Starting phenix.real_space_refine on Sat Jan 18 23:40:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ahx_15452/01_2025/8ahx_15452.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ahx_15452/01_2025/8ahx_15452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ahx_15452/01_2025/8ahx_15452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ahx_15452/01_2025/8ahx_15452.map" model { file = "/net/cci-nas-00/data/ceres_data/8ahx_15452/01_2025/8ahx_15452.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ahx_15452/01_2025/8ahx_15452.cif" } resolution = 3.11 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 8158 2.51 5 N 2073 2.21 5 O 2338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 12687 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: "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: "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: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1514 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 7, 'TRANS': 189} 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: "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: "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} 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: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 372 Unusual residues: {'FMN': 1, 'LMT': 9, 'RBF': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} 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 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 184 SG CYS A 25 36.955 84.906 50.802 1.00102.81 S ATOM 9154 SG CYS E 122 38.370 82.240 48.485 1.00113.43 S ATOM 844 SG CYS A 113 40.644 85.907 45.869 1.00 96.89 S ATOM 8545 SG CYS E 39 39.697 88.711 48.565 1.00101.07 S ATOM 1798 SG CYS B 119 27.814 44.779 90.307 1.00125.95 S ATOM 1971 SG CYS B 145 22.385 46.145 90.650 1.00126.07 S ATOM 1952 SG CYS B 142 26.271 48.407 85.782 1.00140.38 S ATOM 1935 SG CYS B 139 25.704 51.418 91.308 1.00104.29 S ATOM 1722 SG CYS B 109 20.061 40.010 99.643 1.00148.19 S ATOM 1740 SG CYS B 112 18.807 36.197 94.061 1.00146.84 S ATOM 1764 SG CYS B 115 23.153 40.817 94.676 1.00132.05 S ATOM 2001 SG CYS B 149 16.360 40.766 94.111 1.00160.09 S ATOM 4935 SG CYS C 376 43.011 92.402 90.586 1.00108.55 S ATOM 5250 SG CYS C 419 38.769 93.959 91.338 1.00 74.60 S ATOM 4893 SG CYS C 370 39.659 93.659 84.721 1.00 77.21 S ATOM 4918 SG CYS C 373 42.804 97.958 88.721 1.00 83.32 S ATOM 5181 SG CYS C 409 44.506 81.635 94.360 1.00 84.55 S ATOM 5203 SG CYS C 412 46.572 86.143 98.786 1.00 80.78 S ATOM 5219 SG CYS C 415 43.806 87.799 93.438 1.00 98.49 S ATOM 4961 SG CYS C 380 49.219 86.421 93.141 1.00 89.09 S Time building chain proxies: 7.89, per 1000 atoms: 0.62 Number of scatterers: 12687 At special positions: 0 Unit cell: (84.46, 151.7, 145.14, 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 2338 8.00 N 2073 7.00 C 8158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.53 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 201 " pdb="FE1 FES A 201 " - pdb=" SG CYS E 122 " pdb="FE1 FES A 201 " - pdb=" SG CYS A 25 " pdb="FE2 FES A 201 " - pdb=" SG CYS A 113 " pdb="FE2 FES A 201 " - 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="FE3 SF4 B 202 " - pdb=" SG CYS B 115 " pdb="FE1 SF4 B 202 " - pdb=" SG CYS B 109 " pdb="FE4 SF4 B 202 " - pdb=" SG CYS B 149 " 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="FE4 SF4 C 501 " - pdb=" SG CYS C 373 " pdb="FE3 SF4 C 501 " - pdb=" SG CYS C 370 " 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="FE1 SF4 C 502 " - pdb=" SG CYS C 409 " pdb="FE4 SF4 C 502 " - pdb=" SG CYS C 380 " Number of angles added : 54 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2904 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 11 sheets defined 57.2% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 Processing helix chain 'A' and resid 23 through 31 removed outlier: 3.771A pdb=" N PHE A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.623A 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 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 105 through 110 Processing helix chain 'A' and resid 113 through 126 Proline residue: A 119 - end of helix removed outlier: 3.533A pdb=" N ARG A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 159 removed outlier: 4.002A 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 'B' and resid 3 through 26 removed outlier: 3.855A pdb=" N ALA B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 85 removed outlier: 3.521A pdb=" N LYS B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 162 through 166 Processing helix chain 'C' and resid 119 through 123 removed outlier: 3.806A pdb=" N GLU C 123 " --> pdb=" O PRO C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 134 removed outlier: 3.541A pdb=" N LEU C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.534A pdb=" N LYS C 150 " --> pdb=" O PRO C 146 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.803A 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: 3.600A pdb=" N MET C 239 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 4.031A 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: 3.557A pdb=" N GLN C 247 " --> pdb=" O LYS C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.513A pdb=" N VAL C 263 " --> pdb=" O SER C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 283 removed outlier: 3.656A pdb=" N TYR C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 319 removed outlier: 3.657A 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: 3.597A pdb=" N GLU C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.876A pdb=" N VAL C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) 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 Processing helix chain 