Starting phenix.real_space_refine on Sun Aug 4 18:23:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbm_19032/08_2024/8rbm_19032.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbm_19032/08_2024/8rbm_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbm_19032/08_2024/8rbm_19032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbm_19032/08_2024/8rbm_19032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbm_19032/08_2024/8rbm_19032.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rbm_19032/08_2024/8rbm_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 Residue "E GLU 225": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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 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 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: 6.95, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.82 Conformation dependent library (CDL) restraints added in 2.0 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: 1.33 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: 3.08 Time building geometry restraints manager: 5.02 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 1.610 1.819 -0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C4A FMN C 500 " pdb=" N5 FMN C 500 " ideal model delta sigma weight residual 1.380 1.297 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C10 FMN C 500 " pdb=" C4A FMN C 500 " ideal model delta sigma weight residual 1.390 1.470 -0.080 2.00e-02 2.50e+03 1.60e+01 bond pdb=" C4A FMN G 301 " pdb=" N5 FMN G 301 " ideal model delta sigma weight residual 1.380 1.300 0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" C4A FMN D 411 " pdb=" N5 FMN D 411 " ideal model delta sigma weight residual 1.380 1.301 0.079 2.00e-02 2.50e+03 1.57e+01 ... (remaining 11508 not shown) Histogram of bond angle deviations from ideal: 73.55 - 85.65: 26 85.65 - 97.74: 1 97.74 - 109.83: 1594 109.83 - 121.92: 11872 121.92 - 134.01: 2184 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=" O1P FMN D 411 " pdb=" P FMN D 411 " pdb=" O2P FMN D 411 " ideal model delta sigma weight residual 109.50 119.69 -10.19 3.00e+00 1.11e-01 1.15e+01 angle pdb=" O1P FMN C 500 " pdb=" P FMN C 500 " pdb=" O5' FMN C 500 " ideal model delta sigma weight residual 108.20 98.10 10.10 3.00e+00 1.11e-01 1.13e+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 ... (remaining 15672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.95: 6989 33.95 - 67.90: 192 67.90 - 101.85: 52 101.85 - 135.80: 35 135.80 - 169.75: 2 Dihedral angle restraints: 7270 sinusoidal: 3258 harmonic: 4012 Sorted by residual: dihedral pdb=" C10 FMN D 411 " pdb=" C1' FMN D 411 " pdb=" N10 FMN D 411 " pdb=" C2' FMN D 411 " ideal model delta sinusoidal sigma weight residual 257.59 87.84 169.75 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' FMN G 301 " pdb=" O5' FMN G 301 " pdb=" P FMN G 301 " pdb=" O1P FMN G 301 " ideal model delta sinusoidal sigma weight residual 75.26 -144.69 -140.06 1 2.00e+01 2.50e-03 4.24e+01 dihedral pdb=" C5' FMN C 500 " pdb=" O5' FMN C 500 " pdb=" P FMN C 500 " pdb=" O1P FMN C 500 " ideal model delta sinusoidal sigma weight residual 75.26 176.68 -101.42 1 2.00e+01 2.50e-03 2.88e+01 ... (remaining 7267 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.003: 1905 1.003 - 2.007: 0 2.007 - 3.010: 0 3.010 - 4.014: 0 4.014 - 5.017: 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 -2.47 2.55 -5.02 2.00e-01 2.50e+01 6.29e+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 -2.47 2.43 -4.90 2.00e-01 2.50e+01 6.00e+02 ... (remaining 1906 not shown) Planarity restraints: 1881 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G 301 " 0.122 2.00e-02 2.50e+03 3.35e-02 5.33e+01 pdb=" C10 FMN G 301 " -0.012 2.00e-02 2.50e+03 pdb=" C2 FMN G 301 " -0.023 2.00e-02 2.50e+03 pdb=" C4 FMN G 301 " 0.009 2.00e-02 2.50e+03 pdb=" C4A FMN G 301 " 0.002 2.00e-02 2.50e+03 pdb=" C5A FMN G 301 " 0.003 2.00e-02 2.50e+03 pdb=" C6 FMN G 301 " 0.008 2.00e-02 2.50e+03 pdb=" C7 FMN G 301 " -0.000 2.00e-02 2.50e+03 pdb=" C7M FMN G 301 " 0.009 2.00e-02 2.50e+03 pdb=" C8 FMN G 301 " -0.015 2.00e-02 2.50e+03 pdb=" C8M FMN G 301 " -0.038 2.00e-02 2.50e+03 pdb=" C9 FMN G 301 " -0.020 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 " -0.004 2.00e-02 2.50e+03 pdb=" N3 FMN G 301 " -0.005 2.00e-02 2.50e+03 pdb=" N5 