Starting phenix.real_space_refine on Thu Sep 26 11:24:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ahx_15452/09_2024/8ahx_15452.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ahx_15452/09_2024/8ahx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ahx_15452/09_2024/8ahx_15452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ahx_15452/09_2024/8ahx_15452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ahx_15452/09_2024/8ahx_15452.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ahx_15452/09_2024/8ahx_15452.cif" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 18 7.16 5 P 3 5.49 5 S 97 5.16 5 C 8158 2.51 5 N 2073 2.21 5 O 2338 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 12687 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1394 Classifications: {'peptide': 189} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 179} Chain: "B" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 811 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain breaks: 2 Chain: "C" Number of atoms: 3511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 476, 3511 Classifications: {'peptide': 476} Link IDs: {'PTRANS': 37, 'TRANS': 438} Chain: "D" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2629 Classifications: {'peptide': 349} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 325} Chain: "E" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1601 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 203} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1514 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain: "H" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 548 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 4, 'TRANS': 66} Chain: "A" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 74 Unusual residues: {'FES': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 47 Unusual residues: {'FMN': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 372 Unusual residues: {'FMN': 1, 'LMT': 9, 'RBF': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'LMT': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 184 SG CYS A 25 36.955 84.906 50.802 1.00102.81 S ATOM 9154 SG CYS E 122 38.370 82.240 48.485 1.00113.43 S ATOM 844 SG CYS A 113 40.644 85.907 45.869 1.00 96.89 S ATOM 8545 SG CYS E 39 39.697 88.711 48.565 1.00101.07 S ATOM 1798 SG CYS B 119 27.814 44.779 90.307 1.00125.95 S ATOM 1971 SG CYS B 145 22.385 46.145 90.650 1.00126.07 S ATOM 1952 SG CYS B 142 26.271 48.407 85.782 1.00140.38 S ATOM 1935 SG CYS B 139 25.704 51.418 91.308 1.00104.29 S ATOM 1722 SG CYS B 109 20.061 40.010 99.643 1.00148.19 S ATOM 1740 SG CYS B 112 18.807 36.197 94.061 1.00146.84 S ATOM 1764 SG CYS B 115 23.153 40.817 94.676 1.00132.05 S ATOM 2001 SG CYS B 149 16.360 40.766 94.111 1.00160.09 S ATOM 4935 SG CYS C 376 43.011 92.402 90.586 1.00108.55 S ATOM 5250 SG CYS C 419 38.769 93.959 91.338 1.00 74.60 S ATOM 4893 SG CYS C 370 39.659 93.659 84.721 1.00 77.21 S ATOM 4918 SG CYS C 373 42.804 97.958 88.721 1.00 83.32 S ATOM 5181 SG CYS C 409 44.506 81.635 94.360 1.00 84.55 S ATOM 5203 SG CYS C 412 46.572 86.143 98.786 1.00 80.78 S ATOM 5219 SG CYS C 415 43.806 87.799 93.438 1.00 98.49 S ATOM 4961 SG CYS C 380 49.219 86.421 93.141 1.00 89.09 S Time building chain proxies: 7.96, per 1000 atoms: 0.63 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: 2.97 Conformation dependent library (CDL) restraints added in 1.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 201 " pdb="FE1 FES A 201 " - pdb=" SG CYS E 122 " pdb="FE1 FES A 201 " - pdb=" SG CYS A 25 " pdb="FE2 FES A 201 " - pdb=" SG CYS A 113 " pdb="FE2 FES A 201 " - pdb=" SG CYS E 39 " pdb=" SF4 B 201 " pdb="FE3 SF4 B 201 " - pdb=" SG CYS B 142 " pdb="FE2 SF4 B 201 " - pdb=" SG CYS B 145 " pdb="FE4 SF4 B 201 " - pdb=" SG CYS B 139 " pdb="FE1 SF4 B 201 " - pdb=" SG CYS B 119 " pdb=" SF4 B 202 " pdb="FE2 SF4 B 202 " - pdb=" SG CYS B 112 " pdb="FE3 SF4 B 202 " - pdb=" SG CYS B 115 " pdb="FE1 SF4 B 202 " - pdb=" SG CYS B 109 " pdb="FE4 SF4 B 202 " - pdb=" SG CYS B 149 " pdb=" SF4 C 501 " pdb="FE1 SF4 C 501 " - pdb=" SG CYS C 376 " pdb="FE2 SF4 C 501 " - pdb=" SG CYS C 419 " pdb="FE4 SF4 C 501 " - pdb=" SG CYS C 373 " pdb="FE3 SF4 C 501 " - pdb=" SG CYS C 370 " pdb=" SF4 C 502 " pdb="FE3 SF4 C 502 " - pdb=" SG CYS C 415 " pdb="FE2 SF4 C 502 " - pdb=" SG CYS C 412 " pdb="FE1 SF4 C 502 " - pdb=" SG CYS C 409 " pdb="FE4 SF4 C 502 " - pdb=" SG CYS C 380 " Number of angles added : 54 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2904 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 11 sheets defined 57.2% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 Processing helix chain 'A' and resid 23 through 31 removed outlier: 3.771A pdb=" N PHE A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER A 31 " --> pdb=" O PHE A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 62 Processing helix chain 'A' and resid 62 through 67 Processing helix chain 'A' and resid 71 through 90 Processing helix chain 'A' and resid 91 through 93 No H-bonds generated for 'chain 'A' and resid 91 through 93' Processing helix chain 'A' and resid 105 through 110 Processing helix chain 'A' and resid 113 through 126 Proline residue: A 119 - end of helix removed outlier: 3.533A pdb=" N ARG A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 159 removed outlier: 4.002A pdb=" N LEU A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'B' and resid 3 through 26 removed outlier: 3.855A pdb=" N ALA