'D' and resid 69 through 75 removed outlier: 3.738A pdb=" N ASP D 75 " --> pdb=" O ARG D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.735A pdb=" N THR D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 106 removed outlier: 3.771A 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: 4.159A 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: 3.608A pdb=" N ILE D 195 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY D 198 " --> pdb=" O GLU D 194 " (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 280 Processing helix chain 'D' and resid 284 through 288 Processing helix chain 'D' and resid 291 through 312 removed outlier: 3.530A pdb=" N ARG D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) 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: 4.235A pdb=" N PHE E 21 " --> pdb=" O PRO E 17 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU E 25 " --> pdb=" O PHE E 21 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TRP E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 44 removed outlier: 3.612A 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: 3.654A 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: 3.992A pdb=" N VAL E 92 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.590A pdb=" N VAL E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 117 removed outlier: 4.389A pdb=" N ALA E 116 " --> pdb=" O GLY E 112 " (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: 4.468A pdb=" N TRP E 184 " --> pdb=" O HIS E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 201 removed outlier: 3.535A pdb=" N ALA E 199 " --> pdb=" O ILE E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 228 removed outlier: 3.912A pdb=" N PHE E 206 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 79 removed outlier: 4.190A pdb=" N GLN G 39 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLY G 63 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N THR G 64 " --> pdb=" O MET G 60 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 86 removed outlier: 3.509A pdb=" N LEU G 85 " --> pdb=" O PRO G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 93 removed outlier: 3.814A pdb=" N ASP G 93 " --> pdb=" O PRO G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 163 removed outlier: 4.190A pdb=" N ILE G 162 " --> pdb=" O ALA G 159 " (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 'G' and resid 223 through 228 Processing helix chain 'H' and resid 25 through 34 Processing helix chain 'H' and resid 34 through 39 removed outlier: 3.564A pdb=" N CYS H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.702A pdb=" N ALA C 84 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLU C 104 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE C 82 " --> pdb=" O GLU C 104 " (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 204 through 208 Processing sheet with id=AA7, first strand: chain 'C' and resid 288 through 293 Processing sheet with id=AA8, first strand: chain 'C' and resid 328 through 330 Processing sheet with id=AA9, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AB1, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.566A pdb=" N ALA G 118 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU G 133 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER G 137 " --> pdb=" O GLY G 146 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLY G 146 " --> pdb=" O SER G 137 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP G 139 " --> pdb=" O ILE G 144 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE G 144 " --> pdb=" O ASP G 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 14 through 18 removed outlier: 6.104A pdb=" N SER H 4 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE H 70 " --> pdb=" O SER H 4 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL H 6 " --> pdb=" O ILE H 70 " (cutoff:3.500A) 655 hydrogen bonds defined for protein. 1845 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: 3.60 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 5029 1.41 - 1.63: 7766 1.63 - 1.85: 121 1.85 - 2.07: 0 2.07 - 2.28: 52 Bond restraints: 12968 Sorted by residual: bond pdb=" O5' FMN C 500 " pdb=" P FMN C 500 " ideal model delta sigma weight residual 1.610 1.826 -0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" CA VAL C 204 " pdb=" C VAL C 204 " ideal model delta sigma weight residual 1.523 1.460 0.063 1.27e-02 6.20e+03 2.48e+01 bond pdb=" C THR E 45 " pdb=" O THR E 45 " ideal model delta sigma weight residual 1.235 1.199 0.036 7.50e-03 1.78e+04 2.24e+01 bond pdb=" CA LEU A 74 " pdb=" C LEU A 74 " ideal model delta sigma weight residual 1.523 1.466 0.057 1.34e-02 5.57e+03 1.83e+01 bond pdb=" C4A FMN C 500 " pdb=" N5 FMN C 500 " ideal model delta sigma weight residual 1.380 1.295 0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 12963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 17037 2.04 - 4.07: 427 4.07 - 6.11: 133 6.11 - 8.14: 19 8.14 - 10.18: 47 Bond angle restraints: 17663 Sorted by residual: angle pdb=" C VAL A 30 " pdb=" CA VAL A 30 " pdb=" CB VAL A 30 " ideal model delta sigma weight residual 110.84 104.94 5.90 1.25e+00 6.40e-01 2.22e+01 angle pdb=" C ASN A 112 " pdb=" N CYS A 113 " pdb=" CA CYS A 113 " ideal model delta sigma weight residual 121.54 129.34 -7.80 1.91e+00 2.74e-01 1.67e+01 angle pdb=" N THR G 202 " pdb=" CA THR G 202 " pdb=" C THR G 202 " ideal model delta sigma weight residual 114.04 109.19 4.85 1.24e+00 6.50e-01 1.53e+01 angle pdb=" C ALA D 170 " pdb=" CA ALA D 170 " pdb=" CB ALA D 170 " ideal model delta sigma weight residual 115.89 110.80 5.09 1.32e+00 5.74e-01 1.49e+01 angle pdb=" CA ARG A 92 " pdb=" C ARG A 92 " pdb=" O ARG A 92 " ideal model delta sigma weight residual 119.34 123.21 -3.87 