Starting phenix.real_space_refine on Tue Jul 29 07:39:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rbm_19032/07_2025/8rbm_19032.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rbm_19032/07_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_19032/07_2025/8rbm_19032.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rbm_19032/07_2025/8rbm_19032.map" model { file = "/net/cci-nas-00/data/ceres_data/8rbm_19032/07_2025/8rbm_19032.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rbm_19032/07_2025/8rbm_19032.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.58, per 1000 atoms: 0.67 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: 3.24 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.35 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: 3.02 Time building geometry restraints manager: 3.70 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: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 31.410 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.060 ------------------------------------------------------------------------------- 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 : 6.53 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (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 TRP 0.009 0.001 TRP D 83 HIS 0.001 0.000 HIS C 268 PHE 0.013 0.001 PHE E 171 TYR 0.010 0.001 TYR C 237 ARG 0.002 0.000 ARG D 128 Details of bonding type rmsd hydrogen bonds : bond 0.14313 ( 579) hydrogen bonds : angle 6.74671 ( 1671) metal coordination : bond 0.01140 ( 12) metal coordination : angle 11.19042 ( 30) covalent geometry : bond 0.00639 (11513) covalent geometry : angle 0.88388 (15677) 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 : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash 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: 0.7173 (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: 0.8691 (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: 0.2697 time to fit residues: 67.6025 Evaluate side-chains 131 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 123 time to evaluate : 1.218 ------------------------------------------------------------------------------- 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 117 optimal weight: 50.0000 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 108 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- 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 = 0.3544 r_free = 0.3544 target = 0.091995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.068145 restraints weight = 27262.375| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.86 r_work: 0.2947 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11528 Z= 0.136 Angle : 0.847 33.402 15707 Z= 0.311 Chirality : 0.045 0.353 1909 Planarity : 0.005 0.039 1884 Dihedral : 16.157 91.126 2353 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.53 % Favored : 94.19 % Rotamer: Outliers : 2.95 % Allowed : 9.83 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.24), residues: 1411 helix: 1.71 (0.20), residues: 752 sheet: 0.13 (0.73), residues: 73 loop : -0.82 (0.27), residues: 586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 96 HIS 0.002 0.001 HIS C 224 PHE 0.011 0.001 PHE G 218 TYR 0.016 0.001 TYR C 237 ARG 0.005 0.000 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 579) hydrogen bonds : angle 4.71968 ( 1671) metal coordination : bond 0.01560 ( 12) metal coordination : angle 11.52803 ( 30) covalent geometry : bond 0.00306 (11513) covalent geometry : angle 0.68108 (15677) Misc. bond : bond 0.00140 ( 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 176 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8373 (mmm-85) cc_final: 0.7814 (mmm-85) REVERT: A 100 ARG cc_start: 0.8566 (mmt180) cc_final: 0.8361 (mmt180) REVERT: A 125 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7637 (mp0) REVERT: C 19 ASP cc_start: 0.8265 (p0) cc_final: 0.7891 (p0) REVERT: C 354 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8931 (tt) REVERT: D 68 GLN cc_start: 0.9019 (mp10) cc_final: 0.8624 (mp10) REVERT: E 109 LYS cc_start: 0.9370 (mtmm) cc_final: 0.9092 (mtmm) REVERT: E 131 PHE cc_start: 0.8432 (t80) cc_final: 0.8034 (t80) REVERT: E 212 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8321 (mm) REVERT: G 67 