B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 85 removed outlier: 3.521A pdb=" N LYS B 82 " --> pdb=" O GLY B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 Processing helix chain 'B' and resid 162 through 166 Processing helix chain 'C' and resid 119 through 123 removed outlier: 3.806A pdb=" N GLU C 123 " --> pdb=" O PRO C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 134 removed outlier: 3.541A pdb=" N LEU C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 157 removed outlier: 3.534A pdb=" N LYS C 150 " --> pdb=" O PRO C 146 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N HIS C 157 " --> pdb=" O GLN C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 183 Processing helix chain 'C' and resid 183 through 198 Processing helix chain 'C' and resid 211 through 222 Processing helix chain 'C' and resid 236 through 240 removed outlier: 3.600A pdb=" N MET C 239 " --> pdb=" O LEU C 236 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLY C 240 " --> pdb=" O TYR C 237 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 236 through 240' Processing helix chain 'C' and resid 241 through 250 removed outlier: 3.557A pdb=" N GLN C 247 " --> pdb=" O LYS C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 263 removed outlier: 3.513A pdb=" N VAL C 263 " --> pdb=" O SER C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 283 removed outlier: 3.656A pdb=" N TYR C 274 " --> pdb=" O ALA C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 319 removed outlier: 3.657A pdb=" N LEU C 315 " --> pdb=" O PRO C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 395 Processing helix chain 'C' and resid 397 through 404 removed outlier: 3.597A pdb=" N GLU C 403 " --> pdb=" O ASP C 399 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N TYR C 404 " --> pdb=" O GLY C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 413 through 418 removed outlier: 3.876A pdb=" N VAL C 418 " --> pdb=" O CYS C 414 " (cutoff:3.500A) Processing helix chain 'C' and resid 424 through 478 Processing helix chain 'D' and resid 17 through 41 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 41 through 67 Processing helix chain 'D' and resid 69 through 75 removed outlier: 3.738A pdb=" N ASP D 75 " --> pdb=" O ARG D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 89 removed outlier: 3.735A pdb=" N THR D 81 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 106 removed outlier: 3.771A pdb=" N GLY D 98 " --> pdb=" O PRO D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 114 Processing helix chain 'D' and resid 122 through 135 Processing helix chain 'D' and resid 137 through 141 removed outlier: 4.159A pdb=" N THR D 141 " --> pdb=" O GLN D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 164 Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 191 through 198 removed outlier: 3.608A pdb=" N ILE D 195 " --> pdb=" O THR D 191 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLY D 198 " --> pdb=" O GLU D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 201 through 208 Processing helix chain 'D' and resid 220 through 232 Processing helix chain 'D' and resid 237 through 258 Processing helix chain 'D' and resid 265 through 270 Processing helix chain 'D' and resid 273 through 280 Processing helix chain 'D' and resid 284 through 288 Processing helix chain 'D' and resid 291 through 312 removed outlier: 3.530A pdb=" N ARG D 295 " --> pdb=" O SER D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 337 Proline residue: D 331 - end of helix Processing helix chain 'E' and resid 17 through 27 removed outlier: 4.235A pdb=" N PHE E 21 " --> pdb=" O PRO E 17 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU E 25 " --> pdb=" O PHE E 21 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TRP E 26 " --> pdb=" O THR E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 44 removed outlier: 3.612A pdb=" N THR E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 72 Processing helix chain 'E' and resid 73 through 76 removed outlier: 3.654A pdb=" N ILE E 76 " --> pdb=" O ARG E 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 73 through 76' Processing helix chain 'E' and resid 77 through 79 No H-bonds generated for 'chain 'E' and resid 77 through 79' Processing helix chain 'E' and resid 80 through 101 removed outlier: 3.992A pdb=" N VAL E 92 " --> pdb=" O VAL E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.590A pdb=" N VAL E 110 " --> pdb=" O GLU E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 117 removed outlier: 4.389A pdb=" N ALA E 116 " --> pdb=" O GLY E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'E' and resid 136 through 168 Processing helix chain 'E' and resid 173 through 179 Processing helix chain 'E' and resid 180 through 186 removed outlier: 4.468A pdb=" N TRP E 184 " --> pdb=" O HIS E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 196 through 201 removed outlier: 3.535A pdb=" N ALA E 199 " --> pdb=" O ILE E 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 228 removed outlier: 3.912A pdb=" N PHE E 206 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ILE E 207 " --> pdb=" O PRO E 203 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 79 removed outlier: 4.190A pdb=" N GLN G 39 " --> pdb=" O MET G 35 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N GLY G 63 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N THR G 64 " --> pdb=" O MET G 60 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU G 79 " --> pdb=" O ALA G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 