Starting phenix.real_space_refine on Mon Aug 5 04:32:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb8_19028/08_2024/8rb8_19028.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb8_19028/08_2024/8rb8_19028.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb8_19028/08_2024/8rb8_19028.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb8_19028/08_2024/8rb8_19028.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb8_19028/08_2024/8rb8_19028.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8rb8_19028/08_2024/8rb8_19028.cif" } resolution = 3.41 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= 0.002 sd= 0.020 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 18 7.16 5 P 3 5.49 5 S 97 5.16 5 C 8088 2.51 5 N 2066 2.21 5 O 2313 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 12585 Number of models: 1 Model: "" Number of chains: 13 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: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3511 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 37, 'TRANS': 438} 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: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1601 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 203} 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: "H" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 548 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain: "B" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 811 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain breaks: 2 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FES': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 337 Unusual residues: {'FMN': 1, 'LMT': 8, 'RBF': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'LMT': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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 Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 184 SG CYS A 25 47.481 69.234 56.532 1.00 52.97 S ATOM 8343 SG CYS E 122 45.949 72.224 54.666 1.00 69.51 S ATOM 844 SG CYS A 113 43.755 68.914 51.369 1.00 46.34 S ATOM 7734 SG CYS E 39 44.883 65.904 53.712 1.00 58.14 S ATOM 4124 SG CYS C 376 41.300 55.611 94.622 1.00 68.33 S ATOM 4439 SG CYS C 419 45.656 53.952 95.133 1.00 37.38 S ATOM 4082 SG CYS C 370 44.811 55.253 88.580 1.00 52.12 S ATOM 4107 SG CYS C 373 41.805 50.423 91.849 1.00 37.47 S ATOM 4370 SG CYS C 409 39.574 65.611 99.934 1.00 39.39 S ATOM 4392 SG CYS C 412 37.528 60.572 103.661 1.00 39.61 S ATOM 4408 SG CYS C 415 40.675 59.820 98.074 1.00 64.07 S ATOM 4150 SG CYS C 380 35.062 60.836 97.926 1.00 59.97 S ATOM 11569 SG CYS B 119 55.784 103.085 101.718 1.00 75.59 S ATOM 11742 SG CYS B 145 61.255 101.617 101.791 1.00 78.49 S ATOM 11723 SG CYS B 142 57.360 100.128 96.634 1.00 64.43 S ATOM 11706 SG CYS B 139 57.965 96.390 101.721 1.00 60.88 S ATOM 11493 SG CYS B 109 63.621 106.228 111.629 1.00 91.95 S ATOM 11511 SG CYS B 112 64.811 110.948 106.685 1.00 77.36 S ATOM 11535 SG CYS B 115 60.418 106.339 106.542 1.00 79.14 S ATOM 11772 SG CYS B 149 67.251 106.638 106.114 1.00100.00 S Time building chain proxies: 7.99, per 1000 atoms: 0.63 Number of scatterers: 12585 At special positions: 0 Unit cell: (85.28, 148.42, 154.16, 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 18 26.01 S 97 16.00 P 3 15.00 O 2313 8.00 N 2066 7.00 C 8088 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.28 Conformation dependent library (CDL) restraints added in 2.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 200 " pdb="FE1 FES A 200 " - pdb=" SG CYS E 122 " pdb="FE1 FES A 200 " - pdb=" SG CYS A 25 " pdb="FE2 FES A 200 " - pdb=" SG CYS A 113 " pdb="FE2 FES A 200 " - pdb=" SG CYS E 39 " pdb=" SF4 B 201 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 142 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 145 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 139 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 119 " pdb=" SF4 B 202 " pdb="FE2 SF4 B 202 " - pdb=" SG CYS B 112 " pdb="FE4 SF4 B 202 " - pdb=" SG CYS B 149 " pdb="FE3 SF4 B 202 " - pdb=" SG CYS B 115 " pdb="FE1 SF4 B 202 " - pdb=" SG CYS B 109 " 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 : 54 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2898 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 11 sheets defined 55.1% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 removed outlier: 4.078A pdb=" N PHE A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 31 removed outlier: 3.728A