FMN G 301 " 0.006 2.00e-02 2.50e+03 pdb=" O2 FMN G 301 " -0.037 2.00e-02 2.50e+03 pdb=" O4 FMN G 301 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN D 411 " 0.016 2.00e-02 2.50e+03 1.21e-02 6.96e+00 pdb=" C10 FMN D 411 " -0.001 2.00e-02 2.50e+03 pdb=" C2 FMN D 411 " -0.013 2.00e-02 2.50e+03 pdb=" C4 FMN D 411 " 0.003 2.00e-02 2.50e+03 pdb=" C4A FMN D 411 " 0.003 2.00e-02 2.50e+03 pdb=" C5A FMN D 411 " 0.011 2.00e-02 2.50e+03 pdb=" C6 FMN D 411 " 0.003 2.00e-02 2.50e+03 pdb=" C7 FMN D 411 " -0.003 2.00e-02 2.50e+03 pdb=" C7M FMN D 411 " -0.032 2.00e-02 2.50e+03 pdb=" C8 FMN D 411 " 0.001 2.00e-02 2.50e+03 pdb=" C8M FMN D 411 " -0.003 2.00e-02 2.50e+03 pdb=" C9 FMN D 411 " 0.008 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 " 0.006 2.00e-02 2.50e+03 pdb=" N3 FMN D 411 " -0.008 2.00e-02 2.50e+03 pdb=" N5 FMN D 411 " 0.008 2.00e-02 2.50e+03 pdb=" O2 FMN D 411 " -0.019 2.00e-02 2.50e+03 pdb=" O4 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 1878 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: 1.120 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 33.910 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.470 ------------------------------------------------------------------------------- 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 : 0.007 0.209 11513 Z= 0.403 Angle : 0.913 10.236 15677 Z= 0.383 Chirality : 0.232 5.017 1909 Planarity : 0.005 0.044 1881 Dihedral : 19.316 169.748 4706 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 *********************** 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 fitting. rotamer outliers: 23 poor density : 164 time to evaluate : 1.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7430 (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: 0.7780 (mm) REVERT: G 95 PHE cc_start: 0.7645 (m-10) cc_final: 0.7217 (m-10) outliers start: 23 outliers final: 4 residues processed: 182 average time/residue: 0.2673 time to fit residues: 66.7199 Evaluate side-chains 129 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 1.128 ------------------------------------------------------------------------------- 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 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: 0.8980 chunk 35 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 126 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 G 125 ASN G 225 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11513 Z= 0.209 Angle : 0.685 8.540 15677 Z= 0.310 Chirality : 0.046 0.342 1909 Planarity : 0.004 0.039 1881 Dihedral : 17.055 170.320 2346 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.60 % Favored : 94.12 % Rotamer: Outliers : 2.86 % Allowed : 10.10 % Favored : 87.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.24), residues: 1411 helix: 1.69 (0.20), residues: 752 sheet: 0.12 (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 0.003 0.001 HIS C 224 PHE 0.011 0.001 PHE E 114 TYR 0.016 0.001 TYR C 237 ARG 0.006 0.000 ARG b 167 *********************** 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 173 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 1.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8119 (mmm-85) cc_final: 0.7642 (mmm-85) REVERT: A 125 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7502 (mp0) REVERT: C 19 ASP cc_start: 0.7598 (p0) cc_final: 0.7210 (p0) REVERT: C 354 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8749 (tt) REVERT: E 66 ASN cc_start: 0.8093 (m-40) cc_final: 0.7880 (m-40) REVERT: E 212 LEU cc_start: 0.8153 (OUTLIER) cc_final: 0.7901 (mm) REVERT: G 67 GLU cc_start: 0.8821 (tp30) cc_final: 0.8524 (tp30) outliers start: 32 outliers final: 14 residues processed: 159 average time/residue: 0.2690 time to fit residues: 59.0453 Evaluate side-chains 141 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 124 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 41 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 0.0470 chunk 85 optimal weight: 0.0060 chunk 34 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 chunk 136 optimal weight: 10.0000 chunk 112 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 101 optimal weight: 9.9990 overall best weight: 0.9898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 189 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11513 Z= 0.175 Angle : 