86 removed outlier: 3.509A pdb=" N LEU G 85 " --> pdb=" O PRO G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 93 removed outlier: 3.814A pdb=" N ASP G 93 " --> pdb=" O PRO G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 163 removed outlier: 4.190A pdb=" N ILE G 162 " --> pdb=" O ALA G 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 172 Processing helix chain 'G' and resid 188 through 192 Processing helix chain 'G' and resid 202 through 222 Processing helix chain 'G' and resid 223 through 228 Processing helix chain 'H' and resid 25 through 34 Processing helix chain 'H' and resid 34 through 39 removed outlier: 3.564A pdb=" N CYS H 38 " --> pdb=" O GLY H 34 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 101 Processing sheet with id=AA2, first strand: chain 'C' and resid 34 through 38 removed outlier: 3.702A pdb=" N ALA C 84 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N GLU C 104 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N ILE C 82 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 34 through 38 Processing sheet with id=AA4, first strand: chain 'C' and resid 48 through 49 Processing sheet with id=AA5, first strand: chain 'C' and resid 161 through 165 Processing sheet with id=AA6, first strand: chain 'C' and resid 204 through 208 Processing sheet with id=AA7, first strand: chain 'C' and resid 288 through 293 Processing sheet with id=AA8, first strand: chain 'C' and resid 328 through 330 Processing sheet with id=AA9, first strand: chain 'E' and resid 169 through 170 Processing sheet with id=AB1, first strand: chain 'G' and resid 108 through 111 removed outlier: 3.566A pdb=" N ALA G 118 " --> pdb=" O ALA G 110 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU G 133 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER G 137 " --> pdb=" O GLY G 146 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLY G 146 " --> pdb=" O SER G 137 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ASP G 139 " --> pdb=" O ILE G 144 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE G 144 " --> pdb=" O ASP G 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 14 through 18 removed outlier: 6.104A pdb=" N SER H 4 " --> pdb=" O ILE H 68 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE H 70 " --> pdb=" O SER H 4 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL H 6 " --> pdb=" O ILE H 70 " (cutoff:3.500A) 655 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.26 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.41: 5029 1.41 - 1.63: 7766 1.63 - 1.85: 121 1.85 - 2.07: 0 2.07 - 2.28: 52 Bond restraints: 12968 Sorted by residual: bond pdb=" O5' FMN C 500 " pdb=" P FMN C 500 " ideal model delta sigma weight residual 1.610 1.826 -0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" CA VAL C 204 " pdb=" C VAL C 204 " ideal model delta sigma weight residual 1.523 1.460 0.063 1.27e-02 6.20e+03 2.48e+01 bond pdb=" C THR E 45 " pdb=" O THR E 45 " ideal model delta sigma weight residual 1.235 1.199 0.036 7.50e-03 1.78e+04 2.24e+01 bond pdb=" CA LEU A 74 " pdb=" C LEU A 74 " ideal model delta sigma weight residual 1.523 1.466 0.057 1.34e-02 5.57e+03 1.83e+01 bond pdb=" C4A FMN C 500 " pdb=" N5 FMN C 500 " ideal model delta sigma weight residual 1.380 1.295 0.085 2.00e-02 2.50e+03 1.79e+01 ... (remaining 12963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 17037 2.04 - 4.07: 427 4.07 - 6.11: 133 6.11 - 8.14: 19 8.14 - 10.18: 47 Bond angle restraints: 17663 Sorted by residual: angle pdb=" C VAL A 30 " pdb=" CA VAL A 30 " pdb=" CB VAL A 30 " ideal model delta sigma weight residual 110.84 104.94 5.90 1.25e+00 6.40e-01 2.22e+01 angle pdb=" C ASN A 112 " pdb=" N CYS A 113 " pdb=" CA CYS A 113 " ideal model delta sigma weight residual 121.54 129.34 -7.80 1.91e+00 2.74e-01 1.67e+01 angle pdb=" N THR G 202 " pdb=" CA THR G 202 " pdb=" C THR G 202 " ideal model delta sigma weight residual 114.04 109.19 4.85 1.24e+00 6.50e-01 1.53e+01 angle pdb=" C ALA D 170 " pdb=" CA ALA D 170 " pdb=" CB ALA D 170 " ideal model delta sigma weight residual 115.89 110.80 5.09 1.32e+00 5.74e-01 1.49e+01 angle pdb=" CA ARG A 92 " pdb=" C ARG A 92 " pdb=" O ARG A 92 " ideal model delta sigma weight residual 119.34 123.21 -3.87 1.09e+00 8.42e-01 1.26e+01 ... (remaining 17658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.94: 7935 33.94 - 67.87: 234 67.87 - 101.81: 63 101.81 - 135.74: 43 135.74 - 169.68: 1 Dihedral angle restraints: 8276 sinusoidal: 3740 harmonic: 4536 Sorted by residual: dihedral pdb=" C10 FMN D 411 " pdb=" C1' FMN D 411 " pdb=" N10 FMN D 411 " pdb=" C2' FMN D 411 " ideal model delta sinusoidal sigma weight residual 257.59 87.91 169.68 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C5' FMN G 301 " pdb=" O5' FMN G 301 " pdb=" P FMN G 301 " pdb=" O1P FMN G 301 " ideal model delta sinusoidal sigma weight residual 75.26 -151.91 -132.83 1 2.00e+01 2.50e-03 4.03e+01 dihedral pdb=" C4' FMN D 411 " pdb=" C5' FMN D 411 " pdb=" O5' FMN D 411 " pdb=" P FMN D 411 " ideal model delta sinusoidal sigma weight residual -172.30 -80.18 -92.12 1 2.00e+01 2.50e-03 2.49e+01 ... (remaining 8273 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.004: 2155 1.004 - 2.007: 0 2.007 - 3.011: 0 3.011 - 4.015: 0 4.015 - 5.019: 4 Chirality restraints: 2159 Sorted by residual: chirality pdb=" C2' FMN G 301 " pdb=" C1' FMN G 301 " pdb=" C3' FMN G 301 " pdb=" O2' FMN G 301 " both_signs ideal model delta sigma weight residual False -2.47 2.55 -5.02 