1.09e+00 8.42e-01 1.26e+01 ... (remaining 17658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.94: 7935 33.94 - 67.87: 234 67.87 - 101.81: 63 101.81 - 135.74: 43 135.74 - 169.68: 1 Dihedral angle restraints: 8276 sinusoidal: 3740 harmonic: 4536 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 87.91 169.68 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 -151.91 -132.83 1 2.00e+01 2.50e-03 4.03e+01 dihedral pdb=" C4' FMN D 411 " pdb=" C5' FMN D 411 " pdb=" O5' FMN D 411 " pdb=" P FMN D 411 " ideal model delta sinusoidal sigma weight residual -172.30 -80.18 -92.12 1 2.00e+01 2.50e-03 2.49e+01 ... (remaining 8273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.004: 2155 1.004 - 2.007: 0 2.007 - 3.011: 0 3.011 - 4.015: 0 4.015 - 5.019: 4 Chirality restraints: 2159 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 411 " pdb=" C3' FMN D 411 " pdb=" C5' FMN D 411 " pdb=" O4' FMN D 411 " 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 2156 not shown) Planarity restraints: 2125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G 301 " 0.144 2.00e-02 2.50e+03 4.51e-02 9.66e+01 pdb=" C10 FMN G 301 " 0.005 2.00e-02 2.50e+03 pdb=" C2 FMN G 301 " -0.039 2.00e-02 2.50e+03 pdb=" C4 FMN G 301 " 0.007 2.00e-02 2.50e+03 pdb=" C4A FMN G 301 " 0.016 2.00e-02 2.50e+03 pdb=" C5A FMN G 301 " 0.017 2.00e-02 2.50e+03 pdb=" C6 FMN G 301 " 0.008 2.00e-02 2.50e+03 pdb=" C7 FMN G 301 " -0.012 2.00e-02 2.50e+03 pdb=" C7M FMN G 301 " -0.006 2.00e-02 2.50e+03 pdb=" C8 FMN G 301 " -0.023 2.00e-02 2.50e+03 pdb=" C8M FMN G 301 " -0.070 2.00e-02 2.50e+03 pdb=" C9 FMN G 301 " -0.012 2.00e-02 2.50e+03 pdb=" C9A FMN G 301 " 0.009 2.00e-02 2.50e+03 pdb=" N1 FMN G 301 " -0.022 2.00e-02 2.50e+03 pdb=" N10 FMN G 301 " 0.017 2.00e-02 2.50e+03 pdb=" N3 FMN G 301 " -0.024 2.00e-02 2.50e+03 pdb=" N5 FMN G 301 " 0.019 2.00e-02 2.50e+03 pdb=" O2 FMN G 301 " -0.079 2.00e-02 2.50e+03 pdb=" O4 FMN G 301 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS E 74 " 0.024 2.00e-02 2.50e+03 4.73e-02 2.24e+01 pdb=" C HIS E 74 " -0.082 2.00e-02 2.50e+03 pdb=" O HIS E 74 " 0.031 2.00e-02 2.50e+03 pdb=" N THR E 75 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 223 " -0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C ALA G 223 " 0.060 2.00e-02 2.50e+03 pdb=" O ALA G 223 " -0.023 2.00e-02 2.50e+03 pdb=" N GLU G 224 " -0.020 2.00e-02 2.50e+03 ... (remaining 2122 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1280 2.74 - 3.28: 12557 3.28 - 3.82: 20725 3.82 - 4.36: 23462 4.36 - 4.90: 42249 Nonbonded interactions: 100273 Sorted by model distance: nonbonded pdb=" OG SER C 202 " pdb=" O ALA C 227 " model vdw 2.203 3.040 nonbonded pdb=" OG SER H 25 " pdb=" OE1 GLN H 28 " model vdw 2.208 3.040 nonbonded pdb=" OG SER D 201 " pdb=" OG SER D 204 " model vdw 2.212 3.040 nonbonded pdb=" O THR D 184 " pdb=" OG1 THR D 187 " model vdw 2.223 3.040 nonbonded pdb=" O SER D 314 " pdb=" OH TYR G 128 " model vdw 2.226 3.040 ... (remaining 100268 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: 1.130 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: 0.500 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 33.100 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 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 0.216 12968 Z= 0.446 Angle : 0.919 10.177 17663 Z= 0.390 Chirality : 0.219 5.019 2159 Planarity : 0.005 0.048 2125 Dihedral : 19.651 169.681 5372 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.09 % Favored : 94.65 % Rotamer: Outliers : 0.71 % Allowed : 6.74 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 0.91 (0.23), residues: 1590 helix: 1.79 (0.19), residues: 808 sheet: -0.60 (0.58), residues: 107 loop : -0.63 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 83 HIS 0.002 0.001 HIS G 152 PHE 0.017 0.001 PHE G 173 TYR 0.012 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) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 182 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8602 (tm-30) REVERT: A 93 LYS cc_start: 0.8566 (tttt) cc_final: 0.8262 (mptt) REVERT: A 125 GLU cc_start: 0.9101 (mp0) cc_final: 0.8774 (mp0) REVERT: A 161 ASN cc_start: 0.9082 (t0) cc_final: 0.8582 (t0) REVERT: B 3 GLU cc_start: 0.7802 (mt-10) cc_final: 0.6649 (tp30) REVERT: B 105 GLU cc_start: 0.7423 (mp0) cc_final: 0.6596 (mp0) REVERT: B 122 ASP cc_start: 0.8077 (t0) cc_final: 0.7418 (t0) REVERT: B 155 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8893 (mp) REVERT: B 158 PRO cc_start: 0.9004 (Cg_exo) cc_final: 0.8654 (Cg_endo) REVERT: C 3 PHE cc_start: 0.6129 (m-80) cc_final: 0.5725 (m-80) REVERT: C 225 PHE cc_start: 0.8869 (m-80) cc_final: 0.8501 (m-80) REVERT: D 197 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8388 (mm-30) REVERT: E 19 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7727 (tm-30) REVERT: E 163 GLU cc_start: 0.8632 (tt0) cc_final: 0.8301 (tt0) REVERT: E 192 ASP cc_start: 0.7415 (t0) cc_final: 0.7178 (t0) REVERT: E 222 LYS cc_start: 0.7340 (mttt) cc_final: 0.7097 (mptt) REVERT: G 67 GLU cc_start: 0.8926 (tp30) cc_final: 0.8605 (tp30) REVERT: G 89 ASN cc_start: 0.8876 (t0) cc_final: 0.8507 (t0) REVERT: H 18 CYS cc_start: 0.8648 (p) cc_final: 0.8401 (m) REVERT: H 32 GLN cc_start: 0.9121 (tt0) cc_final: 0.8849 (tm-30) REVERT: H 37 ARG cc_start: 0.8622 (ptp-110) cc_final: 0.8247 (ptm-80) REVERT: H 57 LYS cc_start: 0.8525 (ttpp) cc_final: 0.8003 (ttpp) outliers start: 9 outliers final: 3 residues processed: 191 average time/residue: 0.3080 time to fit residues: 80.5244 Evaluate side-chains 149 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 145 time to evaluate : 1.