Starting phenix.real_space_refine on Sat Aug 23 15:28:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ahx_15452/08_2025/8ahx_15452.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ahx_15452/08_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_15452/08_2025/8ahx_15452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ahx_15452/08_2025/8ahx_15452.map" model { file = "/net/cci-nas-00/data/ceres_data/8ahx_15452/08_2025/8ahx_15452.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ahx_15452/08_2025/8ahx_15452.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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 Unresolved non-hydrogen dihedrals: 1 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 Unresolved non-hydrogen dihedrals: 1 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: 3.49, per 1000 atoms: 0.28 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: 1.26 Conformation dependent library (CDL) restraints added in 699.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.42 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: 2.08 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 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 1.676 1.826 -0.150 2.00e-02 2.50e+03 5.60e+01 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=" O5' FMN D 411 " pdb=" P FMN D 411 " ideal model delta sigma weight residual 1.676 1.592 0.084 2.00e-02 2.50e+03 1.75e+01 ... (remaining 12963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 17036 1.98 - 3.95: 435 3.95 - 5.93: 125 5.93 - 7.91: 22 7.91 - 9.88: 45 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 - 24.70: 7712 24.70 - 49.40: 382 49.40 - 74.10: 91 74.10 - 98.80: 49 98.80 - 123.50: 46 Dihedral angle restraints: 8280 sinusoidal: 3744 harmonic: 4536 Sorted by residual: dihedral pdb=" CA ILE D 106 " pdb=" C ILE D 106 " pdb=" N GLY D 107 " pdb=" CA GLY D 107 " ideal model delta harmonic sigma weight residual -180.00 -158.25 -21.75 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA ALA G 223 " pdb=" C ALA G 223 " pdb=" N GLU G 224 " pdb=" CA GLU G 224 " ideal model delta harmonic sigma weight residual 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" C2B LMT E 302 " pdb=" C1B LMT E 302 " pdb=" O5B LMT E 302 " pdb=" C5B LMT E 302 " ideal model delta sinusoidal sigma weight residual -57.12 66.38 -123.50 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 8277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.014: 2155 1.014 - 2.029: 0 2.029 - 3.043: 0 3.043 - 4.057: 0 4.057 - 5.071: 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 -2.52 2.55 -5.07 2.00e-01 2.50e+01 6.43e+02 chirality pdb=" CB THR G 202 " pdb=" CA THR G 202 " pdb=" OG1 THR G 202 " pdb=" CG2 THR G 202 " both_signs ideal model delta sigma weight residual False 2.55 -2.46 5.01 2.00e-01 2.50e+01 6.28e+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 -2.50 2.42 -4.92 2.00e-01 2.50e+01 6.05e+02 ... (remaining 2156 not shown) Planarity restraints: 2128 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G 301 " 0.135 2.00e-02 2.50e+03 4.47e-02 9.00e+01 pdb=" C10 FMN G 301 " 0.007 2.00e-02 2.50e+03 pdb=" C2 FMN G 301 " -0.035 2.00e-02 2.50e+03 pdb=" C4 FMN G 301 " 0.020 2.00e-02 2.50e+03 pdb=" C4A FMN G 301 " 0.024 2.00e-02 2.50e+03 pdb=" C5A FMN G 301 " 0.023 2.00e-02 2.50e+03 pdb=" C6 FMN G 301 " 0.015 2.00e-02 2.50e+03 pdb=" C7 FMN G 301 " -0.008 2.00e-02 2.50e+03 pdb=" C7M FMN G 301 " -0.000 2.00e-02 2.50e+03 pdb=" C8 FMN G 301 " -0.026 2.00e-02 2.50e+03 pdb=" C8M FMN G 301 " -0.078 2.00e-02 2.50e+03 pdb=" C9 FMN G 301 " -0.017 2.00e-02 2.50e+03 pdb=" C9A FMN G 301 " 0.008 2.00e-02 2.50e+03 pdb=" N1 FMN G 301 " -0.023 2.00e-02 2.50e+03 pdb=" N10 FMN G 301 " 0.014 2.00e-02 2.50e+03 pdb=" N3 FMN G 301 " -0.013 2.00e-02 2.50e+03 pdb=" N5 FMN G 301 " 0.029 2.00e-02 2.50e+03 pdb=" O2 FMN G 301 " -0.076 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 2125 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: 1.850 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: 0.260 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 15.190 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.850 ------------------------------------------------------------------------------- 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 0.150 12990 Z= 0.375 Angle : 1.157 42.563 17717 Z= 0.388 Chirality : 0.220 5.071 2159 Planarity : 0.005 0.048 2128 Dihedral : 19.362 123.502 5376 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.69 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.91 (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 ARG 0.002 0.000 ARG E 221 TYR 0.012 0.001 TYR C 237 PHE 0.017 0.001 PHE G 173 TRP 0.009 0.001 TRP D 83 HIS 0.002 0.001 HIS G 152 Details of bonding type rmsd covalent geometry : bond 0.00690 (12968) covalent geometry : angle 0.89296 (17663) hydrogen bonds : bond 