2.00e-01 2.50e+01 6.30e+02 chirality pdb=" CB THR G 202 " pdb=" CA THR G 202 " pdb=" OG1 THR G 202 " pdb=" CG2 THR G 202 " both_signs ideal model delta sigma weight residual False 2.55 -2.46 5.01 2.00e-01 2.50e+01 6.28e+02 chirality pdb=" C4' FMN D 411 " pdb=" C3' FMN D 411 " pdb=" C5' FMN D 411 " pdb=" O4' FMN D 411 " both_signs ideal model delta sigma weight residual False -2.47 2.42 -4.89 2.00e-01 2.50e+01 5.98e+02 ... (remaining 2156 not shown) Planarity restraints: 2125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' FMN G 301 " 0.144 2.00e-02 2.50e+03 4.51e-02 9.66e+01 pdb=" C10 FMN G 301 " 0.005 2.00e-02 2.50e+03 pdb=" C2 FMN G 301 " -0.039 2.00e-02 2.50e+03 pdb=" C4 FMN G 301 " 0.007 2.00e-02 2.50e+03 pdb=" C4A FMN G 301 " 0.016 2.00e-02 2.50e+03 pdb=" C5A FMN G 301 " 0.017 2.00e-02 2.50e+03 pdb=" C6 FMN G 301 " 0.008 2.00e-02 2.50e+03 pdb=" C7 FMN G 301 " -0.012 2.00e-02 2.50e+03 pdb=" C7M FMN G 301 " -0.006 2.00e-02 2.50e+03 pdb=" C8 FMN G 301 " -0.023 2.00e-02 2.50e+03 pdb=" C8M FMN G 301 " -0.070 2.00e-02 2.50e+03 pdb=" C9 FMN G 301 " -0.012 2.00e-02 2.50e+03 pdb=" C9A FMN G 301 " 0.009 2.00e-02 2.50e+03 pdb=" N1 FMN G 301 " -0.022 2.00e-02 2.50e+03 pdb=" N10 FMN G 301 " 0.017 2.00e-02 2.50e+03 pdb=" N3 FMN G 301 " -0.024 2.00e-02 2.50e+03 pdb=" N5 FMN G 301 " 0.019 2.00e-02 2.50e+03 pdb=" O2 FMN G 301 " -0.079 2.00e-02 2.50e+03 pdb=" O4 FMN G 301 " 0.043 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS E 74 " 0.024 2.00e-02 2.50e+03 4.73e-02 2.24e+01 pdb=" C HIS E 74 " -0.082 2.00e-02 2.50e+03 pdb=" O HIS E 74 " 0.031 2.00e-02 2.50e+03 pdb=" N THR E 75 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA G 223 " -0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C ALA G 223 " 0.060 2.00e-02 2.50e+03 pdb=" O ALA G 223 " -0.023 2.00e-02 2.50e+03 pdb=" N GLU G 224 " -0.020 2.00e-02 2.50e+03 ... (remaining 2122 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1280 2.74 - 3.28: 12557 3.28 - 3.82: 20725 3.82 - 4.36: 23462 4.36 - 4.90: 42249 Nonbonded interactions: 100273 Sorted by model distance: nonbonded pdb=" OG SER C 202 " pdb=" O ALA C 227 " model vdw 2.203 3.040 nonbonded pdb=" OG SER H 25 " pdb=" OE1 GLN H 28 " model vdw 2.208 3.040 nonbonded pdb=" OG SER D 201 " pdb=" OG SER D 204 " model vdw 2.212 3.040 nonbonded pdb=" O THR D 184 " pdb=" OG1 THR D 187 " model vdw 2.223 3.040 nonbonded pdb=" O SER D 314 " pdb=" OH TYR G 128 " model vdw 2.226 3.040 ... (remaining 100268 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 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: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 31.500 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.216 12968 Z= 0.446 Angle : 0.919 10.177 17663 Z= 0.390 Chirality : 0.219 5.019 2159 Planarity : 0.005 0.048 2125 Dihedral : 19.651 169.681 5372 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.09 % Favored : 94.65 % Rotamer: Outliers : 0.71 % Allowed : 6.74 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.23), residues: 1590 helix: 1.79 (0.19), residues: 808 sheet: -0.60 (0.58), residues: 107 loop : -0.63 (0.26), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 83 HIS 0.002 0.001 HIS G 152 PHE 0.017 0.001 PHE G 173 TYR 0.012 0.001 TYR C 237 ARG 0.002 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 182 time to evaluate : 1.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8863 (tm-30) cc_final: 0.8602 (tm-30) REVERT: A 93 LYS cc_start: 0.8566 (tttt) cc_final: 0.8262 (mptt) REVERT: A 125 GLU cc_start: 0.9101 (mp0) cc_final: 0.8774 (mp0) REVERT: A 161 ASN cc_start: 0.9082 (t0) cc_final: 0.8582 (t0) REVERT: B 3 GLU cc_start: 0.7802 (mt-10) cc_final: 0.6649 (tp30) REVERT: B 105 GLU cc_start: 0.7423 (mp0) cc_final: 0.6596 (mp0) REVERT: B 122 ASP cc_start: 0.8077 (t0) cc_final: 0.7418 (t0) REVERT: B 155 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8893 (mp) REVERT: B 158 PRO cc_start: 0.9004 (Cg_exo) cc_final: 0.8654 (Cg_endo) REVERT: C 3 PHE cc_start: 0.6129 (m-80) cc_final: 0.5725 (m-80) REVERT: C 225 PHE cc_start: 0.8869 (m-80) cc_final: 0.8501 (m-80) REVERT: D 197 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8388 (mm-30) REVERT: E 19 GLN cc_start: 0.8176 (tm-30) cc_final: 0.7727 (tm-30) REVERT: E 163 GLU cc_start: 0.8632 (tt0) cc_final: 0.8301 (tt0) REVERT: E 192 ASP cc_start: 0.7415 (t0) cc_final: 0.7178 (t0) REVERT: E 222 LYS cc_start: 0.7340 (mttt) cc_final: 0.7097 (mptt) REVERT: G 67 GLU cc_start: 0.8926 (tp30) cc_final: 0.8605 (tp30) REVERT: G 89 ASN cc_start: 0.8876 (t0) cc_final: 0.8507 (t0) REVERT: H 18 CYS cc_start: 0.8648 (p) cc_final: 0.8401 (m) REVERT: H 32 GLN cc_start: 0.9121 (tt0) cc_final: 0.8849 (tm-30) REVERT: H 37 ARG cc_start: 0.8622 (ptp-110) cc_final: 0.8247 (ptm-80) REVERT: H 57 LYS cc_start: 0.8525 (ttpp) cc_final: 0.8003 (ttpp) outliers start: 9 outliers final: 3 residues processed: 191 average time/residue: 0.2968 time to fit residues: 77.8335 Evaluate side-chains 149 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 145 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain G residue 202 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 40 optimal weight: 0.0050 chunk 80 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 91 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 430 GLN D 327 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 12968 Z= 0.219 Angle : 0.658 8.654 17663 Z= 0.299 Chirality : 0.044 0.297 2159 Planarity : 0.004 0.049 2125 Dihedral : 17.444 172.669 2677 