pdb=" N PHE A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.594A 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 90 Processing helix chain 'A' and resid 105 through 110 removed outlier: 3.511A pdb=" N THR A 110 " --> pdb=" O PRO A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 126 Proline residue: A 119 - end of helix removed outlier: 3.505A pdb=" N ARG A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 159 removed outlier: 4.048A 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 124 through 134 removed outlier: 3.567A pdb=" N LEU C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.535A pdb=" N LYS C 150 " --> pdb=" O PRO C 146 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 183 removed outlier: 3.515A pdb=" N ARG C 183 " --> pdb=" O ILE C 179 " (cutoff:3.500A) 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: 3.543A pdb=" N MET C 239 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 4.088A 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 250 removed outlier: 3.618A pdb=" N GLN C 247 " --> pdb=" O LYS C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 Processing helix chain 'C' and resid 270 through 283 removed outlier: 3.597A pdb=" N TYR C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 319 removed outlier: 3.668A pdb=" N LEU C 315 " --> pdb=" O PRO C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 395 Processing helix chain 'C' and resid 397 through 404 removed outlier: 3.632A pdb=" N GLU C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.570A pdb=" N TYR C 417 " --> pdb=" O GLY C 413 " (cutoff:3.500A) removed outlier: 3.904A 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 478 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 removed outlier: 3.534A pdb=" N ILE D 45 " --> pdb=" O GLY D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 69 through 75 removed outlier: 3.710A pdb=" N ASP D 75 " --> pdb=" O ARG D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.693A pdb=" N THR D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 106 removed outlier: 3.832A pdb=" N GLY D 98 " --> pdb=" O PRO D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 114 Processing helix chain 'D' and resid 122 through 135 Processing helix chain 'D' and resid 137 through 141 removed outlier: 4.122A pdb=" N THR D 141 " --> pdb=" O GLN D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 164 Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 191 through 198 removed outlier: 3.656A pdb=" N ILE D 195 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU D 196 " --> pdb=" O ALA D 192 " (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 292 through 312 Processing helix chain 'D' and resid 318 through 337 Proline residue: D 331 - end of helix Processing helix chain 'E' and resid 17 through 27 removed outlier: 4.246A pdb=" N PHE E 21 " --> pdb=" O PRO E 17 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU E 25 " --> pdb=" O PHE E 21 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N TRP E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 44 removed outlier: 3.656A pdb=" N THR E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 72 Processing helix chain 'E' and resid 73 through 76 removed outlier: 3.657A pdb=" N ILE E 76 " --> pdb=" O ARG E 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 73 through 76' 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 101 removed outlier: 4.113A pdb=" N VAL E 92 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.555A 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 136 through 168 Processing helix chain 'E' and resid 173 through 179 Processing helix chain 'E' and resid 180 through 186 removed outlier: 4.554A pdb=" N TRP E 184 " --> pdb=" O HIS E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 228 removed outlier: 3.993A pdb=" N PHE E 206 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ILE E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N VAL E 208 " --> pdb=" O GLY E 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 79 removed outlier: 5.508A pdb=" N GLY G 63 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N THR G 64 " --> pdb=" O MET G 60 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 86 Processing helix chain 'G' and resid 89 through 93 removed outlier: 3.826A pdb=" N ASP G 93 " --> pdb=" O PRO G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 163 removed outlier: 4.253A pdb=" N ILE G 162 " --> pdb=" O ALA G 159 