0.14488 ( 651) hydrogen bonds : angle 5.89494 ( 1845) metal coordination : bond 0.01034 ( 20) metal coordination : angle 13.34389 ( 54) Misc. bond : bond 0.06844 ( 2) *********************** 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 : 0.489 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: 0.7786 (p0) REVERT: B 155 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8890 (mp) REVERT: B 158 PRO cc_start: 0.9004 (Cg_exo) cc_final: 0.8754 (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: 0.8250 (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: 0.8402 (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: 0.1512 time to fit residues: 39.6170 Evaluate side-chains 147 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 143 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 98 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.080670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.058546 restraints weight = 30505.957| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.29 r_work: 0.2802 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12990 Z= 0.133 Angle : 0.979 41.864 17717 Z= 0.302 Chirality : 0.044 0.288 2159 Planarity : 0.004 0.049 2128 Dihedral : 17.044 91.363 2681 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.03 % Favored : 94.84 % Rotamer: Outliers : 2.30 % Allowed : 8.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.22), residues: 1590 helix: 1.90 (0.19), residues: 829 sheet: -0.64 (0.57), residues: 113 loop : -0.72 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 81 TYR 0.019 0.001 TYR H 7 PHE 0.013 0.001 PHE A 143 TRP 0.008 0.001 TRP D 83 HIS 0.002 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00300 (12968) covalent geometry : angle 0.65082 (17663) hydrogen bonds : bond 0.04195 ( 651) hydrogen bonds : angle 4.47874 ( 1845) metal coordination : bond 0.01129 ( 20) metal coordination : angle 13.26271 ( 54) Misc. bond : bond 0.00260 ( 2) *********************** 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: 29 poor density : 162 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8621 (tttt) cc_final: 0.8395 (mptt) REVERT: A 161 ASN cc_start: 0.9175 (t0) cc_final: 0.8669 (t0) REVERT: B 3 GLU cc_start: 0.7833 (mt-10) cc_final: 0.6463 (tp30) REVERT: B 105 GLU cc_start: 0.7364 (mp0) cc_final: 0.6419 (mp0) REVERT: B 122 ASP cc_start: 0.8262 (t0) cc_final: 0.7497 (t0) REVERT: B 155 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8748 (mp) REVERT: C 225 PHE cc_start: 0.8619 (m-80) cc_final: 0.8317 (m-80) REVERT: D 59 GLU cc_start: 0.8881 (tp30) cc_final: 0.8542 (tp30) REVERT: D 197 GLU cc_start: 0.8745 (mm-30) cc_final: 0.8438 (mm-30) REVERT: E 27 GLN cc_start: 0.8673 (tt0) cc_final: 0.8159 (tt0) REVERT: E 28 TYR cc_start: 0.8561 (m-80) cc_final: 0.8087 (m-10) REVERT: E 32 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8973 (mp) REVERT: E 79 GLU cc_start: 0.8496 (pm20) cc_final: 0.8274 (pm20) REVERT: E 163 GLU cc_start: 0.8806 (tt0) cc_final: 0.8541 (tt0) REVERT: E 222 LYS cc_start: 0.7694 (mttt) cc_final: 0.7401 (mptt) REVERT: G 67 GLU cc_start: 0.9080 (tp30) cc_final: 0.8822 (tp30) REVERT: G 89 ASN cc_start: 0.8844 (t0) cc_final: 0.8610 (t0) REVERT: H 7 TYR cc_start: 0.9002 (t80) cc_final: 0.8607 (t80) REVERT: H 18 CYS cc_start: 0.8875 (p) cc_final: 0.7990 (p) REVERT: H 32 GLN cc_start: 0.9430 (tt0) cc_final: 0.8785 (tm-30) REVERT: H 37 ARG cc_start: 0.8698 (ptp-110) cc_final: 0.8321 (ptm-80) outliers start: 29 outliers final: 13 residues processed: 186 average time/residue: 0.1290 time to fit residues: 33.7747 Evaluate side-chains 163 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 148 time to evaluate : 0.484 ------------------------------------------------------------------------------- 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 140 LEU Chi-restraints excluded: chain C residue 204 VAL 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 130 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 119 optimal weight: 6.9990 chunk 146 optimal weight: 7.9990 chunk 156 optimal weight: 20.0000 chunk 148 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.078394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.055414 restraints weight = 30549.140| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.42 r_work: 0.2678 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 12990 Z= 0.193 Angle : 1.005 44.052 17717 Z= 0.313 Chirality : 0.045 0.335 2159 Planarity : 0.004 0.049 2128 Dihedral : 13.320 72.736 2681 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.53 % Favored : 94.34 % Rotamer: Outliers : 2.93 % Allowed : 9.60 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.22), residues: 1590 helix: 1.93 (0.19), residues: 829 sheet: -0.73 (0.56), residues: 113 loop : -0.71 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 81 TYR 0.014 0.001 TYR C 237 