0.664 9.128 15677 Z= 0.300 Chirality : 0.045 0.380 1909 Planarity : 0.004 0.040 1881 Dihedral : 13.947 169.729 2345 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.24 % Favored : 94.47 % Rotamer: Outliers : 2.86 % Allowed : 10.90 % Favored : 86.24 % 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: 1.08 (0.24), residues: 1411 helix: 1.91 (0.20), residues: 752 sheet: 0.29 (0.74), residues: 71 loop : -0.82 (0.27), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 96 HIS 0.003 0.000 HIS C 224 PHE 0.011 0.001 PHE C 121 TYR 0.016 0.001 TYR C 237 ARG 0.004 0.000 ARG A 156 *********************** 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 169 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 137 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.8089 (mmm-85) cc_final: 0.7666 (mmm-85) REVERT: A 125 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.7466 (mp0) REVERT: C 19 ASP cc_start: 0.7532 (p0) cc_final: 0.7135 (p0) REVERT: C 354 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8712 (tt) REVERT: E 212 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7952 (mm) outliers start: 32 outliers final: 16 residues processed: 154 average time/residue: 0.2489 time to fit residues: 54.2506 Evaluate side-chains 144 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 1.204 ------------------------------------------------------------------------------- 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 C residue 140 LEU 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 277 CYS 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 E residue 212 LEU Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain B residue 19 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 13 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 120 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 66 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11513 Z= 0.223 Angle : 0.654 8.889 15677 Z= 0.300 Chirality : 0.045 0.354 1909 Planarity : 0.004 0.039 1881 Dihedral : 12.224 170.955 2343 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.39 % Favored : 94.33 % Rotamer: Outliers : 2.14 % Allowed : 12.51 % Favored : 85.34 % 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: 2.01 (0.20), residues: 751 sheet: 0.20 (0.72), residues: 71 loop : -0.77 (0.27), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 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 0.005 0.000 ARG G 73 *********************** 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 156 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.8567 (OUTLIER) cc_final: 0.7440 (mp0) REVERT: A 161 ASN cc_start: 0.8798 (t0) cc_final: 0.8463 (t0) REVERT: C 19 ASP cc_start: 0.7518 (p0) cc_final: 0.7137 (p0) REVERT: C 354 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8761 (tt) REVERT: G 65 ILE cc_start: 0.8791 (mt) cc_final: 0.8520 (mt) outliers start: 24 outliers final: 16 residues processed: 143 average time/residue: 0.2636 time to fit residues: 52.4087 Evaluate side-chains 144 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 106 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain C residue 140 LEU 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 194 GLU 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 100 MET Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 26 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 100 optimal weight: 0.6980 chunk 55 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 33 optimal weight: 7.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 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 : 0.005 0.048 11513 Z= 0.320 Angle : 0.688 11.192 15677 Z= 0.321 Chirality : 0.045 0.341 1909 Planarity : 0.004 0.040 1881 Dihedral : 11.505 171.780 2340 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.53 % Favored : 94.26 % Rotamer: Outliers : 2.77 % Allowed : 13.05 % Favored : 84.18 % 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: 1.14 (0.24), residues: 1411 helix: 1.95 (0.19), residues: 758 sheet: 0.16 (0.72), residues: 71 loop : -0.78 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 96 HIS 0.005 0.001 HIS E 105 PHE 0.018 0.002 PHE B 26 TYR 0.014 0.001 TYR C 237 ARG 0.008 0.000 ARG E 134 *********************** 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 162 