GLU cc_start: 0.9326 (tp30) cc_final: 0.8825 (tp30) REVERT: G 106 GLU cc_start: 0.7997 (tp30) cc_final: 0.7741 (tp30) outliers start: 33 outliers final: 14 residues processed: 162 average time/residue: 0.2583 time to fit residues: 58.3257 Evaluate side-chains 146 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 1.216 ------------------------------------------------------------------------------- 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 15 LEU 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 71 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 22 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 31 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.090393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.066380 restraints weight = 27967.888| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 2.89 r_work: 0.2906 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11528 Z= 0.161 Angle : 0.865 34.502 15707 Z= 0.315 Chirality : 0.046 0.376 1909 Planarity : 0.004 0.039 1884 Dihedral : 13.222 82.828 2347 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.24 % Favored : 94.47 % Rotamer: Outliers : 2.86 % Allowed : 11.35 % Favored : 85.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.24), residues: 1411 helix: 1.79 (0.19), residues: 757 sheet: 0.23 (0.73), residues: 71 loop : -0.82 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 96 HIS 0.003 0.001 HIS C 224 PHE 0.011 0.001 PHE E 114 TYR 0.015 0.001 TYR C 237 ARG 0.004 0.000 ARG A 156 Details of bonding type rmsd hydrogen bonds : bond 0.03872 ( 579) hydrogen bonds : angle 4.59473 ( 1671) metal coordination : bond 0.01938 ( 12) metal coordination : angle 11.99400 ( 30) covalent geometry : bond 0.00376 (11513) covalent geometry : angle 0.68828 (15677) Misc. bond : bond 0.00060 ( 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 168 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8444 (mmm-85) cc_final: 0.7937 (mmm-85) REVERT: A 100 ARG cc_start: 0.8563 (mmt180) cc_final: 0.8347 (mmt180) REVERT: A 125 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.7670 (mp0) REVERT: C 19 ASP cc_start: 0.8223 (p0) cc_final: 0.7847 (p0) REVERT: C 50 MET cc_start: 0.7822 (ppp) cc_final: 0.7534 (ppp) REVERT: C 354 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8893 (tt) REVERT: D 68 GLN cc_start: 0.9052 (mp10) cc_final: 0.8515 (mp10) REVERT: E 109 LYS cc_start: 0.9374 (mtmm) cc_final: 0.9152 (mtmm) REVERT: E 132 CYS cc_start: 0.8151 (m) cc_final: 0.7672 (m) REVERT: G 79 GLU cc_start: 0.8221 (tm-30) cc_final: 0.8016 (tm-30) REVERT: G 106 GLU cc_start: 0.8081 (tp30) cc_final: 0.7864 (tp30) outliers start: 32 outliers final: 17 residues processed: 154 average time/residue: 0.2361 time to fit residues: 51.5599 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 : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 89 MET 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 217 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 100 MET 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 46 optimal weight: 6.9990 chunk 89 optimal weight: 0.6980 chunk 124 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 123 optimal weight: 0.3980 chunk 50 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- 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 = 0.3432 r_free = 0.3432 target = 0.086144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.062417 restraints weight = 27535.116| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.86 r_work: 0.2821 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11528 Z= 0.225 Angle : 0.900 36.204 15707 Z= 0.330 Chirality : 0.046 0.361 1909 Planarity : 0.005 0.051 1884 Dihedral : 11.739 83.725 2345 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.53 % Favored : 94.19 % Rotamer: Outliers : 2.77 % Allowed : 12.15 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.24), residues: 1411 helix: 1.83 (0.19), residues: 758 sheet: 0.20 (0.73), residues: 71 loop : -0.79 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 96 HIS 0.003 0.001 HIS C 75 PHE 0.013 0.001 PHE A 27 TYR 0.015 0.001 TYR C 237 ARG 0.011 0.001 ARG E 227 Details of bonding type rmsd hydrogen bonds : bond 0.04193 ( 579) hydrogen bonds : angle 4.63057 ( 1671) metal coordination : bond 0.02692 ( 12) metal coordination : angle 12.68029 ( 30) covalent geometry : bond 0.00532 (11513) covalent geometry : angle 0.70943 (15677) Misc. bond : bond 0.00107 ( 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 162 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 131 time to evaluate : 1.