PHE 0.012 0.001 PHE E 206 TRP 0.007 0.001 TRP D 83 HIS 0.004 0.001 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.00466 (12968) covalent geometry : angle 0.67067 (17663) hydrogen bonds : bond 0.04288 ( 651) hydrogen bonds : angle 4.39489 ( 1845) metal coordination : bond 0.01769 ( 20) metal coordination : angle 13.57575 ( 54) Misc. bond : bond 0.00112 ( 2) *********************** 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: 37 poor density : 157 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8645 (tttt) cc_final: 0.8281 (mptt) REVERT: A 125 GLU cc_start: 0.9035 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: B 3 GLU cc_start: 0.7703 (mt-10) cc_final: 0.6223 (tp30) REVERT: B 105 GLU cc_start: 0.6912 (mp0) cc_final: 0.6132 (mp0) REVERT: B 122 ASP cc_start: 0.8377 (t0) cc_final: 0.7519 (t0) REVERT: B 155 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8617 (mp) REVERT: C 225 PHE cc_start: 0.8823 (m-80) cc_final: 0.8415 (m-80) REVERT: D 173 MET cc_start: 0.9037 (mtp) cc_final: 0.8555 (mtt) REVERT: D 197 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8324 (mm-30) REVERT: D 214 LEU cc_start: 0.9281 (OUTLIER) cc_final: 0.9068 (tt) REVERT: E 27 GLN cc_start: 0.8579 (tt0) cc_final: 0.8017 (tt0) REVERT: E 28 TYR cc_start: 0.8477 (m-80) cc_final: 0.7954 (m-10) REVERT: E 32 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9037 (mp) REVERT: E 163 GLU cc_start: 0.8528 (tt0) cc_final: 0.8113 (tt0) REVERT: E 222 LYS cc_start: 0.7410 (mttt) cc_final: 0.7102 (mptt) REVERT: G 67 GLU cc_start: 0.8980 (tp30) cc_final: 0.8729 (tp30) REVERT: G 89 ASN cc_start: 0.8833 (t0) cc_final: 0.8571 (t0) REVERT: G 133 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8222 (tp30) REVERT: H 7 TYR cc_start: 0.8706 (t80) cc_final: 0.8401 (t80) REVERT: H 18 CYS cc_start: 0.8863 (p) cc_final: 0.8425 (p) REVERT: H 32 GLN cc_start: 0.9423 (tt0) cc_final: 0.8816 (tm-30) REVERT: H 37 ARG cc_start: 0.8732 (ptp-110) cc_final: 0.8268 (mtm180) outliers start: 37 outliers final: 20 residues processed: 185 average time/residue: 0.1280 time to fit residues: 33.8064 Evaluate side-chains 177 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.481 ------------------------------------------------------------------------------- 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 155 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 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 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 63 optimal weight: 5.9990 chunk 130 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 150 optimal weight: 8.9990 chunk 108 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3335 r_free = 0.3335 target = 0.079526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.056608 restraints weight = 30311.763| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 2.40 r_work: 0.2705 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 12990 Z= 0.131 Angle : 0.941 42.716 17717 Z= 0.283 Chirality : 0.042 0.362 2159 Planarity : 0.004 0.049 2128 Dihedral : 10.969 58.567 2681 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.03 % Favored : 94.84 % Rotamer: Outliers : 2.62 % Allowed : 11.97 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.22), residues: 1590 helix: 2.06 (0.19), residues: 830 sheet: -0.72 (0.58), residues: 103 loop : -0.70 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 117 TYR 0.015 0.001 TYR C 237 PHE 0.012 0.001 PHE E 114 TRP 0.008 0.001 TRP D 83 HIS 0.002 0.000 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.00306 (12968) covalent geometry : angle 0.58978 (17663) hydrogen bonds : bond 0.03729 ( 651) hydrogen bonds : angle 4.23836 ( 1845) metal coordination : bond 0.01120 ( 20) metal coordination : angle 13.30250 ( 54) Misc. bond : bond 0.00039 ( 2) *********************** 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 195 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 LYS cc_start: 0.8679 (tttt) cc_final: 0.8256 (mptt) REVERT: A 125 GLU cc_start: 0.9061 (OUTLIER) cc_final: 0.7952 (mp0) REVERT: A 155 GLU cc_start: 0.9074 (mt-10) cc_final: 0.8803 (mt-10) REVERT: B 3 GLU cc_start: 0.7722 (mt-10) cc_final: 0.6276 (tp30) REVERT: B 103 ARG cc_start: 0.8234 (tpp80) cc_final: 0.7522 (ttm110) REVERT: B 105 GLU cc_start: 0.6723 (mp0) cc_final: 0.5785 (mp0) REVERT: B 122 ASP cc_start: 0.8379 (t0) cc_final: 0.7527 (t0) REVERT: B 146 ARG cc_start: 0.9461 (OUTLIER) cc_final: 0.9233 (ptp-110) REVERT: B 155 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8606 (mp) REVERT: C 225 PHE cc_start: 0.8750 (m-80) cc_final: 0.8399 (m-80) REVERT: D 59 GLU cc_start: 0.8650 (tp30) cc_final: 0.8281 (tp30) REVERT: D 113 TYR cc_start: 0.9477 (m-80) cc_final: 0.9250 (m-80) REVERT: D 173 MET cc_start: 0.9045 (mtp) cc_final: 0.8573 (mtt) REVERT: D 197 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8289 (mm-30) REVERT: D 214 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9070 (tt) REVERT: E 27 GLN cc_start: 0.8518 (tt0) cc_final: 0.7955 (tt0) REVERT: E 28 TYR cc_start: 0.8421 (m-80) cc_final: 0.7899 (m-10) REVERT: E 32 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9024 (mp) REVERT: E 79 GLU cc_start: 0.8318 (mp0) cc_final: 0.8068 (pm20) REVERT: E 163 GLU cc_start: 0.8521 (tt0) cc_final: 0.8163 (tt0) REVERT: E 222 LYS cc_start: 0.7393 (mttt) cc_final: 0.7133 (mptt) REVERT: G 67 GLU cc_start: 0.8968 (tp30) cc_final: 0.8709 (tp30) REVERT: G 89 ASN cc_start: 0.8793 (t0) cc_final: 0.8499 (t0) REVERT: G 133 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8203 (tp30) REVERT: H 7 TYR cc_start: 0.8706 (t80) cc_final: 0.8461 (t80) REVERT: H 18 CYS cc_start: 0.8852 (p) cc_final: 0.8409 (p) REVERT: H 32 GLN cc_start: 0.9421 (tt0) cc_final: 0.8801 (tm-30) REVERT: H 37 ARG cc_start: 0.8739 (ptp-110) cc_final: 0.8079 (ptm-80) outliers start: 33 outliers final: 24 residues processed: 183 average time/residue: 0.1353 time to fit residues: 34.8304 Evaluate side-chains 184 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 154 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 117 ARG Chi-restraints excluded: chain B residue 146 ARG Chi-restraints excluded: chain B residue 155 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 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 16 VAL Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain E residue 60 LEU 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 138 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 chunk 20 optimal weight: 20.0000 chunk 127 optimal weight: 0.9980 chunk 98 optimal weight: 0.9980 chunk 31 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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 = 0.3315 r_free = 0.3315 target = 0.078603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.055544 restraints weight = 30492.293| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.41 r_work: 0.2681 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12990 Z= 0.159 Angle : 0.942 43.845 17717 Z= 0.287 Chirality : 0.042 0.338 2159 Planarity : 0.004 0.048 2128 Dihedral : 10.246 59.243 2680 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.53 % Favored : 94.34 % Rotamer: Outliers : 3.09 % Allowed : 12.53 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.22), residues: 1590 helix: 2.09 (0.19), residues: 831 sheet: -0.69 (0.57), residues: 113 loop : -0.71 (0.25), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 100 TYR 0.015 0.001 TYR C 237 PHE 0.012 0.001 PHE E 114 TRP 0.008 0.001 TRP B 166 HIS 0.003 0.001 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.00380 (12968) covalent geometry : angle 0.59400 (17663) hydrogen bonds : bond 0.03908 ( 651) hydrogen bonds : angle 4.21923 ( 1845) metal coordination : bond 0.01461 ( 20) metal coordination : angle 13.25985 ( 54) Misc. bond : bond 0.00069 ( 2) *********************** 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 198 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 159 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 MET cc_start: 0.8615 (mtp) cc_final: 0.8306 (mtm) REVERT: A 93 LYS cc_start: 0.8705 (tttt) cc_final: 0.8240 (mptt) REVERT: A 125 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: B 3 GLU cc_start: 0.7715 (mt-10) cc_final: 0.6306 (tp30) REVERT: B 105 GLU cc_start: 0.6733 (mp0) cc_final: 0.6302 (mp0) REVERT: B 122 ASP cc_start: 0.8346 (t0) cc_final: 0.7466 (t0) REVERT: C 225 PHE cc_start: 0.8768 (m-80) cc_final: 0.8394 (m-80) REVERT: D 59 GLU cc_start: 0.8644 (tp30) cc_final: 0.8248 (tp30) REVERT: D 113 TYR cc_start: 0.9487 (m-80) cc_final: 0.9274 (m-80) REVERT: D 173 MET cc_start: 0.9009 (mtp) cc_final: 0.8532 (mtt) REVERT: D 197 GLU cc_start: 0.8711 (mm-30) cc_final: 0.8291 (mm-30) REVERT: D 214 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9065 (tt) REVERT: E 27 GLN cc_start: 0.8526 (tt0) cc_final: 0.7954 (tt0) REVERT: E 28 TYR cc_start: 0.8470 (m-80) cc_final: 0.7933 (m-10) REVERT: E 32 LEU cc_start: 0.9270 (OUTLIER) cc_final: 0.9061 (mp) REVERT: E 163 GLU cc_start: 0.8539 (tt0) cc_final: 0.8162 (tt0) REVERT: E 222 LYS cc_start: 0.7521 (mttt) cc_final: 0.7228 (mptt) REVERT: G 67 GLU cc_start: 0.8975 (tp30) cc_final: 0.8717 (tp30) REVERT: G 89 ASN cc_start: 0.8807 (t0) cc_final: 0.8507 (t0) REVERT: G 133 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8186 (tp30) REVERT: H 18 CYS cc_start: 0.8898 (p) cc_final: 0.8427 (p) REVERT: H 32 GLN cc_start: 0.9426 (tt0) cc_final: 0.8796 (tm-30) REVERT: H 37 ARG cc_start: 0.8721 (ptp-110) cc_final: 0.8277 (mtm180) outliers start: 39 outliers final: 23 residues processed: 188 average time/residue: 0.1350 time to fit residues: 35.8134 Evaluate side-chains 180 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 