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 449 ILE 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: 3.9990 chunk 118 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 0.0050 chunk 80 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 430 GLN D 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.080539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.058571 restraints weight = 30258.427| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 2.26 r_work: 0.2796 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2669 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8903 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12968 Z= 0.219 Angle : 0.658 8.654 17663 Z= 0.299 Chirality : 0.044 0.297 2159 Planarity : 0.004 0.049 2125 Dihedral : 17.444 172.669 2677 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.03 % Favored : 94.84 % Rotamer: Outliers : 2.38 % Allowed : 8.56 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 1.01 (0.23), residues: 1590 helix: 1.90 (0.19), residues: 829 sheet: -0.69 (0.56), residues: 113 loop : -0.69 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 83 HIS 0.002 0.001 HIS C 360 PHE 0.013 0.001 PHE A 143 TYR 0.018 0.001 TYR H 7 ARG 0.005 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 1.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8627 (tttt) cc_final: 0.8417 (mptt) REVERT: A 161 ASN cc_start: 0.9177 (t0) cc_final: 0.8665 (t0) REVERT: B 3 GLU cc_start: 0.7832 (mt-10) cc_final: 0.6462 (tp30) REVERT: B 105 GLU cc_start: 0.7351 (mp0) cc_final: 0.6909 (mp0) REVERT: B 122 ASP cc_start: 0.8274 (t0) cc_final: 0.7569 (t0) REVERT: B 146 ARG cc_start: 0.8902 (mtp85) cc_final: 0.8658 (ptp-110) REVERT: C 225 PHE cc_start: 0.8645 (m-80) cc_final: 0.8335 (m-80) REVERT: C 266 LEU cc_start: 0.9211 (OUTLIER) cc_final: 0.9009 (tp) REVERT: D 59 GLU cc_start: 0.8878 (tp30) cc_final: 0.8536 (tp30) REVERT: D 197 GLU cc_start: 0.8751 (mm-30) cc_final: 0.8441 (mm-30) REVERT: E 27 GLN cc_start: 0.8684 (tt0) cc_final: 0.8178 (tt0) REVERT: E 28 TYR cc_start: 0.8567 (m-80) cc_final: 0.8105 (m-10) REVERT: E 32 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8988 (mp) REVERT: E 79 GLU cc_start: 0.8514 (pm20) cc_final: 0.8267 (pm20) REVERT: E 163 GLU cc_start: 0.8808 (tt0) cc_final: 0.8538 (tt0) REVERT: E 222 LYS cc_start: 0.7672 (mttt) cc_final: 0.7390 (mptt) REVERT: G 67 GLU cc_start: 0.9084 (tp30) cc_final: 0.8826 (tp30) REVERT: G 89 ASN cc_start: 0.8842 (t0) cc_final: 0.8612 (t0) REVERT: H 7 TYR cc_start: 0.9000 (t80) cc_final: 0.8596 (t80) REVERT: H 18 CYS cc_start: 0.8864 (p) cc_final: 0.8374 (p) REVERT: H 32 GLN cc_start: 0.9434 (tt0) cc_final: 0.8895 (tm-30) REVERT: H 37 ARG cc_start: 0.8710 (ptp-110) cc_final: 0.8322 (ptm-80) outliers start: 30 outliers final: 14 residues processed: 186 average time/residue: 0.2674 time to fit residues: 69.9845 Evaluate side-chains 163 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 103 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 chunk 69 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 140 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 268 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.078295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.055331 restraints weight = 30298.496| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.40 r_work: 0.2675 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 12968 Z= 0.306 Angle : 0.670 8.911 17663 Z= 0.308 Chirality : 0.045 0.345 2159 Planarity : 0.004 0.049 2125 Dihedral : 13.461 173.435 2675 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.47 % Favored : 94.40 % Rotamer: Outliers : 2.85 % Allowed : 9.75 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 1.04 (0.22), residues: 1590 helix: 1.94 (0.19), residues: 828 sheet: -0.78 (0.56), residues: 113 loop : -0.67 (0.26), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 83 HIS 0.003 0.001 HIS C 196 PHE 0.012 0.001 PHE E 206 TYR 0.014 0.001 TYR C 237 ARG 0.005 0.000 ARG E 81 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 1.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8659 (tttt) cc_final: 0.8278 (mptt) REVERT: A 125 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: B 3 GLU cc_start: 0.7715 (mt-10) cc_final: 0.6245 (tp30) REVERT: B 122 ASP cc_start: 0.8385 (t0) cc_final: 0.7529 (t0) REVERT: C 225 PHE cc_start: 0.8790 (m-80) cc_final: 0.8399 (m-80) REVERT: C 266 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8643 (tp) REVERT: D 173 MET cc_start: 0.9045 (mtp) cc_final: 0.8582 (mtt) REVERT: D 197 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8313 (mm-30) REVERT: D 214 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9077 (tt) REVERT: E 27 GLN cc_start: 0.8584 (tt0) cc_final: 0.8003 (tt0) REVERT: E 28 TYR cc_start: 0.8485 (m-80) cc_final: 0.7982 (m-10) REVERT: E 32 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9050 (mp) REVERT: E 163 GLU cc_start: 0.8533 (tt0) cc_final: 0.8122 (tt0) REVERT: E 222 LYS cc_start: 0.7414 (mttt) cc_final: 0.7148 (mptt) REVERT: G 67 GLU cc_start: 0.8990 (tp30) cc_final: 0.8737 (tp30) REVERT: G 89 ASN cc_start: 0.8834 (t0) cc_final: 0.8567 (t0) REVERT: G 133 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8226 (tp30) REVERT: H 7 TYR cc_start: 0.8711 (t80) cc_final: 0.8413 (t80) REVERT: H 18 CYS cc_start: 0.8843 (p) cc_final: 0.8428 (p) REVERT: H 32 GLN cc_start: 0.9425 (tt0) cc_final: 0.8824 (tm-30) REVERT: H 37 ARG cc_start: 0.8735 (ptp-110) cc_final: 0.8096 (ptm-80) outliers start: 36 outliers final: 20 residues processed: 185 average time/residue: 0.2762 time to fit residues: 72.3283 Evaluate side-chains 179 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 154 time to evaluate : 1.