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU G 163 " --> pdb=" O ASP G 160 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 159 through 163' Processing helix chain 'G' and resid 168 through 172 Processing helix chain 'G' and resid 202 through 222 Processing helix chain 'G' and resid 223 through 227 removed outlier: 3.590A pdb=" N LEU G 226 " --> pdb=" O ALA G 223 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 34 Processing helix chain 'H' and resid 34 through 39 removed outlier: 3.593A pdb=" N CYS H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.867A pdb=" N ALA B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 113 through 118 Processing sheet with id=AA1, first strand: chain 'C' and resid 34 through 38 removed outlier: 6.562A pdb=" N VAL C 102 " --> pdb=" O VAL C 83 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 38 Processing sheet with id=AA3, first strand: chain 'C' and resid 48 through 49 Processing sheet with id=AA4, first strand: chain 'C' and resid 161 through 165 Processing sheet with id=AA5, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AA6, first strand: chain 'C' and resid 288 through 293 Processing sheet with id=AA7, first strand: chain 'C' and resid 328 through 330 removed outlier: 3.930A pdb=" N GLN C 328 " --> pdb=" O LEU C 357 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AA9, first strand: chain 'G' and resid 108 through 109 removed outlier: 6.674A pdb=" N GLU G 133 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N SER G 137 " --> pdb=" O GLY G 146 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N GLY G 146 " --> pdb=" O SER G 137 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP G 139 " --> pdb=" O ILE G 144 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE G 144 " --> pdb=" O ASP G 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 14 through 18 removed outlier: 6.195A pdb=" N SER H 4 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N ILE H 70 " --> pdb=" O SER H 4 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N VAL H 6 " --> pdb=" O ILE H 70 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 100 through 101 641 hydrogen bonds defined for protein. 1830 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: 3.72 Time building geometry restraints manager: 5.62 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: 5077 1.42 - 1.64: 7611 1.64 - 1.85: 121 1.85 - 2.07: 0 2.07 - 2.28: 52 Bond restraints: 12861 Sorted by residual: bond pdb=" O5' FMN C 500 " pdb=" P FMN C 500 " ideal model delta sigma weight residual 1.610 1.827 -0.217 2.00e-02 2.50e+03 1.18e+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 1.73e+01 bond pdb=" C10 FMN C 500 " pdb=" C4A FMN C 500 " ideal model delta sigma weight residual 1.390 1.471 -0.081 2.00e-02 2.50e+03 1.66e+01 bond pdb=" C4A FMN G 301 " pdb=" N5 FMN G 301 " ideal model delta sigma weight residual 1.380 1.301 0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" C4A FMN D 410 " pdb=" N5 FMN D 410 " ideal model delta sigma weight residual 1.380 1.301 0.079 2.00e-02 2.50e+03 1.57e+01 ... (remaining 12856 not shown) Histogram of bond angle deviations from ideal: 73.50 - 85.61: 50 85.61 - 97.71: 0 97.71 - 109.81: 1686 109.81 - 121.92: 13349 121.92 - 134.02: 2435 Bond angle restraints: 17520 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 121.54 129.03 -7.49 1.91e+00 2.74e-01 1.54e+01 angle pdb=" C ALA D 170 " pdb=" CA ALA D 170 " pdb=" CB ALA D 170 " ideal model delta sigma weight residual 115.89 110.85 5.04 1.32e+00 5.74e-01 1.46e+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 97.81 10.39 3.00e+00 1.11e-01 1.20e+01 angle pdb=" O1P FMN D 410 " pdb=" P FMN D 410 " pdb=" O2P FMN D 410 " ideal model delta sigma weight residual 109.50 119.58 -10.08 3.00e+00 1.11e-01 1.13e+01 angle pdb=" C2 LMT E 304 " pdb=" C3 LMT E 304 " pdb=" C4 LMT E 304 " ideal model delta sigma weight residual 117.09 107.02 10.07 3.00e+00 1.11e-01 1.13e+01 ... (remaining 17515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.89: 7846 33.89 - 67.78: 191 67.78 - 101.68: 53 101.68 - 135.57: 43 135.57 - 169.46: 2 Dihedral angle restraints: 8135 sinusoidal: 3608 harmonic: 4527 Sorted by residual: dihedral pdb=" C10 FMN D 410 " pdb=" C1' FMN D 410 " pdb=" N10 FMN D 410 " pdb=" C2' FMN D 410 " ideal model delta sinusoidal sigma weight residual 257.59 88.13 169.46 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 -147.08 -137.66 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" C4' FMN D 410 " pdb=" C5' FMN