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 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 53 optimal weight: 0.8980 chunk 145 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 72 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 = 0.3333 r_free = 0.3333 target = 0.079511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.056554 restraints weight = 30181.096| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.42 r_work: 0.2701 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12990 Z= 0.117 Angle : 0.910 42.794 17717 Z= 0.275 Chirality : 0.041 0.303 2159 Planarity : 0.004 0.047 2128 Dihedral : 9.813 59.526 2678 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.91 % Favored : 94.97 % Rotamer: Outliers : 2.62 % Allowed : 13.48 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.22), residues: 1590 helix: 2.22 (0.19), residues: 828 sheet: -0.73 (0.58), residues: 103 loop : -0.66 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 78 TYR 0.015 0.001 TYR C 237 PHE 0.011 0.001 PHE E 114 TRP 0.011 0.001 TRP B 166 HIS 0.003 0.000 HIS G 222 Details of bonding type rmsd covalent geometry : bond 0.00271 (12968) covalent geometry : angle 0.56339 (17663) hydrogen bonds : bond 0.03607 ( 651) hydrogen bonds : angle 4.13726 ( 1845) metal coordination : bond 0.00961 ( 20) metal coordination : angle 12.96458 ( 54) Misc. bond : bond 0.00027 ( 2) *********************** 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 192 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8304 (tm-30) REVERT: A 93 LYS cc_start: 0.8705 (tttt) cc_final: 0.8229 (mptt) REVERT: A 125 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.8000 (mp0) REVERT: A 155 GLU cc_start: 0.9004 (mt-10) cc_final: 0.8779 (mt-10) REVERT: B 3 GLU cc_start: 0.7680 (mt-10) cc_final: 0.6266 (tp30) REVERT: B 122 ASP cc_start: 0.8299 (t0) cc_final: 0.7399 (t0) REVERT: C 225 PHE cc_start: 0.8734 (m-80) cc_final: 0.8383 (m-80) REVERT: D 59 GLU cc_start: 0.8671 (tp30) cc_final: 0.8269 (tp30) REVERT: D 113 TYR cc_start: 0.9470 (m-80) cc_final: 0.9248 (m-80) REVERT: D 173 MET cc_start: 0.9018 (mtp) cc_final: 0.8548 (mtt) REVERT: D 197 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8282 (mm-30) REVERT: D 214 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.9054 (tt) REVERT: E 27 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: E 28 TYR cc_start: 0.8404 (m-80) cc_final: 0.7843 (m-10) REVERT: E 32 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9024 (mp) REVERT: E 163 GLU cc_start: 0.8512 (tt0) cc_final: 0.8138 (tt0) REVERT: E 222 LYS cc_start: 0.7503 (mttt) cc_final: 0.7179 (mptt) REVERT: G 35 MET cc_start: 0.4609 (ttm) cc_final: 0.4387 (ttt) REVERT: G 67 GLU cc_start: 0.8967 (tp30) cc_final: 0.8668 (tp30) REVERT: G 89 ASN cc_start: 0.8749 (t0) cc_final: 0.8438 (t0) REVERT: G 133 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8160 (tp30) REVERT: H 18 CYS cc_start: 0.8939 (p) cc_final: 0.8449 (p) REVERT: H 32 GLN cc_start: 0.9431 (tt0) cc_final: 0.8791 (tm-30) REVERT: H 37 ARG cc_start: 0.8678 (ptp-110) cc_final: 0.8240 (mtm180) outliers start: 33 outliers final: 22 residues processed: 181 average time/residue: 0.1334 time to fit residues: 34.0472 Evaluate side-chains 180 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 153 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 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 447 ASP Chi-restraints excluded: chain C residue 449 ILE 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 27 GLN 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 103 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 28 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 43 optimal weight: 9.9990 chunk 13 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3300 r_free = 0.3300 target = 0.077730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.054598 restraints weight = 30549.500| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 2.46 r_work: 0.2648 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12990 Z= 0.199 Angle : 0.965 45.211 17717 Z= 0.303 Chirality : 0.043 0.282 2159 Planarity : 0.004 0.045 2128 Dihedral : 9.796 59.597 2678 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.72 % Favored : 94.15 % Rotamer: Outliers : 2.70 % Allowed : 14.35 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.22), residues: 1590 helix: 2.04 (0.19), residues: 835 sheet: -0.56 (0.60), residues: 98 loop : -0.82 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 78 TYR 0.015 0.001 TYR C 237 PHE 0.014 0.001 PHE E 206 TRP 0.009 0.001 TRP B 166 HIS 0.003 0.001 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00478 (12968) covalent geometry : angle 0.62217 (17663) hydrogen bonds : bond 0.04181 ( 651) hydrogen bonds : angle 4.23964 ( 1845) metal coordination : bond 0.01837 ( 20) metal coordination : angle 13.37036 ( 54) Misc. bond : bond 0.00076 ( 2) *********************** 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 187 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 153 time to evaluate : 0.