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.03 % Favored : 94.84 % Rotamer: Outliers : 2.38 % Allowed : 8.56 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1590 helix: 1.90 (0.19), residues: 829 sheet: -0.69 (0.56), residues: 113 loop : -0.69 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 83 HIS 0.002 0.001 HIS C 360 PHE 0.013 0.001 PHE A 143 TYR 0.018 0.001 TYR H 7 ARG 0.005 0.000 ARG B 146 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 ASN cc_start: 0.9071 (t0) cc_final: 0.8546 (t0) REVERT: B 3 GLU cc_start: 0.7769 (mt-10) cc_final: 0.6591 (tp30) REVERT: B 105 GLU cc_start: 0.7366 (mp0) cc_final: 0.7120 (mp0) REVERT: B 122 ASP cc_start: 0.8114 (t0) cc_final: 0.7529 (t0) REVERT: C 225 PHE cc_start: 0.8838 (m-80) cc_final: 0.8486 (m-80) REVERT: C 266 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.9011 (tp) REVERT: D 59 GLU cc_start: 0.8697 (tp30) cc_final: 0.8291 (tp30) REVERT: D 197 GLU cc_start: 0.8676 (mm-30) cc_final: 0.8332 (mm-30) REVERT: E 27 GLN cc_start: 0.8532 (tt0) cc_final: 0.7949 (tt0) REVERT: E 28 TYR cc_start: 0.8456 (m-80) cc_final: 0.7916 (m-10) REVERT: E 32 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8975 (mp) REVERT: E 79 GLU cc_start: 0.8521 (pm20) cc_final: 0.8290 (pm20) REVERT: E 163 GLU cc_start: 0.8679 (tt0) cc_final: 0.8333 (tt0) REVERT: E 222 LYS cc_start: 0.7350 (mttt) cc_final: 0.7104 (mptt) REVERT: G 67 GLU cc_start: 0.8944 (tp30) cc_final: 0.8662 (tp30) REVERT: G 89 ASN cc_start: 0.8827 (t0) cc_final: 0.8598 (t0) REVERT: H 7 TYR cc_start: 0.8955 (t80) cc_final: 0.8677 (t80) REVERT: H 18 CYS cc_start: 0.8752 (p) cc_final: 0.8271 (p) REVERT: H 32 GLN cc_start: 0.9222 (tt0) cc_final: 0.8760 (tm-30) REVERT: H 37 ARG cc_start: 0.8638 (ptp-110) cc_final: 0.8270 (ptm-80) outliers start: 30 outliers final: 14 residues processed: 186 average time/residue: 0.2691 time to fit residues: 70.4484 Evaluate side-chains 163 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 147 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 204 VAL Chi-restraints excluded: chain C residue 266 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 316 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain E residue 32 LEU Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 118 optimal weight: 8.9990 chunk 97 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 142 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 127 optimal weight: 8.9990 chunk 141 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 12968 Z= 0.306 Angle : 0.673 8.876 17663 Z= 0.308 Chirality : 0.045 0.343 2159 Planarity : 0.004 0.049 2125 Dihedral : 13.557 173.460 2675 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.60 % Favored : 94.28 % Rotamer: Outliers : 2.93 % Allowed : 9.75 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.22), residues: 1590 helix: 1.93 (0.19), residues: 829 sheet: -0.73 (0.56), residues: 113 loop : -0.68 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 83 HIS 0.003 0.001 HIS E 74 PHE 0.012 0.001 PHE E 206 TYR 0.014 0.001 TYR C 237 ARG 0.006 0.000 ARG B 146 *********************** 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 195 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 158 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: B 3 GLU cc_start: 0.7782 (mt-10) cc_final: 0.6605 (tp30) REVERT: B 122 ASP cc_start: 0.8100 (t0) cc_final: 0.7420 (t0) REVERT: C 225 PHE cc_start: 0.8837 (m-80) cc_final: 0.8462 (m-80) REVERT: D 173 MET cc_start: 0.9019 (mtp) cc_final: 0.8552 (mtt) REVERT: D 197 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8305 (mm-30) REVERT: D 214 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9147 (tt) REVERT: E 27 GLN cc_start: 0.8504 (tt0) cc_final: 0.7896 (tt0) REVERT: E 28 TYR cc_start: 0.8462 (m-80) cc_final: 0.7911 (m-10) REVERT: E 163 GLU cc_start: 0.8699 (tt0) cc_final: 0.8306 (tt0) REVERT: E 222 LYS cc_start: 0.7393 (mttt) cc_final: 0.7136 (mptt) REVERT: G 67 GLU cc_start: 0.8969 (tp30) cc_final: 0.8711 (tp30) REVERT: G 89 ASN cc_start: 0.8868 (t0) cc_final: 0.8601 (t0) REVERT: G 133 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8240 (tp30) REVERT: H 18 CYS cc_start: 0.8845 (p) cc_final: 0.8369 (p) REVERT: H 32 GLN cc_start: 0.9219 (tt0) cc_final: 0.8708 (tm-30) REVERT: H 37 ARG cc_start: 0.8697 (ptp-110) cc_final: 0.8165 (ptm-80) outliers start: 37 outliers final: 21 residues processed: 186 average time/residue: 0.2631 time to fit residues: 69.1067 Evaluate side-chains 180 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 156 time to evaluate : 1.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 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 G residue 94 SER Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 141 optimal weight: 3.9990 chunk 107 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 143 optimal weight: 2.9990 chunk 151 optimal weight: 10.0000 chunk 135 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 12968 Z= 0.328 Angle : 0.645 7.230 17663 Z= 0.303 Chirality : 0.044 0.359 2159 Planarity : 0.004 0.049 2125 Dihedral : 11.755 173.494 2674 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.60 % Favored : 94.28 % Rotamer: Outliers : 2.78 % Allowed : 12.37 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.22), residues: 1590 helix: 1.92 (0.18), residues: 829 sheet: -0.85 (0.55), residues: 113 loop : -0.70 (0.26), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 83 HIS 0.004 0.001 HIS E 74 PHE 0.013 0.001 PHE E 206 TYR 0.014 0.001 