D 410 " pdb=" O5' FMN D 410 " pdb=" P FMN D 410 " ideal model delta sinusoidal sigma weight residual -172.30 -82.33 -89.97 1 2.00e+01 2.50e-03 2.40e+01 ... (remaining 8132 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.004: 2132 1.004 - 2.008: 0 2.008 - 3.011: 0 3.011 - 4.015: 0 4.015 - 5.019: 4 Chirality restraints: 2136 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 6.30e+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 6.28e+02 chirality pdb=" C4' FMN D 410 " pdb=" C3' FMN D 410 " pdb=" C5' FMN D 410 " pdb=" O4' FMN D 410 " both_signs ideal model delta sigma weight residual False -2.47 2.42 -4.89 2.00e-01 2.50e+01 5.98e+02 ... (remaining 2133 not shown) Planarity restraints: 2119 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G 301 " -0.119 2.00e-02 2.50e+03 4.17e-02 8.24e+01 pdb=" C10 FMN G 301 " -0.014 2.00e-02 2.50e+03 pdb=" C2 FMN G 301 " 0.038 2.00e-02 2.50e+03 pdb=" C4 FMN G 301 " -0.010 2.00e-02 2.50e+03 pdb=" C4A FMN G 301 " -0.025 2.00e-02 2.50e+03 pdb=" C5A FMN G 301 " -0.021 2.00e-02 2.50e+03 pdb=" C6 FMN G 301 " -0.008 2.00e-02 2.50e+03 pdb=" C7 FMN G 301 " 0.014 2.00e-02 2.50e+03 pdb=" C7M FMN G 301 " 0.028 2.00e-02 2.50e+03 pdb=" C8 FMN G 301 " 0.022 2.00e-02 2.50e+03 pdb=" C8M FMN G 301 " 0.056 2.00e-02 2.50e+03 pdb=" C9 FMN G 301 " 0.007 2.00e-02 2.50e+03 pdb=" C9A FMN G 301 " -0.014 2.00e-02 2.50e+03 pdb=" N1 FMN G 301 " 0.016 2.00e-02 2.50e+03 pdb=" N10 FMN G 301 " -0.021 2.00e-02 2.50e+03 pdb=" N3 FMN G 301 " 0.023 2.00e-02 2.50e+03 pdb=" N5 FMN G 301 " -0.026 2.00e-02 2.50e+03 pdb=" O2 FMN G 301 " 0.089 2.00e-02 2.50e+03 pdb=" O4 FMN G 301 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' FMN D 410 " 0.006 2.00e-02 2.50e+03 1.31e-02 8.18e+00 pdb=" C10 FMN D 410 " -0.004 2.00e-02 2.50e+03 pdb=" C2 FMN D 410 " -0.012 2.00e-02 2.50e+03 pdb=" C4 FMN D 410 " 0.005 2.00e-02 2.50e+03 pdb=" C4A FMN D 410 " 0.002 2.00e-02 2.50e+03 pdb=" C5A FMN D 410 " 0.009 2.00e-02 2.50e+03 pdb=" C6 FMN D 410 " 0.002 2.00e-02 2.50e+03 pdb=" C7 FMN D 410 " -0.002 2.00e-02 2.50e+03 pdb=" C7M FMN D 410 " -0.042 2.00e-02 2.50e+03 pdb=" C8 FMN D 410 " 0.003 2.00e-02 2.50e+03 pdb=" C8M FMN D 410 " 0.014 2.00e-02 2.50e+03 pdb=" C9 FMN D 410 " 0.009 2.00e-02 2.50e+03 pdb=" C9A FMN D 410 " 0.010 2.00e-02 2.50e+03 pdb=" N1 FMN D 410 " -0.012 2.00e-02 2.50e+03 pdb=" N10 FMN D 410 " 0.002 2.00e-02 2.50e+03 pdb=" N3 FMN D 410 " -0.005 2.00e-02 2.50e+03 pdb=" N5 FMN D 410 " 0.007 2.00e-02 2.50e+03 pdb=" O2 FMN D 410 " -0.013 2.00e-02 2.50e+03 pdb=" O4 FMN D 410 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 78 " -0.011 2.00e-02 2.50e+03 2.11e-02 4.43e+00 pdb=" C VAL A 78 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL A 78 " -0.014 2.00e-02 2.50e+03 pdb=" N VAL A 79 " -0.012 2.00e-02 2.50e+03 ... (remaining 2116 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 383 2.72 - 3.26: 12564 3.26 - 3.81: 20070 3.81 - 4.35: 23997 4.35 - 4.90: 42045 Nonbonded interactions: 99059 Sorted by model distance: nonbonded pdb=" OG1 THR D 191 " pdb=" OE1 GLU D 194 " model vdw 2.169 3.040 nonbonded pdb=" OG SER H 25 " pdb=" OE1 GLN H 28 " model vdw 2.210 3.040 nonbonded pdb=" OG SER C 202 " pdb=" O ALA C 227 " model vdw 2.225 3.040 nonbonded pdb=" O THR D 184 " pdb=" OG1 THR D 187 " model vdw 2.249 3.040 nonbonded pdb=" OG SER D 201 " pdb=" OG SER D 204 " model vdw 2.261 3.040 ... (remaining 99054 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 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: 0.670 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 39.030 Find NCS groups from input model: 0.140 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 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 0.217 12861 Z= 0.435 Angle : 0.869 10.394 17520 Z= 0.366 Chirality : 0.220 5.019 2136 Planarity : 0.004 0.042 2119 Dihedral : 18.996 169.458 5237 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.47 % Favored : 95.34 % Rotamer: Outliers : 1.51 % Allowed : 5.09 % Favored : 93.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 0.92 (0.23), residues: 1587 helix: 1.83 (0.19), residues: 805 sheet: -0.62 (0.57), residues: 106 loop : -0.67 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 83 HIS 0.002 0.000 HIS C 268 PHE 0.015 0.001 PHE G 95 TYR 0.009 0.001 TYR C 237 ARG 0.002 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 197 time to evaluate : 1.