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.8587 (mmt180) cc_final: 0.8367 (mmt180) REVERT: A 125 GLU cc_start: 0.8816 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: A 161 ASN cc_start: 0.9129 (t0) cc_final: 0.8657 (t0) REVERT: C 19 ASP cc_start: 0.8211 (p0) cc_final: 0.7871 (p0) REVERT: C 354 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8960 (tt) REVERT: D 68 GLN cc_start: 0.9157 (mp10) cc_final: 0.8598 (mp10) REVERT: E 73 ARG cc_start: 0.6551 (OUTLIER) cc_final: 0.5827 (ttm-80) REVERT: E 109 LYS cc_start: 0.9372 (mtmm) cc_final: 0.9147 (mtmm) REVERT: E 147 MET cc_start: 0.8642 (mmt) cc_final: 0.8406 (tpt) REVERT: E 185 MET cc_start: 0.9025 (mtm) cc_final: 0.8813 (mtm) REVERT: E 186 GLU cc_start: 0.8481 (tp30) cc_final: 0.8184 (tp30) REVERT: G 79 GLU cc_start: 0.8300 (tm-30) cc_final: 0.8045 (tm-30) REVERT: G 95 PHE cc_start: 0.7527 (m-10) cc_final: 0.7165 (m-10) outliers start: 31 outliers final: 19 residues processed: 148 average time/residue: 0.2457 time to fit residues: 51.5750 Evaluate side-chains 145 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 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 73 ARG 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 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 77 optimal weight: 0.9980 chunk 108 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 117 optimal weight: 50.0000 chunk 24 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 80 optimal weight: 4.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 105 HIS G 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.086983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.063364 restraints weight = 27381.760| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.82 r_work: 0.2845 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11528 Z= 0.162 Angle : 0.863 36.440 15707 Z= 0.309 Chirality : 0.044 0.342 1909 Planarity : 0.004 0.041 1884 Dihedral : 10.893 83.495 2344 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.32 % Favored : 94.47 % Rotamer: Outliers : 2.14 % Allowed : 14.03 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.24), residues: 1411 helix: 1.89 (0.19), residues: 762 sheet: 0.20 (0.73), residues: 71 loop : -0.74 (0.27), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 96 HIS 0.003 0.001 HIS C 224 PHE 0.025 0.001 PHE B 26 TYR 0.018 0.001 TYR C 237 ARG 0.004 0.000 ARG E 227 Details of bonding type rmsd hydrogen bonds : bond 0.03874 ( 579) hydrogen bonds : angle 4.51343 ( 1671) metal coordination : bond 0.01891 ( 12) metal coordination : angle 12.73094 ( 30) covalent geometry : bond 0.00382 (11513) covalent geometry : angle 0.66033 (15677) Misc. bond : bond 0.00066 ( 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 156 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: A 89 MET cc_start: 0.8221 (tmm) cc_final: 0.7932 (tmm) REVERT: A 100 ARG cc_start: 0.8548 (mmt180) cc_final: 0.8295 (mmt180) REVERT: A 124 ARG cc_start: 0.9181 (tpp80) cc_final: 0.8910 (ttm170) REVERT: A 125 GLU cc_start: 0.8810 (OUTLIER) cc_final: 0.7711 (mp0) REVERT: A 161 ASN cc_start: 0.9076 (t0) cc_final: 0.8595 (t0) REVERT: C 19 ASP cc_start: 0.8155 (p0) cc_final: 0.7810 (p0) REVERT: C 354 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8913 (tt) REVERT: D 68 GLN cc_start: 0.9150 (mp10) cc_final: 0.8592 (mp10) REVERT: E 73 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6560 (ttm170) REVERT: E 85 MET cc_start: 0.8667 (mmm) cc_final: 0.8370 (mmm) REVERT: E 109 LYS cc_start: 0.9356 (mtmm) cc_final: 0.9082 (mtmm) REVERT: E 147 MET cc_start: 0.8545 (mmt) cc_final: 0.8317 (tpt) REVERT: E 185 MET cc_start: 0.9006 (mtm) cc_final: 0.8732 (mtm) REVERT: E 186 GLU cc_start: 0.8485 (tp30) cc_final: 0.8232 (tp30) REVERT: G 79 GLU cc_start: 0.8282 (tm-30) cc_final: 0.8034 (tm-30) REVERT: G 95 PHE cc_start: 0.7540 (m-10) cc_final: 0.7296 (m-10) outliers start: 24 outliers final: 15 residues processed: 147 average time/residue: 0.2931 time to fit residues: 60.4438 