TYR C 237 ARG 0.005 0.000 ARG B 103 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 161 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.9093 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: A 155 GLU cc_start: 0.9007 (mt-10) cc_final: 0.8801 (mt-10) REVERT: B 3 GLU cc_start: 0.7825 (mt-10) cc_final: 0.6620 (tp30) REVERT: B 122 ASP cc_start: 0.8014 (t0) cc_final: 0.7380 (t0) REVERT: C 225 PHE cc_start: 0.8889 (m-80) cc_final: 0.8527 (m-80) REVERT: D 59 GLU cc_start: 0.8697 (tp30) cc_final: 0.8322 (tp30) REVERT: D 173 MET cc_start: 0.8991 (mtp) cc_final: 0.8485 (mtt) REVERT: D 194 GLU cc_start: 0.8203 (mp0) cc_final: 0.7946 (mp0) REVERT: D 197 GLU cc_start: 0.8687 (mm-30) cc_final: 0.8276 (mm-30) REVERT: D 214 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9151 (tt) REVERT: E 27 GLN cc_start: 0.8523 (tt0) cc_final: 0.7902 (tt0) REVERT: E 28 TYR cc_start: 0.8488 (m-80) cc_final: 0.7940 (m-10) REVERT: E 163 GLU cc_start: 0.8679 (tt0) cc_final: 0.8286 (tt0) REVERT: E 222 LYS cc_start: 0.7488 (mttt) cc_final: 0.7140 (mptt) REVERT: G 67 GLU cc_start: 0.8992 (tp30) cc_final: 0.8776 (tp30) REVERT: G 89 ASN cc_start: 0.8835 (t0) cc_final: 0.8545 (t0) REVERT: G 133 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8247 (tp30) REVERT: H 7 TYR cc_start: 0.9000 (t80) cc_final: 0.8763 (t80) REVERT: H 18 CYS cc_start: 0.8915 (p) cc_final: 0.8409 (p) REVERT: H 32 GLN cc_start: 0.9218 (tt0) cc_final: 0.8669 (tm-30) REVERT: H 37 ARG cc_start: 0.8716 (ptp-110) cc_final: 0.8292 (mtm180) outliers start: 35 outliers final: 26 residues processed: 185 average time/residue: 0.2807 time to fit residues: 72.6972 Evaluate side-chains 184 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 1.399 ------------------------------------------------------------------------------- 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 13 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 312 VAL Chi-restraints excluded: chain C residue 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 60 LEU 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 20 VAL Chi-restraints excluded: chain H residue 42 ILE 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 86 optimal weight: 0.0870 chunk 2 optimal weight: 0.9980 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 104 optimal weight: 0.0000 chunk 0 optimal weight: 10.0000 chunk 77 optimal weight: 0.7980 chunk 136 optimal weight: 9.9990 chunk 38 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 overall best weight: 0.7764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.067 12968 Z= 0.157 Angle : 0.566 7.087 17663 Z= 0.267 Chirality : 0.041 0.326 2159 Planarity : 0.004 0.048 2125 Dihedral : 10.679 171.313 2674 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.03 % Favored : 94.84 % Rotamer: Outliers : 2.62 % Allowed : 13.16 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.22), residues: 1590 helix: 2.02 (0.19), residues: 842 sheet: -0.73 (0.56), residues: 113 loop : -0.87 (0.25), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 83 HIS 0.002 0.000 HIS B 132 PHE 0.014 0.001 PHE A 143 TYR 0.016 0.001 TYR C 237 ARG 0.007 0.000 ARG G 78 *********************** 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 200 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 167 time to evaluate : 1.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8388 (tm-30) REVERT: A 125 GLU cc_start: 0.9056 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: B 3 GLU cc_start: 0.7745 (mt-10) cc_final: 0.6625 (tp30) REVERT: B 122 ASP cc_start: 0.8033 (t0) cc_final: 0.7318 (t0) REVERT: C 225 PHE cc_start: 0.8779 (m-80) cc_final: 0.8478 (m-80) REVERT: D 59 GLU cc_start: 0.8701 (tp30) cc_final: 0.8320 (tp30) REVERT: D 197 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8249 (mm-30) REVERT: E 27 GLN cc_start: 0.8449 (tt0) cc_final: 0.7838 (tt0) REVERT: E 28 TYR cc_start: 0.8410 (m-80) cc_final: 0.7778 (m-10) REVERT: E 163 GLU cc_start: 0.8681 (tt0) cc_final: 0.8322 (tt0) REVERT: E 222 LYS cc_start: 0.7497 (mttt) cc_final: 0.7177 (mptt) REVERT: G 67 GLU cc_start: 0.8928 (tp30) cc_final: 0.8625 (tp30) REVERT: G 89 ASN cc_start: 0.8788 (t0) cc_final: 0.8509 (t0) REVERT: G 133 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8207 (tp30) REVERT: H 7 TYR cc_start: 0.8915 (t80) cc_final: 0.8680 (t80) REVERT: H 18 CYS cc_start: 0.8924 (p) cc_final: 0.8372 (p) REVERT: H 32 GLN cc_start: 0.9212 (tt0) cc_final: 0.8661 (tm-30) REVERT: H 37 ARG cc_start: 0.8643 (ptp-110) cc_final: 0.8270 (mtm180) outliers start: 33 outliers final: 20 residues processed: 189 average time/residue: 0.2677 time to fit residues: 71.6392 Evaluate side-chains 179 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 157 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 319 CYS Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 136 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 151 optimal weight: 7.9990 chunk 126 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 12 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 12968 Z= 0.262 Angle : 0.599 8.126 17663 Z= 0.284 Chirality : 0.042 0.297 2159 Planarity : 0.004 0.047 2125 Dihedral : 10.505 173.639 2674 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.53 % Favored : 94.34 % Rotamer: Outliers : 2.62 % Allowed : 13.80 % Favored : 83.