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 131 time to evaluate : 1.281 Fit side-chains revert: symmetry clash REVERT: A 124 ARG cc_start: 0.8857 (tpp80) cc_final: 0.8648 (ttm170) REVERT: A 125 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: A 161 ASN cc_start: 0.8818 (t0) cc_final: 0.8500 (t0) REVERT: C 19 ASP cc_start: 0.7552 (p0) cc_final: 0.7203 (p0) REVERT: C 354 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8802 (tt) REVERT: G 65 ILE cc_start: 0.8854 (mt) cc_final: 0.8596 (mt) outliers start: 31 outliers final: 19 residues processed: 147 average time/residue: 0.2529 time to fit residues: 51.5348 Evaluate side-chains 144 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 1.185 ------------------------------------------------------------------------------- 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 106 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 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 32 LEU 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 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 45 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 134 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 11 optimal weight: 0.0770 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 0.0470 overall best weight: 0.6236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.078 11513 Z= 0.163 Angle : 0.631 9.396 15677 Z= 0.294 Chirality : 0.042 0.321 1909 Planarity : 0.004 0.052 1881 Dihedral : 10.838 169.368 2340 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.32 % Favored : 94.47 % Rotamer: Outliers : 2.41 % Allowed : 14.12 % Favored : 83.47 % 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: 1.27 (0.24), residues: 1411 helix: 2.09 (0.20), residues: 755 sheet: 0.19 (0.72), residues: 71 loop : -0.75 (0.27), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 96 HIS 0.003 0.000 HIS C 224 PHE 0.014 0.001 PHE B 26 TYR 0.018 0.001 TYR C 237 ARG 0.003 0.000 ARG E 73 *********************** 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 163 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 136 time to evaluate : 1.153 Fit side-chains revert: symmetry clash REVERT: A 89 MET cc_start: 0.8110 (tmm) cc_final: 0.7646 (tmm) REVERT: A 93 LYS cc_start: 0.7154 (pttm) cc_final: 0.6878 (pttm) REVERT: A 125 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.7391 (mp0) REVERT: A 161 ASN cc_start: 0.8734 (t0) cc_final: 0.8397 (t0) REVERT: C 19 ASP cc_start: 0.7497 (p0) cc_final: 0.7142 (p0) REVERT: C 354 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8736 (tt) REVERT: G 35 MET cc_start: 0.3487 (ttt) cc_final: 0.3208 (tpt) REVERT: G 65 ILE cc_start: 0.8837 (mt) cc_final: 0.8567 (mt) outliers start: 27 outliers final: 18 residues processed: 152 average time/residue: 0.2458 time to fit residues: 52.5388 Evaluate side-chains 150 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 130 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 161 THR Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain E residue 170 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 113 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 133 optimal weight: 0.6980 chunk 83 optimal weight: 4.9990 chunk 81 optimal weight: 0.0270 chunk 61 optimal weight: 7.9990 chunk 82 optimal weight: 5.9990 overall best weight: 1.0442 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11513 Z= 0.181 Angle : 0.636 9.893 15677 Z= 0.298 Chirality : 0.041 0.311 1909 Planarity : 0.004 0.040 1881 Dihedral : 10.530 170.411 2340 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.17 % Favored : 94.61 % Rotamer: Outliers : 2.23 % Allowed : 14.92 % 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: 1.33 (0.24), residues: 1411 helix: 2.12 (0.19), residues: 758 sheet: -0.12 (0.69), residues: 77 loop : -0.68 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 96 HIS 0.003 0.000 HIS C 224 PHE 0.015 0.001 PHE E 131 TYR 0.017 0.001 TYR C 237 ARG 0.010 0.000 ARG E 134 *********************** 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 159 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 1.181 Fit side-chains revert: symmetry clash REVERT: A 89 MET cc_start: 0.8119 (tmm) cc_final: 0.7658 (tmm) REVERT: A 93 LYS cc_start: 0.7216 (pttm) cc_final: 0.6978 (pttm) REVERT: A 125 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7379 (mp0) REVERT: A 161 ASN cc_start: 0.8771 (t0) cc_final: 0.8426 (t0) REVERT: C 19 ASP cc_start: 0.7507 (p0) cc_final: 0.7149 (p0) REVERT: C 354 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8737 (tt) REVERT: G 65 ILE cc_start: 0.8830 (mt) cc_final: 0.8568 (mt) REVERT: G 78 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7796 (ptp90) outliers start: 25 outliers final: 16 residues processed: 148 average time/residue: 0.2409 time to fit residues: 50.2832 Evaluate side-chains 146 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 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 50 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 224 HIS Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain 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 97 ASP Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain B residue 19 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 26 optimal weight: 9.9990 chunk 25 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN E 135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11513 Z= 0.197 Angle : 0.657 10.513 15677 Z= 0.304 Chirality : 0.042 0.306 1909 Planarity : 0.004 0.040 1881 Dihedral : 10.347 170.739 2340 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.53 % Favored : 94.26 % Rotamer: Outliers : 2.32 % Allowed : 15.28 % Favored : 82.39 % 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: 2.17 (0.19), residues: 758 sheet: -0.09 (0.69), residues: 77 loop : -0.69 (0.28), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 96 HIS 0.002 0.000 HIS C 224 PHE 0.017 0.001 PHE E 131 TYR 0.016 0.001 TYR C 237 ARG 0.008 0.000 ARG E 81 *********************** 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 fitting. rotamer outliers: 26 poor density : 132 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: A 89 MET cc_start: 0.8111 (tmm) cc_final: 0.7701 (tmm) REVERT: A 125 GLU cc_start: 0.8569 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: A 161 ASN cc_start: 0.8764 (t0) cc_final: 0.8425 (t0) REVERT: C 19 ASP cc_start: 0.7507 (p0) cc_final: 0.7158 (p0) REVERT: C 354 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8732 (tt) REVERT: E 171 PHE cc_start: 0.7303 (m-80) cc_final: 0.7099 (m-80) REVERT: G 65 ILE cc_start: 0.8843 (mt) cc_final: 0.8580 (mt) REVERT: G 67 GLU cc_start: 0.8801 (tp30) cc_final: 0.8382 (tp30) outliers start: 26 outliers final: 21 residues processed: 147 average time/residue: 0.2388 time to fit residues: 49.7898 Evaluate side-chains 153 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 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 D residue 266 LEU 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 97 ASP Chi-restraints excluded: chain E residue 135 ASN Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain E residue 212 LEU Chi-restraints excluded: chain G residue 78 ARG Chi-restraints excluded: chain B residue 19 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 0.0070 chunk 117 optimal weight: 30.0000 chunk 124 optimal weight: 9.9990 chunk 75 optimal weight: 0.4980 chunk 54 optimal weight: 8.9990 chunk 98 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 118 optimal weight: 7.9990 chunk 81 optimal weight: 0.0770 chunk 132 optimal weight: 0.6980 overall best weight: 0.4156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11513 Z= 0.157 Angle : 0.650 11.747 15677 Z= 0.304 Chirality : 0.041 0.298 1909 Planarity : 0.004 0.048 1881 Dihedral : 10.093 169.564 2340 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.17 % Favored : 94.61 % Rotamer: Outliers : 2.14 % Allowed : 15.37 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.19 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.13 (0.19), residues: 761 sheet: -0.07 (0.69), residues: 77 loop : -0.64 (0.28), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 96 HIS 0.003 0.000 HIS E 105 PHE 0.019 0.001 PHE G 95 TYR 0.016 0.001 TYR C 237 ARG 0.010 0.000 ARG b 167 *********************** 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 158 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.8018 (tmm) cc_final: 0.7592 (tmm) REVERT: A 92 ARG cc_start: 0.7830 (mmm-85) cc_final: 0.7609 (mmm-85) REVERT: A 125 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7360 (mp0) REVERT: A 161 ASN cc_start: 0.8744 (t0) cc_final: 0.8399 (t0) REVERT: C 19 