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 77 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 79 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 85 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 138 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.079318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.056310 restraints weight = 30139.671| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 2.41 r_work: 0.2695 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12968 Z= 0.199 Angle : 0.597 7.447 17663 Z= 0.279 Chirality : 0.042 0.360 2159 Planarity : 0.004 0.049 2125 Dihedral : 11.677 172.230 2674 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.16 % Favored : 94.72 % Rotamer: Outliers : 2.54 % Allowed : 12.29 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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 (0.22), residues: 1590 helix: 2.05 (0.19), residues: 830 sheet: -0.71 (0.58), residues: 103 loop : -0.68 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 83 HIS 0.002 0.001 HIS E 74 PHE 0.012 0.001 PHE A 143 TYR 0.015 0.001 TYR C 237 ARG 0.005 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 1.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8653 (tttt) cc_final: 0.8237 (mptt) REVERT: A 125 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: B 3 GLU cc_start: 0.7712 (mt-10) cc_final: 0.6220 (tp30) REVERT: B 122 ASP cc_start: 0.8345 (t0) cc_final: 0.7500 (t0) REVERT: C 225 PHE cc_start: 0.8743 (m-80) cc_final: 0.8372 (m-80) REVERT: D 59 GLU cc_start: 0.8646 (tp30) cc_final: 0.8274 (tp30) REVERT: D 113 TYR cc_start: 0.9475 (m-80) cc_final: 0.9251 (m-80) REVERT: D 173 MET cc_start: 0.9052 (mtp) cc_final: 0.8575 (mtt) REVERT: D 197 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8281 (mm-30) REVERT: D 214 LEU cc_start: 0.9294 (OUTLIER) cc_final: 0.9087 (tt) REVERT: E 27 GLN cc_start: 0.8523 (tt0) cc_final: 0.7960 (tt0) REVERT: E 28 TYR cc_start: 0.8447 (m-80) cc_final: 0.7932 (m-10) REVERT: E 32 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9023 (mp) REVERT: E 163 GLU cc_start: 0.8525 (tt0) cc_final: 0.8164 (tt0) REVERT: E 222 LYS cc_start: 0.7445 (mttt) cc_final: 0.7132 (mptt) REVERT: G 67 GLU cc_start: 0.8978 (tp30) cc_final: 0.8717 (tp30) REVERT: G 89 ASN cc_start: 0.8788 (t0) cc_final: 0.8507 (t0) REVERT: G 133 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8237 (tp30) REVERT: H 7 TYR cc_start: 0.8719 (t80) cc_final: 0.8476 (t80) REVERT: H 18 CYS cc_start: 0.8851 (p) cc_final: 0.8406 (p) REVERT: H 32 GLN cc_start: 0.9431 (tt0) cc_final: 0.8808 (tm-30) REVERT: H 37 ARG cc_start: 0.8741 (ptp-110) cc_final: 0.8081 (ptm-80) outliers start: 32 outliers final: 23 residues processed: 184 average time/residue: 0.2804 time to fit residues: 72.5285 Evaluate side-chains 181 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 42 optimal weight: 7.9990 chunk 118 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 92 optimal weight: 6.9990 chunk 25 optimal weight: 0.3980 chunk 55 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.078903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.055925 restraints weight = 30147.796| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 2.40 r_work: 0.2692 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12968 Z= 0.226 Angle : 0.587 7.047 17663 Z= 0.277 Chirality : 0.042 0.331 2159 Planarity : 0.004 0.048 2125 Dihedral : 10.722 172.990 2674 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.53 % Favored : 94.34 % Rotamer: Outliers : 2.93 % Allowed : 12.77 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 1.09 (0.22), residues: 1590 helix: 2.04 (0.18), residues: 837 sheet: -0.80 (0.55), residues: 113 loop : -0.78 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 166 HIS 0.002 0.001 HIS E 74 PHE 0.012 0.001 PHE E 114 TYR 0.015 0.001 TYR C 237 ARG 0.010 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 1.391 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8698 (tttt) cc_final: 0.8237 (mptt) REVERT: A 125 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: A 155 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8786 (mt-10) REVERT: B 3 GLU cc_start: 0.7700 (mt-10) cc_final: 0.6263 (tp30) REVERT: B 100 MET cc_start: 0.8361 (tpp) cc_final: 0.8154 (mmm) REVERT: B 122 ASP cc_start: 0.8299 (t0) cc_final: 0.7427 (t0) REVERT: C 225 PHE cc_start: 0.8731 (m-80) cc_final: 0.8374 (m-80) REVERT: D 59 GLU cc_start: 0.8653 (tp30) cc_final: 0.8257 (tp30) REVERT: D 113 TYR cc_start: 0.9484 (m-80) cc_final: 0.9262 (m-80) REVERT: D 173 MET cc_start: 0.9022 (mtp) cc_final: 0.8534 (mtt) REVERT: D 197 GLU cc_start: 0.8703 (mm-30) cc_final: 0.8280 (mm-30) REVERT: D 214 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9081 (tt) REVERT: E 27 GLN cc_start: 0.8506 (tt0) cc_final: 0.7900 (tt0) REVERT: E 28 TYR cc_start: 0.8427 (m-80) cc_final: 0.7886 (m-10) REVERT: E 163 GLU cc_start: 0.8524 (tt0) cc_final: 0.8155 (tt0) REVERT: E 222 LYS cc_start: 0.7516 (mttt) cc_final: 0.7189 (mptt) REVERT: G 67 GLU cc_start: 0.8981 (tp30) cc_final: 0.8724 (tp30) REVERT: G 89 ASN cc_start: 0.8796 (t0) cc_final: 0.8507 (t0) REVERT: G 133 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8177 (tp30) REVERT: H 18 CYS cc_start: 0.8918 (p) cc_final: 0.8439 (p) REVERT: H 32 GLN cc_start: 0.9439 (tt0) cc_final: 0.8809 (tm-30) REVERT: H 37 ARG cc_start: 0.8716 (ptp-110) cc_final: 0.8272 (mtm180) outliers start: 37 outliers final: 25 residues processed: 185 average time/residue: 0.2733 time to fit residues: 71.2068 Evaluate side-chains 185 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 1.