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.22), residues: 1590 helix: 2.05 (0.19), residues: 838 sheet: -0.54 (0.60), residues: 98 loop : -0.79 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 166 HIS 0.003 0.001 HIS G 222 PHE 0.012 0.001 PHE E 206 TYR 0.015 0.001 TYR C 237 ARG 0.006 0.000 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 156 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLU cc_start: 0.9112 (OUTLIER) cc_final: 0.8677 (mp0) REVERT: B 3 GLU cc_start: 0.7772 (mt-10) cc_final: 0.6711 (tp30) REVERT: B 122 ASP cc_start: 0.8094 (t0) cc_final: 0.7399 (t0) REVERT: C 225 PHE cc_start: 0.8819 (m-80) cc_final: 0.8522 (m-80) REVERT: D 59 GLU cc_start: 0.8694 (tp30) cc_final: 0.8294 (tp30) REVERT: D 173 MET cc_start: 0.9004 (mtt) cc_final: 0.8499 (mtt) REVERT: D 197 GLU cc_start: 0.8683 (mm-30) cc_final: 0.8262 (mm-30) REVERT: E 27 GLN cc_start: 0.8465 (tt0) cc_final: 0.7829 (tt0) REVERT: E 28 TYR cc_start: 0.8448 (m-80) cc_final: 0.7811 (m-10) REVERT: E 163 GLU cc_start: 0.8699 (tt0) cc_final: 0.8310 (tt0) REVERT: E 222 LYS cc_start: 0.7546 (mttt) cc_final: 0.7214 (mptt) REVERT: G 67 GLU cc_start: 0.8973 (tp30) cc_final: 0.8680 (tp30) REVERT: G 89 ASN cc_start: 0.8794 (t0) cc_final: 0.8492 (t0) REVERT: G 133 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8165 (tp30) REVERT: H 7 TYR cc_start: 0.8939 (t80) cc_final: 0.8677 (t80) REVERT: H 18 CYS cc_start: 0.8943 (p) cc_final: 0.8462 (p) REVERT: H 32 GLN cc_start: 0.9232 (tt0) cc_final: 0.8658 (tm-30) REVERT: H 37 ARG cc_start: 0.8664 (ptp-110) cc_final: 0.8228 (mtm180) outliers start: 33 outliers final: 24 residues processed: 180 average time/residue: 0.2704 time to fit residues: 67.6710 Evaluate side-chains 177 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 151 time to evaluate : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain 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 447 ASP Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 42 ILE 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 17 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 chunk 110 optimal weight: 0.0870 chunk 85 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 84 optimal weight: 0.0970 chunk 151 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 12968 Z= 0.159 Angle : 0.568 8.811 17663 Z= 0.272 Chirality : 0.041 0.283 2159 Planarity : 0.004 0.046 2125 Dihedral : 10.114 171.485 2674 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.91 % Favored : 94.97 % Rotamer: Outliers : 2.38 % Allowed : 14.59 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.22), residues: 1590 helix: 2.18 (0.19), residues: 833 sheet: -0.51 (0.60), residues: 98 loop : -0.75 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 166 HIS 0.001 0.000 HIS C 17 PHE 0.011 0.001 PHE A 143 TYR 0.015 0.001 TYR C 237 ARG 0.007 0.000 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 163 time to evaluate : 1.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8900 (tm-30) cc_final: 0.8372 (tm-30) REVERT: A 88 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8619 (tm-30) REVERT: A 125 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.7990 (mp0) REVERT: B 3 GLU cc_start: 0.7743 (mt-10) cc_final: 0.6610 (tp30) REVERT: B 122 ASP cc_start: 0.8035 (t0) cc_final: 0.7291 (t0) REVERT: C 225 PHE cc_start: 0.8762 (m-80) cc_final: 0.8495 (m-80) REVERT: D 59 GLU cc_start: 0.8699 (tp30) cc_final: 0.8291 (tp30) REVERT: D 197 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8277 (mm-30) REVERT: E 27 GLN cc_start: 0.8417 (tt0) cc_final: 0.7779 (tt0) REVERT: E 28 TYR cc_start: 0.8403 (m-80) cc_final: 0.7696 (m-10) REVERT: E 163 GLU cc_start: 0.8687 (tt0) cc_final: 0.8342 (tt0) REVERT: E 222 LYS cc_start: 0.7540 (mttt) cc_final: 0.7214 (mptt) REVERT: G 67 GLU cc_start: 0.8937 (tp30) cc_final: 0.8631 (tp30) REVERT: G 89 ASN cc_start: 0.8729 (t0) cc_final: 0.8439 (t0) REVERT: G 133 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8147 (tp30) REVERT: H 7 TYR cc_start: 0.8915 (t80) cc_final: 0.8708 (t80) REVERT: H 9 ASP cc_start: 0.8640 (t0) cc_final: 0.8160 (t0) REVERT: H 16 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8822 (mt) REVERT: H 18 CYS cc_start: 0.8932 (p) cc_final: 0.8425 (p) REVERT: H 32 GLN cc_start: 0.9253 (tt0) cc_final: 0.8685 (tm-30) REVERT: H 37 ARG cc_start: 0.8626 (ptp-110) cc_final: 0.8170 (mtm180) outliers start: 30 outliers final: 22 residues processed: 183 average time/residue: 0.2793 time to fit residues: 71.3778 Evaluate side-chains 183 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 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 23 LEU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 16 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 60 optimal weight: 8.9990 chunk 90 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 103 optimal weight: 0.0570 chunk 74 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 118 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 144 optimal weight: 6.9990 overall best weight: 1.2902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 12968 Z= 0.184 Angle : 0.572 9.132 17663 Z= 0.275 Chirality : 0.041 0.278 2159 Planarity : 0.004 0.044 2125 Dihedral : 9.927 172.368 2674 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.97 % Favored : 94.91 % Rotamer: Outliers : 2.46 % Allowed : 14.83 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.22), residues: 1590 helix: 2.18 (0.19), residues: 836 sheet: -0.66 (0.58), residues: 103 loop : -0.71 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 83 HIS 0.002 0.000 HIS C 17 PHE 0.012 0.001 PHE A 143 TYR 0.015 0.001 TYR C 237 ARG 0.007 0.000 