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 354 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8536 (tt) REVERT: G 67 GLU cc_start: 0.8584 (tp30) cc_final: 0.8299 (tp30) REVERT: B 132 HIS cc_start: 0.5459 (m90) cc_final: 0.5134 (m90) outliers start: 19 outliers final: 4 residues processed: 214 average time/residue: 0.3015 time to fit residues: 86.8729 Evaluate side-chains 124 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 119 time to evaluate : 1.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain G residue 202 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 0.8980 chunk 118 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 63 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 chunk 47 optimal weight: 0.0370 chunk 74 optimal weight: 0.3980 chunk 91 optimal weight: 4.9990 chunk 142 optimal weight: 10.0000 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 GLN G 98 GLN G 225 GLN H 31 GLN H 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12861 Z= 0.164 Angle : 0.649 8.841 17520 Z= 0.295 Chirality : 0.044 0.296 2136 Planarity : 0.005 0.053 2119 Dihedral : 15.701 173.335 2551 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.41 % Favored : 95.46 % Rotamer: Outliers : 1.59 % Allowed : 10.73 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 1.19 (0.22), residues: 1587 helix: 2.10 (0.19), residues: 809 sheet: -0.26 (0.60), residues: 103 loop : -0.67 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 96 HIS 0.002 0.000 HIS C 427 PHE 0.013 0.001 PHE A 143 TYR 0.018 0.001 TYR C 237 ARG 0.011 0.001 ARG H 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 138 time to evaluate : 1.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 227 ARG cc_start: 0.6922 (mtt180) cc_final: 0.6642 (mtt180) REVERT: G 67 GLU cc_start: 0.8554 (tp30) cc_final: 0.8288 (tp30) REVERT: G 95 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.7728 (p90) REVERT: G 101 GLU cc_start: 0.8278 (pt0) cc_final: 0.8073 (pm20) REVERT: B 132 HIS cc_start: 0.5379 (m90) cc_final: 0.5163 (m90) outliers start: 20 outliers final: 10 residues processed: 151 average time/residue: 0.2791 time to fit residues: 59.1137 Evaluate side-chains 123 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 1.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 354 LEU Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 95 PHE Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain B residue 105 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 chunk 118 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 142 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 chunk 127 optimal weight: 10.0000 chunk 141 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 114 optimal weight: 8.9990 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 189 ASN D 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.071 12861 Z= 0.467 Angle : 0.778 8.327 17520 Z= 0.361 Chirality : 0.048 0.299 2136 Planarity : 0.005 0.061 2119 Dihedral : 11.754 174.310 2549 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.54 % Allowed : 11.29 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 1.02 (0.22), residues: 1587 helix: 1.91 (0.19), residues: 805 sheet: -0.60 (0.55), residues: 108 loop : -0.61 (0.25), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 168 HIS 0.005 0.001 HIS C 17 PHE 0.017 0.002 PHE E 114 TYR 0.019 0.002 TYR C 237 ARG 0.019 0.001 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 122 time to evaluate : 1.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 327 ASN cc_start: 0.8824 (m-40) cc_final: 0.8579 (m110) REVERT: E 227 ARG cc_start: 0.6976 (mtt180) cc_final: 0.6724 (mtt180) REVERT: G 67 GLU cc_start: 0.8680 (tp30) cc_final: 0.8460 (tp30) REVERT: G 86 TYR cc_start: 0.8468 (p90) cc_final: 0.8115 (p90) REVERT: G 101 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8199 (pm20) REVERT: H 25 SER cc_start: 0.8007 (p) cc_final: 0.7567 (m) outliers start: 32 outliers final: 15 residues processed: 144 average time/residue: 0.2560 time to fit residues: 53.2938 Evaluate side-chains 128 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain B residue 105 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 5.9990 chunk 107 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 143 optimal weight: 40.0000 chunk 151 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 268 HIS D 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12861 Z= 0.179 Angle : 0.603 7.789 17520 Z= 0.281 Chirality : 0.042 0.360 2136 Planarity : 0.004 0.040 2119 Dihedral : 10.521 171.636 2546 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.75 % Allowed : 12.88 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 1.32 (0.22), residues: 1587 helix: 2.15 (0.19), residues: 815 sheet: -0.36 (0.57), residues: 103 loop : -0.53 (0.25), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 96 HIS 0.001 0.000 HIS A 60 PHE 0.011 0.001 PHE E 114 TYR 0.021 0.001 TYR C 237 ARG 0.006 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 125 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 143 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8205 (t0) REVERT: E 225 GLU cc_start: 0.8761 (mm-30) cc_final: 0.8549 (tp30) REVERT: E 227 ARG cc_start: 0.6842 (mtt180) cc_final: 0.6600 (mtt180) REVERT: G 67 GLU cc_start: 0.8622 (tp30) cc_final: 0.8389 (tp30) REVERT: B 132 HIS cc_start: 0.5739 (m90) cc_final: 0.5178 (m90) outliers start: 22 outliers final: 14 residues processed: 137 average time/residue: 0.2666 time to fit residues: 53.7567 Evaluate side-chains 128 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain B residue 15 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 86 optimal weight: 5.9990 chunk 2 optimal weight: 0.9980 chunk 112 optimal weight: 3.9990 chunk 62 optimal weight: 6.9990 chunk 129 optimal weight: 10.0000 chunk 104 optimal weight: 0.0000 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 136 optimal weight: 6.9990 chunk 38 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 68 GLN E 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12861 Z= 0.217 Angle : 0.595 6.943 17520 Z= 0.281 Chirality : 0.042 0.364 2136 Planarity : 0.004 0.039 2119 Dihedral : 9.854 172.709 2544 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.91 % Allowed : 13.35 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 1.44 (0.22), residues: 1587 helix: 2.30 (0.19), residues: 808 sheet: -0.38 (0.57), residues: 99 loop : -0.50 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 96 HIS 0.002 0.001 HIS C 17 PHE 0.012 0.001 PHE E 114 TYR 0.020 0.001 TYR C 237 ARG 0.006 0.000 ARG A 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 327 ASN cc_start: 0.8723 (m110) cc_final: 0.8482 (m-40) REVERT: E 227 ARG cc_start: 0.6873 (mtt180) cc_final: 0.6621 (mtt180) REVERT: G 67 GLU cc_start: 0.8643 (tp30) cc_final: 0.8411 (tp30) REVERT: H 42 ILE cc_start: 0.8474 (mm) cc_final: 0.8167 (pt) outliers start: 24 outliers final: 17 residues processed: 132 average time/residue: 0.2585 time to fit residues: 49.7046 Evaluate side-chains 129 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 48 MET Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain H residue 62 LEU Chi-restraints excluded: chain B residue 15 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 151 optimal weight: 20.0000 chunk 126 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 50 optimal weight: 0.3980 chunk 79 optimal weight: 0.0470 chunk 146 optimal weight: 5.9990 overall best weight: 1.8884 ------------------------------------------------------------------------------- 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: 0.8533 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12861 Z= 0.193 Angle : 0.574 8.880 17520 Z= 0.273 Chirality : 0.041 0.323 2136 Planarity : 0.004 0.039 2119 Dihedral : 9.249 172.289 2544 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 2.15 % Allowed : 13.83 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 1.53 (0.22), residues: 1587 helix: 2.40 (0.19), residues: 805 sheet: -0.35 (0.56), residues: 100 loop : -0.47 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 96 HIS 0.001 0.000 HIS A 60 PHE 0.010 0.001 PHE E 114 TYR 0.017 0.001 TYR C 237 ARG 0.007 0.000 ARG B 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 327 ASN cc_start: 0.8711 (m110) cc_final: 0.8462 (m-40) REVERT: E 185 MET cc_start: 0.8416 (mmm) cc_final: 0.8077 (mmm) REVERT: E 227 ARG cc_start: 0.6912 (mtt180) cc_final: 0.6679 (mtt180) REVERT: G 67 GLU cc_start: 0.8662 (tp30) cc_final: 0.8434 (tp30) REVERT: G 86 TYR cc_start: 0.8362 (p90) cc_final: 0.8014 (p90) REVERT: H 42 ILE cc_start: 0.8589 (mm) cc_final: 0.8273 (pt) outliers start: 27 outliers final: 17 residues processed: 136 average time/residue: 0.2679 time to fit residues: 52.6966 Evaluate side-chains 128 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 101 GLU Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 131 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 17 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 127 optimal weight: 8.9990 chunk 84 optimal weight: 0.0270 