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 109 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 41 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 150 optimal weight: 0.0030 chunk 70 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.080590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.057806 restraints weight = 30379.348| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 2.43 r_work: 0.2731 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 12968 Z= 0.150 Angle : 0.547 6.946 17663 Z= 0.261 Chirality : 0.040 0.287 2159 Planarity : 0.004 0.047 2125 Dihedral : 10.173 171.429 2674 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.72 % Favored : 95.16 % Rotamer: Outliers : 2.78 % Allowed : 13.56 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 1.22 (0.22), residues: 1590 helix: 2.18 (0.19), residues: 836 sheet: -0.95 (0.54), residues: 115 loop : -0.71 (0.25), residues: 639 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 166 HIS 0.002 0.000 HIS G 222 PHE 0.011 0.001 PHE A 143 TYR 0.015 0.001 TYR C 237 ARG 0.006 0.000 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8291 (tm-30) REVERT: A 88 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8506 (tm-30) REVERT: A 92 ARG cc_start: 0.9022 (ttm-80) cc_final: 0.8590 (tpt-90) REVERT: A 93 LYS cc_start: 0.8687 (tttt) cc_final: 0.8222 (mptt) REVERT: A 125 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: B 3 GLU cc_start: 0.7681 (mt-10) cc_final: 0.6257 (tp30) REVERT: B 122 ASP cc_start: 0.8359 (t0) cc_final: 0.7355 (t0) REVERT: C 225 PHE cc_start: 0.8686 (m-80) cc_final: 0.8363 (m-80) REVERT: D 59 GLU cc_start: 0.8636 (tp30) cc_final: 0.8146 (tp30) REVERT: D 113 TYR cc_start: 0.9461 (m-80) cc_final: 0.9221 (m-80) REVERT: D 197 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8278 (mm-30) REVERT: E 27 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7921 (tt0) REVERT: E 28 TYR cc_start: 0.8391 (m-80) cc_final: 0.7816 (m-10) REVERT: E 54 MET cc_start: 0.8687 (tpt) cc_final: 0.8138 (tpt) REVERT: E 163 GLU cc_start: 0.8514 (tt0) cc_final: 0.8159 (tt0) REVERT: E 222 LYS cc_start: 0.7471 (mttt) cc_final: 0.7175 (mptt) REVERT: G 35 MET cc_start: 0.4595 (ttm) cc_final: 0.4350 (ttt) REVERT: G 67 GLU cc_start: 0.8953 (tp30) cc_final: 0.8650 (tp30) REVERT: G 89 ASN cc_start: 0.8724 (t0) cc_final: 0.8424 (t0) REVERT: G 133 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.7936 (mm-30) REVERT: H 18 CYS cc_start: 0.8962 (p) cc_final: 0.8089 (p) REVERT: H 28 GLN cc_start: 0.9391 (mp10) cc_final: 0.9103 (mp10) REVERT: H 32 GLN cc_start: 0.9440 (tt0) cc_final: 0.8747 (tm-30) REVERT: H 37 ARG cc_start: 0.8662 (ptp-110) cc_final: 0.8225 (mtm180) outliers start: 35 outliers final: 20 residues processed: 188 average time/residue: 0.2743 time to fit residues: 72.0856 Evaluate side-chains 181 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 75 optimal weight: 6.9990 chunk 145 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 156 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.080075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.057236 restraints weight = 30361.891| |-----------------------------------------------------------------------------| r_work (start): 0.2848 rms_B_bonded: 2.43 r_work: 0.2716 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12968 Z= 0.185 Angle : 0.565 6.817 17663 Z= 0.269 Chirality : 0.040 0.281 2159 Planarity : 0.004 0.046 2125 Dihedral : 9.975 172.425 2674 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.09 % Favored : 94.78 % Rotamer: Outliers : 2.14 % Allowed : 14.43 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.22), residues: 1590 helix: 2.26 (0.19), residues: 829 sheet: -0.83 (0.55), residues: 115 loop : -0.59 (0.26), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 83 HIS 0.002 0.000 HIS C 360 PHE 0.012 0.001 PHE A 143 TYR 0.015 0.001 TYR C 237 ARG 0.007 0.000 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8470 (tm-30) REVERT: A 92 ARG cc_start: 0.9064 (ttm-80) cc_final: 0.8677 (tpt-90) REVERT: A 93 LYS cc_start: 0.8677 (tttt) cc_final: 0.8169 (mptt) REVERT: A 125 GLU cc_start: 0.9125 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: A 155 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8751 (mt-10) REVERT: B 3 GLU cc_start: 0.7670 (mt-10) cc_final: 0.6229 (tp30) REVERT: B 103 ARG cc_start: 0.8368 (tpp80) cc_final: 0.7932 (ttm110) REVERT: B 122 ASP cc_start: 0.8357 (t0) cc_final: 0.7352 (t0) REVERT: C 225 PHE cc_start: 0.8710 (m-80) cc_final: 0.8374 (m-80) REVERT: D 59 GLU cc_start: 0.8648 (tp30) cc_final: 0.8239 (tp30) REVERT: D 113 TYR cc_start: 0.9479 (m-80) cc_final: 0.9237 (m-80) REVERT: D 185 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8385 (mm-30) REVERT: D 197 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8290 (mm-30) REVERT: E 27 GLN cc_start: 0.8478 (tt0) cc_final: 0.7943 (tt0) REVERT: E 28 TYR cc_start: 0.8404 (m-80) cc_final: 0.7818 (m-10) REVERT: E 54 MET cc_start: 0.8693 (tpt) cc_final: 0.8144 (tpt) REVERT: E 163 GLU cc_start: 0.8504 (tt0) cc_final: 0.8140 (tt0) REVERT: E 222 LYS cc_start: 0.7484 (mttt) cc_final: 0.7180 (mptt) REVERT: G 67 GLU cc_start: 0.8972 (tp30) cc_final: 0.8676 (tp30) REVERT: G 89 ASN cc_start: 0.8720 (t0) cc_final: 0.8428 (t0) REVERT: G 133 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8104 (tp30) REVERT: H 7 TYR cc_start: 0.8496 (t80) cc_final: 0.8197 (t80) REVERT: H 9 ASP cc_start: 0.8253 (t0) cc_final: 0.7489 (t0) REVERT: H 18 CYS cc_start: 0.8940 (p) cc_final: 0.8112 (p) REVERT: H 32 GLN cc_start: 0.9465 (tt0) cc_final: 0.8745 (tm-30) REVERT: H 37 ARG cc_start: 0.8655 (ptp-110) cc_final: 0.8118 (mtm180) outliers start: 27 outliers final: 21 residues processed: 179 average time/residue: 0.2799 time to fit residues: 70.0343 Evaluate side-chains 182 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 1.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 40 optimal weight: 7.9990 chunk 7 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 22 optimal weight: 7.