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 ARG cc_start: 0.9005 (ttm-80) cc_final: 0.8753 (tpt-90) REVERT: A 93 LYS cc_start: 0.8728 (tttt) cc_final: 0.8234 (mptt) REVERT: A 125 GLU cc_start: 0.9115 (OUTLIER) cc_final: 0.8744 (mp0) REVERT: B 3 GLU cc_start: 0.7708 (mt-10) cc_final: 0.6404 (tp30) REVERT: B 122 ASP cc_start: 0.8335 (t0) cc_final: 0.7459 (t0) REVERT: C 225 PHE cc_start: 0.8816 (m-80) cc_final: 0.8451 (m-80) REVERT: C 319 CYS cc_start: 0.8674 (m) cc_final: 0.8436 (m) REVERT: D 113 TYR cc_start: 0.9492 (m-80) cc_final: 0.9287 (m-80) REVERT: D 173 MET cc_start: 0.8991 (mtp) cc_final: 0.8491 (mtt) REVERT: D 194 GLU cc_start: 0.8189 (mp0) cc_final: 0.7971 (mp0) REVERT: D 197 GLU cc_start: 0.8729 (mm-30) cc_final: 0.8297 (mm-30) REVERT: D 214 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.9045 (tt) REVERT: E 27 GLN cc_start: 0.8542 (tt0) cc_final: 0.7901 (tt0) REVERT: E 28 TYR cc_start: 0.8462 (m-80) cc_final: 0.7883 (m-10) REVERT: E 32 LEU cc_start: 0.9292 (OUTLIER) cc_final: 0.9085 (mp) REVERT: E 163 GLU cc_start: 0.8475 (tt0) cc_final: 0.8061 (tt0) REVERT: G 67 GLU cc_start: 0.9010 (tp30) cc_final: 0.8731 (tp30) REVERT: G 89 ASN cc_start: 0.8756 (t0) cc_final: 0.8442 (t0) REVERT: G 133 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8123 (tp30) REVERT: H 7 TYR cc_start: 0.8453 (t80) cc_final: 0.8068 (t80) REVERT: H 9 ASP cc_start: 0.8212 (t0) cc_final: 0.7463 (t0) REVERT: H 18 CYS cc_start: 0.8895 (p) cc_final: 0.8483 (p) REVERT: H 28 GLN cc_start: 0.9306 (mp10) cc_final: 0.9086 (mp10) REVERT: H 32 GLN cc_start: 0.9431 (tt0) cc_final: 0.8792 (tm-30) REVERT: H 37 ARG cc_start: 0.8687 (ptp-110) cc_final: 0.8214 (mtm180) outliers start: 34 outliers final: 24 residues processed: 179 average time/residue: 0.1214 time to fit residues: 30.3278 Evaluate side-chains 180 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 152 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 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 312 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 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 E residue 60 LEU Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 212 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 H residue 3 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 LYS Chi-restraints excluded: chain H residue 70 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 18 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 52 optimal weight: 0.8980 chunk 134 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 chunk 99 optimal weight: 0.0970 chunk 135 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3341 r_free = 0.3341 target = 0.079894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.057086 restraints weight = 30008.653| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 2.41 r_work: 0.2723 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 12990 Z= 0.104 Angle : 0.904 42.334 17717 Z= 0.277 Chirality : 0.040 0.280 2159 Planarity : 0.004 0.044 2128 Dihedral : 9.365 59.529 2678 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.97 % Favored : 94.91 % Rotamer: Outliers : 2.14 % Allowed : 14.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.22), residues: 1590 helix: 2.17 (0.19), residues: 840 sheet: -0.59 (0.60), residues: 100 loop : -0.87 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 78 TYR 0.015 0.001 TYR C 237 PHE 0.012 0.001 PHE E 114 TRP 0.011 0.001 TRP B 166 HIS 0.001 0.000 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00233 (12968) covalent geometry : angle 0.56007 (17663) hydrogen bonds : bond 0.03462 ( 651) hydrogen bonds : angle 4.08679 ( 1845) metal coordination : bond 0.00740 ( 20) metal coordination : angle 12.86779 ( 54) Misc. bond : bond 0.00018 ( 2) *********************** 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 191 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8912 (tm-30) cc_final: 0.8271 (tm-30) REVERT: A 88 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8660 (tm-30) REVERT: A 92 ARG cc_start: 0.9056 (ttm-80) cc_final: 0.8650 (tpt-90) REVERT: A 93 LYS cc_start: 0.8716 (tttt) cc_final: 0.8212 (mptt) REVERT: A 125 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8742 (mp0) REVERT: B 3 GLU cc_start: 0.7668 (mt-10) cc_final: 0.6309 (tp30) REVERT: B 122 ASP cc_start: 0.8362 (t0) cc_final: 0.7369 (t0) REVERT: C 225 PHE cc_start: 0.8705 (m-80) cc_final: 0.8393 (m-80) REVERT: C 319 CYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8425 (m) REVERT: D 59 GLU cc_start: 0.8640 (tp30) cc_final: 0.8219 (tp30) REVERT: D 113 TYR cc_start: 0.9460 (m-80) cc_final: 0.9243 (m-80) REVERT: D 197 GLU cc_start: 0.8712 (mm-30) cc_final: 0.8289 (mm-30) REVERT: D 214 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.9046 (tt) REVERT: E 27 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.7852 (tt0) REVERT: E 28 TYR cc_start: 0.8355 (m-80) cc_final: 0.7732 (m-10) REVERT: E 32 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9021 (mp) REVERT: G 67 GLU cc_start: 0.8982 (tp30) cc_final: 0.8731 (tp30) REVERT: G 89 ASN cc_start: 0.8671 (t0) cc_final: 0.8369 (t0) REVERT: G 133 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8140 (tp30) REVERT: H 9 ASP cc_start: 0.8139 (t0) cc_final: 0.7336 (t0) REVERT: H 18 CYS cc_start: 0.8931 (p) cc_final: 0.8445 (p) REVERT: H 32 GLN cc_start: 0.9421 (tt0) cc_final: 0.8757 (tm-30) REVERT: H 37 ARG cc_start: 0.8651 (ptp-110) cc_final: 0.8131 (mtm110) outliers start: 27 outliers final: 18 residues processed: 184 average time/residue: 0.1101 time to fit residues: 28.2441 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 : 0.493 ------------------------------------------------------------------------------- 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 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 203 VAL 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 214 LEU 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 32 LEU 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 133 GLU 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 90 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 118 optimal weight: 6.9990 chunk 73 optimal weight: 9.9990 chunk 65 optimal weight: 0.0060 chunk 130 optimal weight: 5.9990 chunk 153 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.079732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.056952 restraints weight = 30291.240| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.42 r_work: 0.2714 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12990 Z= 0.116 Angle : 0.907 42.486 17717 Z= 0.284 Chirality : 0.041 0.276 2159 Planarity : 0.004 0.043 2128 Dihedral : 9.168 59.405 2678 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.09 % Favored : 94.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.22), residues: 1590 helix: 2.22 (0.19), residues: 835 sheet: -0.54 (0.60), residues: 100 loop : -0.79 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 78 TYR 0.016 0.001 TYR C 237 PHE 0.013 0.001 PHE A 143 TRP 0.012 0.001 TRP B 166 HIS 0.002 0.000 HIS C 360 Details of bonding type rmsd covalent geometry : bond 0.00269 (12968) covalent geometry : angle 0.57594 (17663) hydrogen bonds : bond 0.03480 ( 651) hydrogen bonds : angle 4.07892 ( 1845) metal coordination : bond 0.00958 ( 20) metal coordination : angle 12.70118 ( 54) Misc. bond : bond 0.00026 ( 2) *********************** 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 186 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 0.305 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: 0.8281 (tm-30) REVERT: A 88 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8651 (tm-30) REVERT: A 92 ARG cc_start: 0.9067 (ttm-80) cc_final: 0.8703 (tpt-90) REVERT: A 125 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8756 (mp0) REVERT: A 155 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8751 (mt-10) REVERT: B 3 GLU cc_start: 0.7677 (mt-10) cc_final: 0.6302 (tp30) REVERT: B 103 ARG cc_start: 0.8428 (tpp80) cc_final: 0.8209 (ttm110) REVERT: B 122 ASP cc_start: 0.8326 (t0) cc_final: 0.7326 (t0) REVERT: C 225 PHE cc_start: 0.8698 (m-80) cc_final: 0.8369 (m-80) REVERT: D 59 GLU cc_start: 0.8646 (tp30) cc_final: 0.8225 (tp30) REVERT: D 113 TYR cc_start: 0.9469 (m-80) cc_final: 0.9249 (m-80) REVERT: D 197 GLU cc_start: 0.8725 (mm-30) cc_final: 0.8314 (mm-30) REVERT: D 214 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.9043 (tt) REVERT: E 27 GLN cc_start: 0.8466 (OUTLIER) cc_final: 0.7865 (tt0) REVERT: E 28 TYR cc_start: 0.8362 (m-80) cc_final: 0.7724 (m-10) REVERT: E 32 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.9025 (mp) REVERT: E 54 MET cc_start: 0.8677 (tpt) cc_final: 0.8135 (tpt) REVERT: G 67 GLU cc_start: 0.8964 (tp30) cc_final: 0.8711 (tp30) REVERT: G 89 ASN cc_start: 0.8675 (t0) cc_final: 0.8391 (t0) REVERT: G 133 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.8113 (tp30) REVERT: H 9 ASP cc_start: 0.8065 (t0) cc_final: 0.7306 (t0) REVERT: H 17 SER cc_start: 0.9009 (m) cc_final: 0.8673 (t) REVERT: H 18 CYS cc_start: 0.8955 (p) cc_final: 0.8535 (p) REVERT: H 32 GLN cc_start: 0.9421 (tt0) cc_final: 0.8753 (tm-30) REVERT: H 37 ARG cc_start: 0.8660 (ptp-110) cc_final: 0.8209 (mtm180) outliers start: 26 outliers final: 18 residues processed: 183 average time/residue: 0.1061 time to fit residues: 27.1209 Evaluate side-chains 181 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL 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 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 