chunk 151 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 93 optimal weight: 0.3980 overall best weight: 0.8842 ------------------------------------------------------------------------------- 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: 0.8500 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12861 Z= 0.152 Angle : 0.562 8.394 17520 Z= 0.268 Chirality : 0.040 0.245 2136 Planarity : 0.004 0.040 2119 Dihedral : 8.906 171.522 2544 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.35 % Favored : 95.59 % Rotamer: Outliers : 1.51 % Allowed : 14.31 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 1.60 (0.22), residues: 1587 helix: 2.48 (0.19), residues: 805 sheet: -0.24 (0.57), residues: 100 loop : -0.48 (0.25), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 83 HIS 0.002 0.000 HIS G 222 PHE 0.009 0.001 PHE D 35 TYR 0.016 0.001 TYR A 105 ARG 0.006 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 122 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 327 ASN cc_start: 0.8683 (m110) cc_final: 0.8420 (m110) REVERT: E 185 MET cc_start: 0.8381 (mmm) cc_final: 0.8102 (mmm) REVERT: E 227 ARG cc_start: 0.6898 (mtt180) cc_final: 0.6664 (mtt180) REVERT: G 67 GLU cc_start: 0.8651 (tp30) cc_final: 0.8429 (tp30) REVERT: G 95 PHE cc_start: 0.9166 (OUTLIER) cc_final: 0.8789 (p90) REVERT: B 132 HIS cc_start: 0.5567 (m90) cc_final: 0.4812 (m90) outliers start: 19 outliers final: 12 residues processed: 135 average time/residue: 0.2566 time to fit residues: 50.3020 Evaluate side-chains 127 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 114 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 387 LEU Chi-restraints excluded: chain D residue 54 SER Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 95 PHE Chi-restraints excluded: chain G residue 173 PHE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 110 ILE Chi-restraints excluded: chain B residue 131 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 4.9990 chunk 90 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 0.2980 chunk 96 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 137 optimal weight: 0.9980 chunk 144 optimal weight: 0.0670 overall best weight: 0.6120 ------------------------------------------------------------------------------- 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: 0.8480 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 12861 Z= 0.145 Angle : 0.560 8.068 17520 Z= 0.270 Chirality : 0.039 0.166 2136 Planarity : 0.004 0.061 2119 Dihedral : 8.704 171.607 2544 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.47 % Favored : 95.46 % Rotamer: Outliers : 1.59 % Allowed : 14.39 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 1.70 (0.22), residues: 1587 helix: 2.59 (0.19), residues: 798 sheet: -0.06 (0.59), residues: 98 loop : -0.47 (0.25), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 83 HIS 0.002 0.000 HIS G 222 PHE 0.010 0.001 PHE A 143 TYR 0.017 0.001 TYR A 105 ARG 0.010 0.000 ARG H 37 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 327 ASN cc_start: 0.8658 (m110) cc_final: 0.8389 (m110) REVERT: E 185 MET cc_start: 0.8351 (mmm) cc_final: 0.8047 (mmm) REVERT: E 227 ARG cc_start: 0.6929 (mtt180) cc_final: 0.6708 (mtt180) REVERT: G 67 GLU cc_start: 0.8660 (tp30) cc_final: 0.8434 (tp30) REVERT: G 95 PHE cc_start: 0.9137 (OUTLIER) cc_final: 0.8779 (p90) REVERT: B 132 HIS cc_start: 0.5486 (m90) cc_final: 0.4819 (m90) outliers start: 20 outliers final: 14 residues processed: 129 average time/residue: 0.2404 time to fit residues: 45.4813 Evaluate side-chains 129 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 114 time to evaluate : 1.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 95 PHE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 110 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 144 optimal weight: 5.9990 chunk 84 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 110 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 chunk 127 optimal weight: 6.9990 chunk 133 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- 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: 0.8546 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12861 Z= 0.250 Angle : 0.611 9.788 17520 Z= 0.291 Chirality : 0.041 0.176 2136 Planarity : 0.004 0.040 2119 Dihedral : 8.747 173.649 2544 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.91 % Favored : 95.02 % Rotamer: Outliers : 1.59 % Allowed : 14.86 % Favored : 83.