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.080345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.057661 restraints weight = 30341.607| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.42 r_work: 0.2738 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 12968 Z= 0.168 Angle : 0.558 6.725 17663 Z= 0.269 Chirality : 0.040 0.279 2159 Planarity : 0.004 0.044 2125 Dihedral : 9.806 171.993 2674 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.84 % Favored : 95.03 % Rotamer: Outliers : 2.46 % Allowed : 14.43 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 1.29 (0.22), residues: 1590 helix: 2.22 (0.19), residues: 836 sheet: -0.74 (0.57), residues: 105 loop : -0.71 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 166 HIS 0.003 0.000 HIS C 17 PHE 0.010 0.001 PHE E 114 TYR 0.014 0.001 TYR C 237 ARG 0.007 0.000 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8931 (tm-30) cc_final: 0.8266 (tm-30) REVERT: A 88 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8481 (tm-30) REVERT: A 92 ARG cc_start: 0.9058 (ttm-80) cc_final: 0.8678 (tpt-90) REVERT: A 93 LYS cc_start: 0.8680 (tttt) cc_final: 0.8161 (mptt) REVERT: A 125 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: A 155 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8703 (mt-10) REVERT: B 3 GLU cc_start: 0.7640 (mt-10) cc_final: 0.6201 (tp30) REVERT: B 103 ARG cc_start: 0.8300 (tpp80) cc_final: 0.7701 (ttm110) REVERT: B 105 GLU cc_start: 0.7225 (mp0) cc_final: 0.5934 (mp0) REVERT: B 122 ASP cc_start: 0.8375 (t0) cc_final: 0.7351 (t0) REVERT: B 155 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8635 (mp) REVERT: C 225 PHE cc_start: 0.8703 (m-80) cc_final: 0.8409 (m-80) REVERT: D 59 GLU cc_start: 0.8642 (tp30) cc_final: 0.8227 (tp30) REVERT: D 113 TYR cc_start: 0.9474 (m-80) cc_final: 0.9222 (m-80) REVERT: D 197 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8287 (mm-30) REVERT: E 27 GLN cc_start: 0.8456 (tt0) cc_final: 0.7908 (tt0) REVERT: E 28 TYR cc_start: 0.8381 (m-80) cc_final: 0.7772 (m-10) REVERT: E 54 MET cc_start: 0.8680 (tpt) cc_final: 0.8143 (tpt) REVERT: E 163 GLU cc_start: 0.8492 (tt0) cc_final: 0.8135 (tt0) REVERT: E 222 LYS cc_start: 0.7498 (mttt) cc_final: 0.7205 (mptt) REVERT: G 67 GLU cc_start: 0.8969 (tp30) cc_final: 0.8674 (tp30) REVERT: G 89 ASN cc_start: 0.8674 (t0) cc_final: 0.8375 (t0) REVERT: G 133 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8080 (tp30) REVERT: H 9 ASP cc_start: 0.8202 (t0) cc_final: 0.7433 (t0) REVERT: H 18 CYS cc_start: 0.8939 (p) cc_final: 0.8383 (p) REVERT: H 32 GLN cc_start: 0.9470 (tt0) cc_final: 0.8846 (tm-30) REVERT: H 37 ARG cc_start: 0.8644 (ptp-110) cc_final: 0.8093 (mtm180) outliers start: 31 outliers final: 21 residues processed: 186 average time/residue: 0.2925 time to fit residues: 75.8509 Evaluate side-chains 188 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 73 optimal weight: 10.0000 chunk 139 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 63 optimal weight: 0.3980 chunk 113 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 128 optimal weight: 0.0870 chunk 37 optimal weight: 9.9990 chunk 130 optimal weight: 3.9990 chunk 127 optimal weight: 0.0050 overall best weight: 0.8974 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.080742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.057917 restraints weight = 30137.235| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.44 r_work: 0.2734 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 12968 Z= 0.165 Angle : 0.559 7.392 17663 Z= 0.269 Chirality : 0.040 0.275 2159 Planarity : 0.004 0.043 2125 Dihedral : 9.564 171.980 2674 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.78 % Favored : 95.09 % Rotamer: Outliers : 2.38 % Allowed : 14.12 % Favored : 83.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 1.36 (0.22), residues: 1590 helix: 2.26 (0.19), residues: 835 sheet: -0.70 (0.58), residues: 105 loop : -0.64 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 166 HIS 0.002 0.000 HIS C 17 PHE 0.010 0.001 PHE E 114 TYR 0.014 0.001 TYR C 237 ARG 0.007 0.000 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 166 time to evaluate : 1.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8675 (tm-30) REVERT: A 88 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8529 (tm-30) REVERT: A 92 ARG cc_start: 0.9065 (ttm-80) cc_final: 0.8831 (tpp80) REVERT: A 93 LYS cc_start: 0.8666 (tttt) cc_final: 0.8152 (mptt) REVERT: A 125 GLU cc_start: 0.9130 (OUTLIER) cc_final: 0.8023 (mp0) REVERT: A 131 MET cc_start: 0.8845 (tpt) cc_final: 0.8559 (mmm) REVERT: A 155 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8690 (mt-10) REVERT: B 3 GLU cc_start: 0.7628 (mt-10) cc_final: 0.6268 (tp30) REVERT: B 103 ARG cc_start: 0.8312 (tpp80) cc_final: 0.7610 (ttm110) REVERT: B 122 ASP cc_start: 0.8302 (t0) cc_final: 0.7290 (t0) REVERT: B 155 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8441 (mp) REVERT: C 225 PHE cc_start: 0.8674 (m-80) cc_final: 0.8400 (m-80) REVERT: D 59 GLU cc_start: 0.8641 (tp30) cc_final: 0.8136 (tp30) REVERT: D 197 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8304 (mm-30) REVERT: E 27 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7898 (tt0) REVERT: E 28 TYR cc_start: 0.8367 (m-80) cc_final: 0.7702 (m-10) REVERT: E 54 MET cc_start: 0.8683 (tpt) cc_final: 0.8149 (tpt) REVERT: E 163 GLU cc_start: 0.8485 (tt0) cc_final: 0.8123 (tt0) REVERT: E 222 LYS cc_start: 0.7527 (mttt) cc_final: 0.7234 (mptt) REVERT: G 67 GLU cc_start: 0.8973 (tp30) cc_final: 0.8718 (tp30) REVERT: G 89 ASN cc_start: 0.8649 (t0) cc_final: 0.8361 (t0) REVERT: G 133 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.7902 (mm-30) REVERT: H 9 