Evaluate side-chains 144 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 50 LEU 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 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 194 GLU Chi-restraints excluded: chain E residue 73 ARG 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 103 optimal weight: 0.9980 chunk 131 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 137 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 83 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.087756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.063823 restraints weight = 28083.302| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.85 r_work: 0.2829 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11528 Z= 0.167 Angle : 0.866 36.773 15707 Z= 0.310 Chirality : 0.043 0.329 1909 Planarity : 0.004 0.041 1884 Dihedral : 10.419 83.597 2344 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.24 % Favored : 94.54 % Rotamer: Outliers : 2.77 % Allowed : 13.67 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.24), residues: 1411 helix: 1.94 (0.19), residues: 763 sheet: 0.16 (0.72), residues: 71 loop : -0.72 (0.27), residues: 577 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 96 HIS 0.003 0.001 HIS C 224 PHE 0.018 0.001 PHE B 26 TYR 0.016 0.001 TYR C 237 ARG 0.009 0.000 ARG E 134 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 579) hydrogen bonds : angle 4.45485 ( 1671) metal coordination : bond 0.01959 ( 12) metal coordination : angle 12.77488 ( 30) covalent geometry : bond 0.00392 (11513) covalent geometry : angle 0.66246 (15677) Misc. bond : bond 0.00074 ( 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 161 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 130 time to evaluate : 1.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.8533 (mmt180) cc_final: 0.8285 (mmt180) REVERT: A 124 ARG cc_start: 0.9178 (tpp80) cc_final: 0.8913 (ttm170) REVERT: A 125 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.7652 (mp0) REVERT: A 161 ASN cc_start: 0.9071 (t0) cc_final: 0.8584 (t0) REVERT: C 19 ASP cc_start: 0.8182 (p0) cc_final: 0.7841 (p0) REVERT: C 354 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8927 (tt) REVERT: D 68 GLN cc_start: 0.9165 (mp10) cc_final: 0.8624 (mp10) REVERT: E 73 ARG cc_start: 0.7151 (OUTLIER) cc_final: 0.6826 (ttm-80) REVERT: E 85 MET cc_start: 0.8587 (mmm) cc_final: 0.8129 (mmm) REVERT: E 109 LYS cc_start: 0.9353 (mtmm) cc_final: 0.9079 (mtmm) REVERT: E 185 MET cc_start: 0.9070 (mtm) cc_final: 0.8767 (mtm) REVERT: E 186 GLU cc_start: 0.8489 (tp30) cc_final: 0.8178 (tp30) REVERT: G 35 MET cc_start: 0.3127 (ttt) cc_final: 0.2855 (tpt) REVERT: G 79 GLU cc_start: 0.8347 (tm-30) cc_final: 0.8088 (tm-30) REVERT: G 95 PHE cc_start: 0.7581 (m-10) cc_final: 0.7287 (m-10) outliers start: 31 outliers final: 21 residues processed: 150 average time/residue: 0.2997 time to fit residues: 63.9257 Evaluate side-chains 151 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 127 time to evaluate : 1.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 50 LEU 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 34 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 73 ARG Chi-restraints excluded: chain E residue 97 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 111 optimal weight: 6.9990 chunk 43 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 124 optimal weight: 8.9990 chunk 125 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 21 optimal weight: 8.9990 chunk 18 optimal weight: 7.9990 chunk 137 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.086720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.063246 restraints weight = 28020.122| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.79 r_work: 0.2864 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11528 Z= 0.165 Angle : 0.877 36.863 15707 Z= 0.314 Chirality : 0.043 0.321 1909 Planarity : 0.004 0.046 1884 Dihedral : 10.110 83.486 2344 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.39 % Favored : 94.40 % Rotamer: Outliers : 2.41 % Allowed : 14.75 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.24), residues: 1411 helix: 2.00 (0.19), residues: 761 sheet: -0.21 (0.69), residues: 77 loop : -0.72 (0.27), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 