214 LEU 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 32 LEU 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 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 56 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 87 optimal weight: 0.0770 chunk 45 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 85 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.080667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.057920 restraints weight = 30322.085| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.44 r_work: 0.2736 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 12990 Z= 0.105 Angle : 0.888 41.322 17717 Z= 0.281 Chirality : 0.040 0.274 2159 Planarity : 0.004 0.042 2128 Dihedral : 8.927 59.017 2678 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.78 % Favored : 95.09 % Rotamer: Outliers : 1.82 % Allowed : 15.38 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.22), residues: 1590 helix: 2.32 (0.19), residues: 828 sheet: -0.55 (0.60), residues: 100 loop : -0.66 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 78 TYR 0.014 0.001 TYR C 237 PHE 0.012 0.001 PHE A 143 TRP 0.008 0.001 TRP B 166 HIS 0.002 0.000 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00235 (12968) covalent geometry : angle 0.56596 (17663) hydrogen bonds : bond 0.03240 ( 651) hydrogen bonds : angle 4.02471 ( 1845) metal coordination : bond 0.00720 ( 20) metal coordination : angle 12.40985 ( 54) Misc. bond : bond 0.00013 ( 2) ********************** 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 185 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8700 (tm-30) REVERT: A 88 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8685 (tm-30) REVERT: A 93 LYS cc_start: 0.8376 (tttm) cc_final: 0.7652 (mmtm) REVERT: A 125 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.8754 (mp0) REVERT: B 3 GLU cc_start: 0.7654 (mt-10) cc_final: 0.6273 (tp30) REVERT: B 122 ASP cc_start: 0.8313 (t0) cc_final: 0.7296 (t0) REVERT: C 225 PHE cc_start: 0.8644 (m-80) cc_final: 0.8370 (m-80) REVERT: D 59 GLU cc_start: 0.8607 (tp30) cc_final: 0.8097 (tp30) REVERT: D 113 TYR cc_start: 0.9464 (m-80) cc_final: 0.9236 (m-80) REVERT: D 197 GLU cc_start: 0.8706 (mm-30) cc_final: 0.8295 (mm-30) REVERT: E 27 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.7805 (tt0) REVERT: E 28 TYR cc_start: 0.8350 (m-80) cc_final: 0.7692 (m-10) REVERT: E 32 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.9031 (mp) REVERT: E 54 MET cc_start: 0.8675 (tpt) cc_final: 0.8143 (tpt) REVERT: G 67 GLU cc_start: 0.8971 (tp30) cc_final: 0.8720 (tp30) REVERT: G 89 ASN cc_start: 0.8646 (t0) cc_final: 0.8356 (t0) REVERT: G 133 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8102 (tp30) REVERT: H 9 ASP cc_start: 0.8018 (t0) cc_final: 0.7198 (t0) REVERT: H 14 LEU cc_start: 0.8534 (mt) cc_final: 0.8217 (tt) REVERT: H 32 GLN cc_start: 0.9439 (tt0) cc_final: 0.8946 (tm-30) REVERT: H 37 ARG cc_start: 0.8656 (ptp-110) cc_final: 0.8207 (mtm180) outliers start: 23 outliers final: 18 residues processed: 180 average time/residue: 0.1152 time to fit residues: 29.0931 Evaluate side-chains 180 residues out of total 1262 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain B residue 105 GLU 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 32 LEU 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 133 GLU 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 15 optimal weight: 6.9990 chunk 18 optimal weight: 0.3980 chunk 117 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 123 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 = 0.3330 r_free = 0.3330 target = 0.079259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.056448 restraints weight = 30333.463| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.41 r_work: 0.2700 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 12990 Z= 0.138 Angle : 0.904 42.792 17717 Z= 0.289 Chirality : 0.041 0.271 2159 Planarity : 0.004 0.041 2128 Dihedral : 8.869 59.976 2678 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.35 % Favored : 94.53 % Rotamer: Outliers : 1.98 % Allowed : 15.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.37 (0.23), residues: 1590 helix: 2.27 (0.19), residues: 829 sheet: -0.42 (0.60), residues: 98 loop : -0.66 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 78 TYR 0.016 0.001 TYR C 237 PHE 0.011 0.001 PHE A 143 TRP 0.010 0.001 TRP B 166 HIS 0.003 0.001 HIS C 17 Details of bonding type rmsd covalent geometry : bond 0.00328 (12968) covalent geometry : angle 0.58497 (17663) hydrogen bonds : bond 0.03592 ( 651) hydrogen bonds : angle 4.05952 ( 1845) metal coordination : bond 0.01204 ( 20) metal coordination : angle 12.49095 ( 54) Misc. bond : bond 0.00047 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2985.78 seconds wall clock time: 52 minutes 0.16 seconds (3120.16 seconds total)