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 1.72 (0.22), residues: 1587 helix: 2.50 (0.19), residues: 804 sheet: 0.05 (0.59), residues: 96 loop : -0.35 (0.25), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 96 HIS 0.003 0.001 HIS A 60 PHE 0.015 0.001 PHE A 173 TYR 0.022 0.001 TYR A 105 ARG 0.011 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 114 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 327 ASN cc_start: 0.8653 (m110) cc_final: 0.8409 (m-40) REVERT: E 185 MET cc_start: 0.8430 (mmm) cc_final: 0.8138 (mmm) REVERT: E 227 ARG cc_start: 0.6861 (mtt180) cc_final: 0.6641 (mtt180) REVERT: G 67 GLU cc_start: 0.8705 (tp30) cc_final: 0.8473 (tp30) REVERT: G 86 TYR cc_start: 0.8348 (p90) cc_final: 0.8082 (p90) outliers start: 20 outliers final: 16 residues processed: 129 average time/residue: 0.2420 time to fit residues: 45.6411 Evaluate side-chains 126 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain D residue 116 ILE Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 143 ASP Chi-restraints excluded: chain G residue 60 MET Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 167 SER Chi-restraints excluded: chain B residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 8.9990 chunk 91 optimal weight: 0.0870 chunk 70 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 chunk 143 optimal weight: 7.9990 chunk 124 optimal weight: 0.9980 chunk 12 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 98 optimal weight: 8.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- 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: 0.8495 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12861 Z= 0.151 Angle : 0.591 10.325 17520 Z= 0.284 Chirality : 0.040 0.276 2136 Planarity : 0.004 0.046 2119 Dihedral : 8.539 171.802 2544 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.16 % Favored : 95.78 % Rotamer: Outliers : 1.11 % Allowed : 15.50 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 1.77 (0.22), residues: 1587 helix: 2.55 (0.19), residues: 804 sheet: 0.04 (0.59), residues: 98 loop : -0.32 (0.25), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 96 HIS 0.001 0.000 HIS A 60 PHE 0.013 0.001 PHE A 173 TYR 0.018 0.001 TYR A 105 ARG 0.009 0.000 ARG B 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3174 Ramachandran restraints generated. 1587 Oldfield, 0 Emsley, 1587 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 118 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 185 MET cc_start: 0.8418 (mmm) cc_final: 0.8118 (mmm) REVERT: E 227 ARG cc_start: 0.6861 (mtt180) cc_final: 0.6652 (mtt180) REVERT: G 67 GLU cc_start: 0.8648 (tp30) cc_final: 0.8431 (tp30) REVERT: G 70 MET cc_start: 0.8488 (tpp) cc_final: 0.8273 (tpt) REVERT: G 86 TYR cc_start: 0.8302 (p90) cc_final: 0.7999 (p90) outliers start: 14 outliers final: 11 residues processed: 128 average time/residue: 0.2459 time to fit residues: 45.8525 Evaluate side-chains 123 residues out of total 1259 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 112 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 352 THR Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 143 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 8.9990 chunk 38 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 124 optimal weight: 0.0770 chunk 52 optimal weight: 8.9990 chunk 128 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 22 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 overall best weight: 1.3944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 327 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.061366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.044435 restraints weight = 44110.395| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 3.03 r_work: 0.2690 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12861 Z= 0.184 Angle : 0.601 10.619 17520 Z= 0.290 Chirality : 0.040 0.248 2136 Planarity : 0.004 0.044 2119 Dihedral : 8.425 172.592 2544 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.66 % Favored : 95.27 % Rotamer: Outliers : 1.03 % Allowed : 16.22 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: 1.79 (0.22), residues: 1587 helix: 2.56 (0.19), residues: 803 sheet: 0.01 (0.59), residues: 96 loop : -0.30 (0.25), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 96 HIS 0.002 0.000 HIS G 62 PHE 0.012 0.001 PHE A 173 TYR 0.020 0.001 TYR A 105 ARG 0.011 0.000 ARG B 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2564.58 seconds wall clock time: 51 minutes 59.74 seconds (3119.74 seconds total)