96 HIS 0.003 0.000 HIS C 224 PHE 0.012 0.001 PHE E 114 TYR 0.015 0.001 TYR C 237 ARG 0.007 0.000 ARG b 167 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 579) hydrogen bonds : angle 4.45346 ( 1671) metal coordination : bond 0.01916 ( 12) metal coordination : angle 12.82730 ( 30) covalent geometry : bond 0.00389 (11513) covalent geometry : angle 0.67520 (15677) Misc. bond : bond 0.00072 ( 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 162 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 135 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7928 (tmm) cc_final: 0.7515 (tmm) REVERT: A 100 ARG cc_start: 0.8536 (mmt180) cc_final: 0.8277 (mmt180) REVERT: A 124 ARG cc_start: 0.9206 (tpp80) cc_final: 0.8965 (ttm170) REVERT: A 125 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: A 161 ASN cc_start: 0.9046 (t0) cc_final: 0.8548 (t0) REVERT: C 19 ASP cc_start: 0.8170 (p0) cc_final: 0.7826 (p0) REVERT: C 354 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8916 (tt) REVERT: D 68 GLN cc_start: 0.9155 (mp10) cc_final: 0.8591 (mp10) REVERT: D 216 GLU cc_start: 0.8187 (tm-30) cc_final: 0.7905 (tm-30) REVERT: D 336 TYR cc_start: 0.8923 (m-10) cc_final: 0.8675 (m-10) REVERT: E 81 ARG cc_start: 0.7564 (ttm-80) cc_final: 0.7360 (tpp80) REVERT: E 85 MET cc_start: 0.8487 (mmm) cc_final: 0.8100 (mmm) REVERT: E 109 LYS cc_start: 0.9351 (mtmm) cc_final: 0.9050 (mtmm) REVERT: E 185 MET cc_start: 0.9076 (mtm) cc_final: 0.8762 (mtm) REVERT: G 79 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8129 (tm-30) REVERT: G 95 PHE cc_start: 0.7584 (m-10) cc_final: 0.7333 (m-10) REVERT: G 133 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8125 (tp30) REVERT: B 25 LYS cc_start: 0.6533 (ttpt) cc_final: 0.6219 (mmmt) outliers start: 27 outliers final: 21 residues processed: 151 average time/residue: 0.2655 time to fit residues: 56.6242 Evaluate side-chains 148 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 50 LEU 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 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 217 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 32 LEU 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 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 122 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 118 optimal weight: 0.9990 chunk 133 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 53 optimal weight: 10.0000 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.089101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.065051 restraints weight = 28146.213| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 2.86 r_work: 0.2879 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11528 Z= 0.132 Angle : 0.852 36.462 15707 Z= 0.305 Chirality : 0.041 0.310 1909 Planarity : 0.004 0.041 1884 Dihedral : 9.738 82.783 2344 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.17 % Favored : 94.61 % Rotamer: Outliers : 1.97 % Allowed : 15.37 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.24), residues: 1411 helix: 2.05 (0.19), residues: 762 sheet: -0.16 (0.69), residues: 77 loop : -0.71 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 96 HIS 0.002 0.000 HIS C 224 PHE 0.015 0.001 PHE B 26 TYR 0.015 0.001 TYR C 237 ARG 0.007 0.000 ARG b 167 Details of bonding type rmsd hydrogen bonds : bond 0.03512 ( 579) hydrogen bonds : angle 4.36293 ( 1671) metal coordination : bond 0.01354 ( 12) metal coordination : angle 12.64427 ( 30) covalent geometry : bond 0.00305 (11513) covalent geometry : angle 0.64936 (15677) Misc. bond : bond 0.00046 ( 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 158 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7925 (tmm) cc_final: 0.7619 (tmm) REVERT: A 100 ARG cc_start: 0.8499 (mmt180) cc_final: 0.8245 (mmt180) REVERT: A 124 ARG cc_start: 0.9193 (tpp80) cc_final: 0.8940 (ttm170) REVERT: A 125 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.7561 (mp0) REVERT: A 161 ASN cc_start: 0.9019 (t0) cc_final: 0.8554 (t0) REVERT: C 19 ASP cc_start: 0.8104 (p0) cc_final: 0.7751 (p0) REVERT: C 354 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8901 (tt) REVERT: D 68 GLN cc_start: 0.9131 (mp10) cc_final: 0.8624 (mp10) REVERT: D 216 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7900 (tm-30) REVERT: E 85 MET cc_start: 0.8430 (mmm) cc_final: 0.8167 (mmm) REVERT: E 109 LYS cc_start: 0.9357 (mtmm) cc_final: 0.9071 (mtmm) REVERT: E 185 MET cc_start: 0.9079 (mtm) cc_final: 0.8816 (mtm) REVERT: G 79 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8119 (tm-30) REVERT: G 95 PHE cc_start: 0.7632 (m-10) cc_final: 0.7412 (m-10) REVERT: B 25 LYS cc_start: 0.6299 (ttpt) cc_final: 0.5978 (mmmt) outliers start: 22 outliers final: 16 residues processed: 152 average time/residue: 0.2535 time to fit residues: 54.7748 Evaluate side-chains 147 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 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 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 102 SER 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 73 ARG 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 94 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 117 optimal weight: 7.9990 chunk 81 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 40 optimal weight: 9.9990 chunk 86 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN E 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.089136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.065241 restraints weight = 28081.996| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.84 r_work: 0.2887 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2660 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 : 0.842 36.087 15707 Z= 0.305 Chirality : 0.041 0.302 1909 Planarity : 0.004 0.046 1884 Dihedral : 9.512 82.193 2344 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.24 % Favored : 94.54 % Rotamer: Outliers : 1.70 % Allowed : 16.35 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.24), residues: 1411 helix: 2.14 (0.19), residues: 759 sheet: -0.18 (0.68), residues: 77 loop : -0.68 (0.28), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 48 HIS 0.003 0.000 HIS C 224 PHE 0.013 0.001 PHE B 26 TYR 0.016 0.001 TYR C 237 ARG 0.011 0.000 ARG b 167 Details of bonding type rmsd hydrogen bonds : bond 0.03388 ( 579) hydrogen bonds : angle 4.30585 ( 1671) metal coordination : bond 0.01207 ( 12) metal coordination : angle 12.43221 ( 30) covalent geometry : bond 0.00276 (11513) covalent geometry : angle 0.64406 (15677) Misc. bond : bond 0.00036 ( 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: 19 poor density : 132 time to evaluate : 1.151 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7807 (tmm) cc_final: 0.7524 (tmm) REVERT: A 100 ARG cc_start: 0.8524 (mmt180) cc_final: 0.8264 (mmt180) REVERT: A 124 ARG cc_start: 0.9210 (tpp80) cc_final: 0.8955 (ttm170) REVERT: A 125 GLU cc_start: 0.8724 (OUTLIER) cc_final: 0.7564 (mp0) REVERT: A 161 ASN cc_start: 0.9035 (t0) cc_final: 0.8549 (t0) REVERT: C 19 ASP cc_start: 0.8134 (p0) cc_final: 0.7791 (p0) REVERT: C 50 MET cc_start: 0.8364 (ppp) cc_final: 0.7734 (ppp) REVERT: C 354 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8905 (tt) REVERT: D 68 GLN cc_start: 0.9134 (mp10) cc_final: 0.8592 (mp10) REVERT: D 216 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7906 (tm-30) REVERT: E 50 ASN cc_start: 0.8468 (m-40) cc_final: 0.8197 (m110) REVERT: E 85 MET cc_start: 0.8451 (mmm) cc_final: 0.8181 (mmm) REVERT: E 109 LYS cc_start: 0.9346 (mtmm) cc_final: 0.9020 (mtmm) REVERT: E 185 MET cc_start: 0.9058 (mtm) cc_final: 0.8801 (mtm) REVERT: G 67 GLU cc_start: 0.9109 (tp30) cc_final: 0.8627 (tp30) REVERT: G 79 GLU cc_start: 0.8407 (tm-30) cc_final: 0.8124 (tm-30) REVERT: B 25 LYS cc_start: 0.6286 (ttpt) cc_final: 0.5906 (mmmt) outliers start: 19 outliers final: 16 residues processed: 145 average time/residue: 0.2571 time to fit residues: 53.0231 Evaluate side-chains 148 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 102 SER 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 73 ARG 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 61 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 71 optimal weight: 0.8980 chunk 116 optimal weight: 0.0020 chunk 112 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 99 optimal weight: 0.9980 chunk 128 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- 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 = 0.3502 r_free = 0.3502 target = 0.089995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.066303 