 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11528 Z= 0.145 Angle : 0.852 36.580 15707 Z= 0.303 Chirality : 0.042 0.321 1909 Planarity : 0.004 0.041 1884 Dihedral : 10.047 82.637 2344 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.24 % Favored : 94.54 % Rotamer: Outliers : 2.41 % Allowed : 14.21 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1.24 (0.24), residues: 1411 helix: 2.04 (0.19), residues: 762 sheet: -0.15 (0.69), residues: 77 loop : -0.72 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 81 TYR 0.016 0.001 TYR C 237 PHE 0.012 0.001 PHE E 114 TRP 0.008 0.001 TRP D 96 HIS 0.003 0.000 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00337 (11513) covalent geometry : angle 0.64915 (15677) hydrogen bonds : bond 0.03706 ( 579) hydrogen bonds : angle 4.38642 ( 1671) metal coordination : bond 0.01597 ( 12) metal coordination : angle 12.64409 ( 30) Misc. bond : bond 0.00057 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ARG cc_start: 0.9203 (tpp80) cc_final: 0.8949 (ttm170) REVERT: A 125 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.7529 (mp0) REVERT: A 161 ASN cc_start: 0.9044 (t0) cc_final: 0.8549 (t0) REVERT: C 19 ASP cc_start: 0.8161 (p0) cc_final: 0.7819 (p0) REVERT: C 354 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8908 (tt) REVERT: D 68 GLN cc_start: 0.9133 (mp10) cc_final: 0.8562 (mp10) REVERT: D 216 GLU cc_start: 0.8174 (tm-30) cc_final: 0.7876 (tm-30) REVERT: E 81 ARG cc_start: 0.7586 (ttm-80) cc_final: 0.7246 (tpp80) REVERT: E 85 MET cc_start: 0.8609 (mmm) cc_final: 0.8170 (mmm) REVERT: E 109 LYS cc_start: 0.9346 (mtmm) cc_final: 0.9051 (mtmm) REVERT: E 131 PHE cc_start: 0.8550 (t80) cc_final: 0.8311 (t80) REVERT: E 185 MET cc_start: 0.9033 (mtm) cc_final: 0.8747 (mtm) REVERT: G 79 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8018 (tm-30) REVERT: G 95 PHE cc_start: 0.7548 (m-10) cc_final: 0.7264 (m-10) REVERT: G 133 GLU cc_start: 0.8502 (mm-30) cc_final: 0.8106 (tp30) REVERT: B 25 LYS cc_start: 0.6391 (ttpt) cc_final: 0.6052 (mmmt) outliers start: 27 outliers final: 21 residues processed: 152 average time/residue: 0.1131 time to fit residues: 23.9930 Evaluate side-chains 153 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 93 LYS Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 19 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 30.0000 chunk 42 optimal weight: 0.7980 chunk 40 optimal weight: 0.0670 chunk 16 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 106 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 110 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 109 optimal weight: 1.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.090109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.066104 restraints weight = 27698.601| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.85 r_work: 0.2892 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11528 Z= 0.115 Angle : 0.824 36.223 15707 Z= 0.295 Chirality : 0.041 0.308 1909 Planarity : 0.004 0.041 1884 Dihedral : 9.714 81.836 2344 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.24 % Favored : 94.54 % Rotamer: Outliers : 2.23 % Allowed : 15.01 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1.36 (0.24), residues: 1411 helix: 2.16 (0.19), residues: 758 sheet: -0.09 (0.69), residues: 77 loop : -0.69 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 167 TYR 0.016 0.001 TYR C 237 PHE 0.011 0.001 PHE E 114 TRP 0.007 0.001 TRP D 96 HIS 0.002 0.000 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00259 (11513) covalent geometry : angle 0.62182 (15677) hydrogen bonds : bond 0.03388 ( 579) hydrogen bonds : angle 4.30087 ( 1671) metal coordination : bond 0.01116 ( 12) metal coordination : angle 12.40346 ( 30) Misc. bond : bond 0.00034 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ARG cc_start: 0.9180 (tpp80) cc_final: 0.8940 (ttm170) REVERT: A 125 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: A 161 ASN cc_start: 0.9005 (t0) cc_final: 0.8518 (t0) REVERT: C 19 ASP cc_start: 0.8092 (p0) cc_final: 0.7739 (p0) REVERT: C 354 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8908 (tt) REVERT: D 68 GLN cc_start: 0.9147 (mp10) cc_final: 0.8623 (mp10) REVERT: D 216 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7861 (tm-30) REVERT: E 85 MET cc_start: 0.8547 (mmm) cc_final: 0.8284 (mmm) REVERT: E 109 LYS cc_start: 0.9357 (mtmm) cc_final: 0.9044 (mtmm) REVERT: E 185 MET cc_start: 0.8998 (mtm) cc_final: 0.8708 (mtm) REVERT: G 67 GLU cc_start: 0.9094 (tp30) cc_final: 0.8595 (tp30) REVERT: G 79 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7847 (tm-30) REVERT: G 95 PHE cc_start: 0.7592 (m-10) cc_final: 0.7340 (m-10) REVERT: B 25 LYS cc_start: 0.6062 (ttpt) cc_final: 0.5787 (mmmt) outliers start: 25 outliers final: 18 residues processed: 149 average time/residue: 0.0986 time to fit residues: 20.9654 Evaluate side-chains 148 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain B residue 19 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 8 optimal weight: 7.9990 chunk 14 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 25 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 9.9990 chunk 42 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.090201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.066303 restraints weight = 27604.885| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 2.85 r_work: 0.2906 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11528 Z= 0.116 Angle : 0.826 35.956 15707 Z= 0.297 Chirality : 0.041 0.324 1909 Planarity : 0.004 0.047 1884 Dihedral : 9.538 81.234 2344 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.10 % Favored : 94.68 % Rotamer: Outliers : 1.61 % Allowed : 15.91 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1.40 (0.24), residues: 1411 helix: 2.18 (0.19), residues: 759 sheet: -0.07 (0.69), residues: 77 loop : -0.66 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG b 167 TYR 0.016 0.001 TYR C 237 PHE 0.012 0.001 PHE E 131 TRP 0.006 0.001 TRP A 56 HIS 0.002 0.000 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00262 (11513) covalent geometry : angle 0.62908 (15677) hydrogen bonds : bond 0.03309 ( 579) hydrogen bonds : angle 4.28102 ( 1671) metal coordination : bond 0.01136 ( 12) metal coordination : angle 12.25905 ( 30) Misc. bond : bond 0.00032 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8288 (mmm-85) cc_final: 0.8006 (mmm-85) REVERT: A 124 ARG cc_start: 0.9206 (tpp80) cc_final: 0.8971 (ttm170) REVERT: A 125 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: A 161 ASN cc_start: 0.9023 (t0) cc_final: 0.8543 (t0) REVERT: C 19 ASP cc_start: 0.8101 (p0) cc_final: 0.7754 (p0) REVERT: C 50 MET cc_start: 0.8383 (ppp) cc_final: 0.7769 (ppp) REVERT: C 354 LEU cc_start: 0.9186 (OUTLIER) cc_final: 0.8878 (tt) REVERT: D 68 GLN cc_start: 0.9145 (mp10) cc_final: 0.8624 (mp10) REVERT: E 35 MET cc_start: 0.8598 (mmp) cc_final: 0.8166 (mmp) REVERT: E 85 MET cc_start: 0.8596 (mmm) cc_final: 0.8139 (mmp) REVERT: E 109 LYS cc_start: 0.9351 (mtmm) cc_final: 0.9030 (mtmm) REVERT: E 131 PHE cc_start: 0.8238 (t80) cc_final: 0.7927 (t80) REVERT: E 147 MET cc_start: 0.8561 (tpt) cc_final: 0.8254 (tpt) REVERT: G 67 GLU cc_start: 0.9124 (tp30) cc_final: 0.8602 (tp30) REVERT: G 79 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7809 (tm-30) REVERT: G 95 PHE cc_start: 0.7613 (m-10) cc_final: 0.7386 (m-10) outliers start: 18 outliers final: 14 residues processed: 144 average time/residue: 0.1083 time to fit residues: 22.0624 Evaluate side-chains 141 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 71 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.089463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.065684 restraints weight = 27784.411| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.82 r_work: 0.2909 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11528 