ASP cc_start: 0.8057 (t0) cc_final: 0.7228 (t0) REVERT: H 14 LEU cc_start: 0.8547 (mt) cc_final: 0.8216 (tt) REVERT: H 18 CYS cc_start: 0.8930 (p) cc_final: 0.8340 (p) REVERT: H 32 GLN cc_start: 0.9478 (tt0) cc_final: 0.8850 (tm-30) REVERT: H 37 ARG cc_start: 0.8613 (ptp-110) cc_final: 0.8047 (mtm180) outliers start: 30 outliers final: 23 residues processed: 186 average time/residue: 0.2734 time to fit residues: 71.1065 Evaluate side-chains 190 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 8.9990 chunk 156 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 68 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 142 optimal weight: 8.9990 chunk 105 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.077561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.054373 restraints weight = 30497.639| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.48 r_work: 0.2647 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 12968 Z= 0.344 Angle : 0.641 6.539 17663 Z= 0.310 Chirality : 0.043 0.272 2159 Planarity : 0.004 0.041 2125 Dihedral : 9.835 174.572 2674 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.85 % Favored : 94.03 % Rotamer: Outliers : 2.06 % Allowed : 14.99 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % 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: 1.25 (0.22), residues: 1590 helix: 2.11 (0.19), residues: 830 sheet: -0.65 (0.59), residues: 100 loop : -0.59 (0.26), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 168 HIS 0.004 0.001 HIS C 17 PHE 0.016 0.001 PHE E 206 TYR 0.016 0.001 TYR C 237 ARG 0.008 0.000 ARG G 78 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 1.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8671 (tm-30) REVERT: A 88 GLU cc_start: 0.8925 (OUTLIER) cc_final: 0.8440 (tm-30) REVERT: A 125 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8770 (mp0) REVERT: A 131 MET cc_start: 0.8964 (tpt) cc_final: 0.8716 (mmm) REVERT: A 155 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8713 (mt-10) REVERT: B 3 GLU cc_start: 0.7695 (mt-10) cc_final: 0.6405 (tp30) REVERT: B 103 ARG cc_start: 0.8364 (tpp80) cc_final: 0.7843 (ttm110) REVERT: B 105 GLU cc_start: 0.7293 (mp0) cc_final: 0.6658 (pm20) REVERT: B 122 ASP cc_start: 0.8373 (t0) cc_final: 0.7387 (t0) REVERT: B 155 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8643 (mp) REVERT: C 165 ASN cc_start: 0.9328 (OUTLIER) cc_final: 0.9033 (t0) REVERT: C 225 PHE cc_start: 0.8783 (m-80) cc_final: 0.8436 (m-80) REVERT: D 173 MET cc_start: 0.8890 (mtt) cc_final: 0.8595 (mtt) REVERT: D 194 GLU cc_start: 0.8156 (mp0) cc_final: 0.7916 (mp0) REVERT: D 197 GLU cc_start: 0.8736 (mm-30) cc_final: 0.8304 (mm-30) REVERT: E 19 GLN cc_start: 0.8010 (tm-30) cc_final: 0.7544 (tm-30) REVERT: E 27 GLN cc_start: 0.8524 (tt0) cc_final: 0.7921 (tt0) REVERT: E 28 TYR cc_start: 0.8463 (m-80) cc_final: 0.7818 (m-10) REVERT: E 163 GLU cc_start: 0.8469 (tt0) cc_final: 0.8043 (tt0) REVERT: G 67 GLU cc_start: 0.9015 (tp30) cc_final: 0.8769 (tp30) REVERT: G 89 ASN cc_start: 0.8662 (t0) cc_final: 0.8375 (t0) REVERT: G 133 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8089 (tp30) REVERT: H 9 ASP cc_start: 0.7979 (t0) cc_final: 0.7173 (t0) REVERT: H 14 LEU cc_start: 0.8450 (mt) cc_final: 0.8119 (tt) REVERT: H 17 SER cc_start: 0.9014 (m) cc_final: 0.8649 (t) REVERT: H 32 GLN cc_start: 0.9436 (tt0) cc_final: 0.8951 (tm-30) REVERT: H 37 ARG cc_start: 0.8608 (ptp-110) cc_final: 0.8026 (mtm180) outliers start: 26 outliers final: 19 residues processed: 178 average time/residue: 0.2872 time to fit residues: 70.9096 Evaluate side-chains 178 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 165 ASN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 65.4593 > 50: distance: 23 - 83: 28.761 distance: 26 - 80: 29.898 distance: 53 - 59: 29.753 distance: 59 - 60: 8.145 distance: 60 - 63: 17.753 distance: 61 - 62: 34.265 distance: 61 - 67: 53.089 distance: 63 - 64: 4.104 distance: 64 - 65: 19.075 distance: 64 - 66: 20.150 distance: 67 - 68: 51.860 distance: 68 - 69: 28.160 distance: 68 - 71: 10.001 distance: 69 - 70: 28.473 distance: 69 - 75: 31.592 distance: 71 - 72: 52.424 distance: 72 - 73: 47.627 distance: 72 - 74: 41.419 distance: 75 - 76: 41.003 distance: 75 - 149: 36.104 distance: 76 - 77: 46.019 distance: 76 - 79: 47.129 distance: 77 - 78: 41.211 distance: 77 - 80: 59.739 distance: 78 - 146: 34.643 distance: 80 - 81: 51.423 distance: 81 - 82: 43.455 distance: 81 - 84: 40.560 distance: 82 - 83: 43.120 distance: 82 - 91: 33.663 distance: 84 - 85: 24.559 distance: 85 - 86: 31.236 distance: 85 - 87: 42.073 distance: 86 - 88: 29.454 distance: 87 - 89: 11.092 distance: 88 - 90: 7.010 distance: 89 - 90: 31.550 distance: 91 - 92: 15.759 distance: 91 - 97: 24.314 distance: 92 - 93: 29.033 distance: 92 - 95: 12.594 distance: 93 - 94: 40.487 distance: 93 - 98: 41.361 distance: 96 - 97: 8.846 distance: 98 - 99: 28.421 distance: 98 - 104: 13.948 distance: 99 - 100: 7.804 distance: 100 - 101: 31.261 distance: 100 - 105: 28.075 distance: 103 - 104: 40.098 distance: 105 - 106: 39.972 distance: 106 - 107: 13.565 distance: 106 - 109: 21.212 distance: 107 - 108: 48.372 distance: 107 - 112: 22.193 distance: 109 - 111: 8.677 distance: 112 - 113: 17.383 distance: 113 - 114: 15.142 distance: 113 - 116: 45.064 distance: 114 - 115: 44.703 distance: 114 - 121: 9.583 distance: 116 - 117: 53.196 distance: 117 - 118: 35.867 distance: 118 - 119: 28.837 distance: 118 - 120: 27.030 distance: 121 - 122: 34.934 distance: 122 - 125: 40.137 distance: 123 - 124: 40.308 distance: 125 - 126: 38.698 distance: 128 - 129: 27.627 distance: 129 - 130: 41.672 distance: 129 - 132: 12.409 distance: 130 - 131: 28.365 distance: 130 - 134: 28.601 distance: 132 - 133: 44.054