restraints weight = 27998.117| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.85 r_work: 0.2915 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2760 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= 0.112 Angle : 0.828 35.307 15707 Z= 0.300 Chirality : 0.041 0.295 1909 Planarity : 0.004 0.041 1884 Dihedral : 9.291 81.359 2344 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.24 % Favored : 94.54 % Rotamer: Outliers : 1.79 % Allowed : 16.53 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.24), residues: 1411 helix: 2.15 (0.19), residues: 762 sheet: -0.17 (0.68), residues: 77 loop : -0.65 (0.28), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 56 HIS 0.001 0.000 HIS C 224 PHE 0.019 0.001 PHE E 131 TYR 0.015 0.001 TYR C 237 ARG 0.010 0.000 ARG b 167 Details of bonding type rmsd hydrogen bonds : bond 0.03239 ( 579) hydrogen bonds : angle 4.27516 ( 1671) metal coordination : bond 0.01083 ( 12) metal coordination : angle 12.22842 ( 30) covalent geometry : bond 0.00248 (11513) covalent geometry : angle 0.63260 (15677) Misc. bond : bond 0.00025 ( 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 157 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 137 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7733 (tmm) cc_final: 0.7448 (tmm) REVERT: A 92 ARG cc_start: 0.8253 (mmm-85) cc_final: 0.8046 (mmm-85) REVERT: A 100 ARG cc_start: 0.8485 (mmt180) cc_final: 0.8196 (mmt180) REVERT: A 124 ARG cc_start: 0.9242 (tpp80) cc_final: 0.8984 (ttm170) REVERT: A 125 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.7512 (mp0) REVERT: A 161 ASN cc_start: 0.9063 (t0) cc_final: 0.8563 (t0) REVERT: C 19 ASP cc_start: 0.8171 (p0) cc_final: 0.7829 (p0) REVERT: C 50 MET cc_start: 0.8389 (ppp) cc_final: 0.7847 (ppp) REVERT: C 354 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8893 (tt) REVERT: D 68 GLN cc_start: 0.9130 (mp10) cc_final: 0.8577 (mp10) REVERT: E 85 MET cc_start: 0.8436 (mmm) cc_final: 0.8171 (mmm) REVERT: E 109 LYS cc_start: 0.9325 (mtmm) cc_final: 0.8981 (mtmm) REVERT: E 131 PHE cc_start: 0.8546 (t80) cc_final: 0.7307 (t80) REVERT: E 185 MET cc_start: 0.9073 (mtm) cc_final: 0.8798 (mtm) REVERT: G 67 GLU cc_start: 0.9120 (tp30) cc_final: 0.8620 (tp30) REVERT: G 79 GLU cc_start: 0.8434 (tm-30) cc_final: 0.8129 (tm-30) REVERT: G 95 PHE cc_start: 0.7506 (m-10) cc_final: 0.7126 (m-10) REVERT: B 25 LYS cc_start: 0.6256 (ttpt) cc_final: 0.5860 (mmmt) outliers start: 20 outliers final: 15 residues processed: 148 average time/residue: 0.2722 time to fit residues: 57.5596 Evaluate side-chains 146 residues out of total 1120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 73 ARG 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 29 optimal weight: 8.9990 chunk 80 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 129 optimal weight: 0.7980 chunk 104 optimal weight: 10.0000 chunk 47 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 131 optimal weight: 8.9990 chunk 37 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3473 r_free = 0.3473 target = 0.088331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.064595 restraints weight = 28041.624| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.80 r_work: 0.2871 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 11528 Z= 0.163 Angle : 0.854 35.493 15707 Z= 0.315 Chirality : 0.042 0.298 1909 Planarity : 0.004 0.055 1884 Dihedral : 9.353 81.895 2344 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.03 % Favored : 94.76 % Rotamer: Outliers : 2.14 % Allowed : 16.44 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.24), residues: 1411 helix: 2.18 (0.19), residues: 758 sheet: -0.11 (0.68), residues: 77 loop : -0.69 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 56 HIS 0.003 0.000 HIS C 224 PHE 0.018 0.001 PHE E 131 TYR 0.015 0.001 TYR C 237 ARG 0.011 0.000 ARG b 167 Details of bonding type rmsd hydrogen bonds : bond 0.03621 ( 579) hydrogen bonds : angle 4.30807 ( 1671) metal coordination : bond 0.01786 ( 12) metal coordination : angle 12.41180 ( 30) covalent geometry : bond 0.00384 (11513) covalent geometry : angle 0.66065 (15677) Misc. bond : bond 0.00068 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4893.15 seconds wall clock time: 88 minutes 35.38 seconds (5315.38 seconds total)