ASP cc_start: 0.7493 (p0) cc_final: 0.7135 (p0) REVERT: C 354 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8717 (tt) REVERT: E 131 PHE cc_start: 0.6877 (t80) cc_final: 0.6648 (t80) REVERT: G 65 ILE cc_start: 0.8846 (mt) cc_final: 0.8590 (mt) REVERT: G 67 GLU cc_start: 0.8786 (tp30) cc_final: 0.8351 (tp30) REVERT: G 78 ARG cc_start: 0.8335 (OUTLIER) cc_final: 0.7835 (ptp90) outliers start: 24 outliers final: 19 residues processed: 149 average time/residue: 0.2448 time to fit residues: 51.4343 Evaluate side-chains 153 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 131 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 315 LEU Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 266 LEU 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 97 ASP Chi-restraints excluded: chain E residue 170 LEU 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 80 optimal weight: 2.9990 chunk 62 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 138 optimal weight: 1.9990 chunk 127 optimal weight: 0.9990 chunk 110 optimal weight: 3.9990 chunk 11 optimal weight: 0.3980 chunk 85 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 117 optimal weight: 40.0000 overall best weight: 1.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.2718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11513 Z= 0.226 Angle : 0.678 11.608 15677 Z= 0.315 Chirality : 0.042 0.299 1909 Planarity : 0.004 0.043 1881 Dihedral : 10.131 171.697 2340 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.39 % Favored : 94.40 % 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: 1.38 (0.24), residues: 1411 helix: 2.16 (0.19), residues: 761 sheet: -0.05 (0.69), residues: 77 loop : -0.66 (0.28), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 56 HIS 0.002 0.000 HIS C 17 PHE 0.014 0.001 PHE B 26 TYR 0.016 0.001 TYR C 237 ARG 0.010 0.000 ARG b 167 ********************** 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 152 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 130 time to evaluate : 1.253 Fit side-chains revert: symmetry clash REVERT: A 89 MET cc_start: 0.8010 (tmm) cc_final: 0.7649 (tmm) REVERT: A 125 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.7366 (mp0) REVERT: A 161 ASN cc_start: 0.8777 (t0) cc_final: 0.8444 (t0) REVERT: C 19 ASP cc_start: 0.7518 (p0) cc_final: 0.7172 (p0) REVERT: C 354 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8755 (tt) REVERT: G 65 ILE cc_start: 0.8858 (mt) cc_final: 0.8630 (mt) REVERT: G 67 GLU cc_start: 0.8827 (tp30) cc_final: 0.8398 (tp30) outliers start: 22 outliers final: 16 residues processed: 144 average time/residue: 0.2513 time to fit residues: 50.9168 Evaluate side-chains 144 residues out of total 1120 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 126 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 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 354 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 194 GLU Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 97 ASP Chi-restraints excluded: chain B residue 19 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 16 optimal weight: 0.0170 chunk 30 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 113 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 96 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 overall best weight: 1.5622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.089335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.065409 restraints weight = 27695.219| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.80 r_work: 0.2899 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11513 Z= 0.216 Angle : 0.670 11.523 15677 Z= 0.313 Chirality : 0.042 0.300 1909 Planarity : 0.004 0.054 1881 Dihedral : 10.067 171.133 2340 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.24 % Favored : 94.54 % Rotamer: Outliers : 1.79 % Allowed : 15.55 % 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: 1.38 (0.24), residues: 1411 helix: 2.14 (0.19), residues: 761 sheet: -0.06 (0.68), residues: 77 loop : -0.65 (0.28), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 96 HIS 0.005 0.001 HIS E 74 PHE 0.032 0.001 PHE E 131 TYR 0.015 0.001 TYR C 237 ARG 0.012 0.000 ARG b 167 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2290.86 seconds wall clock time: 41 minutes 36.26 seconds (2496.26 seconds total)