Z= 0.121 Angle : 0.833 35.580 15707 Z= 0.304 Chirality : 0.041 0.298 1909 Planarity : 0.004 0.058 1884 Dihedral : 9.452 80.805 2344 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.10 % Favored : 94.68 % Rotamer: Outliers : 1.61 % Allowed : 16.26 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1.43 (0.24), residues: 1411 helix: 2.19 (0.19), residues: 762 sheet: -0.07 (0.69), residues: 77 loop : -0.63 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG b 167 TYR 0.015 0.001 TYR C 237 PHE 0.012 0.001 PHE D 149 TRP 0.008 0.001 TRP b 166 HIS 0.001 0.000 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00277 (11513) covalent geometry : angle 0.64238 (15677) hydrogen bonds : bond 0.03334 ( 579) hydrogen bonds : angle 4.28889 ( 1671) metal coordination : bond 0.01293 ( 12) metal coordination : angle 12.16800 ( 30) Misc. bond : bond 0.00033 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2822 Ramachandran restraints generated. 1411 Oldfield, 0 Emsley, 1411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 124 ARG cc_start: 0.9200 (tpp80) cc_final: 0.8963 (ttm170) REVERT: A 125 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.7593 (mp0) REVERT: A 161 ASN cc_start: 0.9008 (t0) cc_final: 0.8511 (t0) REVERT: C 19 ASP cc_start: 0.8083 (p0) cc_final: 0.7735 (p0) REVERT: C 50 MET cc_start: 0.8364 (ppp) cc_final: 0.7734 (ppp) REVERT: C 218 MET cc_start: 0.8875 (mmm) cc_final: 0.8349 (mpp) REVERT: C 354 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8896 (tt) REVERT: D 68 GLN cc_start: 0.9139 (mp10) cc_final: 0.8616 (mp10) REVERT: E 85 MET cc_start: 0.8600 (mmm) cc_final: 0.8349 (mmm) REVERT: E 109 LYS cc_start: 0.9362 (mtmm) cc_final: 0.9044 (mtmm) REVERT: E 147 MET cc_start: 0.8540 (tpt) cc_final: 0.8236 (tpt) REVERT: E 185 MET cc_start: 0.8961 (mtm) cc_final: 0.8759 (mtm) REVERT: G 67 GLU cc_start: 0.9124 (tp30) cc_final: 0.8595 (tp30) REVERT: G 79 GLU cc_start: 0.8248 (tm-30) cc_final: 0.7772 (tm-30) REVERT: G 95 PHE cc_start: 0.7622 (m-10) cc_final: 0.7400 (m-10) outliers start: 18 outliers final: 14 residues processed: 136 average time/residue: 0.1060 time to fit residues: 20.5159 Evaluate side-chains 137 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain C residue 201 TYR Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain B residue 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 100 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 37 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 23 optimal weight: 8.9990 chunk 109 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.089784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.065974 restraints weight = 28053.436| |-----------------------------------------------------------------------------| r_work (start): 0.3041 rms_B_bonded: 2.84 r_work: 0.2908 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11528 Z= 0.118 Angle : 0.822 35.303 15707 Z= 0.299 Chirality : 0.041 0.295 1909 Planarity : 0.004 0.044 1884 Dihedral : 9.315 80.201 2344 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.10 % Favored : 94.68 % Rotamer: Outliers : 1.79 % Allowed : 15.91 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % 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: 1.46 (0.24), residues: 1411 helix: 2.23 (0.19), residues: 762 sheet: -0.07 (0.69), residues: 77 loop : -0.63 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG b 167 TYR 0.015 0.001 TYR C 237 PHE 0.012 0.001 PHE E 131 TRP 0.006 0.001 TRP A 56 HIS 0.003 0.000 HIS C 224 Details of bonding type rmsd covalent geometry : bond 0.00267 (11513) covalent geometry : angle 0.62983 (15677) hydrogen bonds : bond 0.03272 ( 579) hydrogen bonds : angle 4.25119 ( 1671) metal coordination : bond 0.01142 ( 12) metal coordination : angle 12.10818 ( 30) Misc. bond : bond 0.00031 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2198.02 seconds wall clock time: 38 minutes 36.52 seconds (2316.52 seconds total)