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 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 189 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 158 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8921 (tm-30) cc_final: 0.8366 (tm-30) REVERT: A 88 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8602 (tm-30) REVERT: A 125 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8672 (mp0) REVERT: B 3 GLU cc_start: 0.7759 (mt-10) cc_final: 0.6685 (tp30) REVERT: B 122 ASP cc_start: 0.8066 (t0) cc_final: 0.7321 (t0) REVERT: B 155 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9031 (mp) REVERT: C 225 PHE cc_start: 0.8772 (m-80) cc_final: 0.8492 (m-80) REVERT: D 59 GLU cc_start: 0.8698 (tp30) cc_final: 0.8287 (tp30) REVERT: D 197 GLU cc_start: 0.8682 (mm-30) cc_final: 0.8272 (mm-30) REVERT: E 27 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7788 (tt0) REVERT: E 28 TYR cc_start: 0.8433 (m-80) cc_final: 0.7719 (m-10) REVERT: E 79 GLU cc_start: 0.8353 (mp0) cc_final: 0.7999 (pm20) REVERT: E 163 GLU cc_start: 0.8689 (tt0) cc_final: 0.8330 (tt0) REVERT: G 67 GLU cc_start: 0.8943 (tp30) cc_final: 0.8642 (tp30) REVERT: G 89 ASN cc_start: 0.8700 (t0) cc_final: 0.8400 (t0) REVERT: G 133 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8153 (tp30) REVERT: H 9 ASP cc_start: 0.8638 (t0) cc_final: 0.8187 (t0) REVERT: H 18 CYS cc_start: 0.8938 (p) cc_final: 0.8377 (p) REVERT: H 32 GLN cc_start: 0.9259 (tt0) cc_final: 0.8675 (tm-30) REVERT: H 37 ARG cc_start: 0.8636 (ptp-110) cc_final: 0.8201 (mtm180) outliers start: 31 outliers final: 22 residues processed: 179 average time/residue: 0.2680 time to fit residues: 67.4463 Evaluate side-chains 181 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 154 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 447 ASP Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 42 ILE 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 132 optimal weight: 4.9990 chunk 141 optimal weight: 6.9990 chunk 144 optimal weight: 0.0770 chunk 84 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 127 optimal weight: 0.2980 chunk 133 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 12968 Z= 0.154 Angle : 0.558 8.728 17663 Z= 0.269 Chirality : 0.040 0.276 2159 Planarity : 0.004 0.043 2125 Dihedral : 9.571 171.222 2674 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.72 % Favored : 95.16 % Rotamer: Outliers : 1.90 % Allowed : 15.07 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.22), residues: 1590 helix: 2.22 (0.19), residues: 838 sheet: -0.66 (0.59), residues: 102 loop : -0.71 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 166 HIS 0.001 0.000 HIS C 17 PHE 0.011 0.001 PHE A 143 TYR 0.014 0.001 TYR C 237 ARG 0.007 0.000 ARG G 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3180 Ramachandran restraints generated. 1590 Oldfield, 0 Emsley, 1590 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8654 (tm-30) REVERT: A 125 GLU cc_start: 0.9094 (OUTLIER) cc_final: 0.8016 (mp0) REVERT: B 3 GLU cc_start: 0.7703 (mt-10) cc_final: 0.6632 (tp30) REVERT: B 122 ASP cc_start: 0.8083 (t0) cc_final: 0.7332 (t0) REVERT: C 225 PHE cc_start: 0.8723 (m-80) cc_final: 0.8497 (m-80) REVERT: D 59 GLU cc_start: 0.8670 (tp30) cc_final: 0.8173 (tp30) REVERT: D 197 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8287 (mm-30) REVERT: E 27 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7750 (tt0) REVERT: E 28 TYR cc_start: 0.8388 (m-80) cc_final: 0.7643 (m-10) REVERT: E 54 MET cc_start: 0.8857 (tpt) cc_final: 0.8364 (tpt) REVERT: G 67 GLU cc_start: 0.8940 (tp30) cc_final: 0.8677 (tp30) REVERT: G 89 ASN cc_start: 0.8671 (t0) cc_final: 0.8395 (t0) REVERT: G 133 GLU cc_start: 0.8493 (OUTLIER) cc_final: 0.7914 (mm-30) REVERT: H 9 ASP cc_start: 0.8490 (t0) cc_final: 0.7887 (t0) REVERT: H 14 LEU cc_start: 0.8810 (mt) cc_final: 0.8582 (tt) REVERT: H 18 CYS cc_start: 0.8959 (p) cc_final: 0.8398 (p) REVERT: H 32 GLN cc_start: 0.9229 (tt0) cc_final: 0.8669 (tm-30) REVERT: H 37 ARG cc_start: 0.8609 (ptp-110) cc_final: 0.8127 (mtm180) outliers start: 24 outliers final: 18 residues processed: 183 average time/residue: 0.2659 time to fit residues: 68.4787 Evaluate side-chains 180 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 158 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain 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 281 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 149 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 70 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 156 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 124 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 96 optimal weight: 5.9990 chunk 76 optimal weight: 0.0980 chunk 98 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 12968 Z= 0.162 Angle : 0.567 8.514 17663 Z= 0.274 Chirality : 0.040 0.273 2159 Planarity : 0.004 0.041 2125 Dihedral : 9.417 171.607 2674 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.72 % Favored : 95.16 % Rotamer: Outliers : 1.90 % Allowed : 15.15 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.22), residues: 1590 helix: 2.25 (0.19), residues: 836 sheet: -0.75 (0.55), residues: 112 loop : -0.69 (0.25), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 166 HIS 0.002 0.000 HIS C 17 PHE 0.014 0.001 PHE A 143 TYR 0.022 0.001 TYR H 7 ARG 0.009 0.000 ARG B 167 ********************** 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 183 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 159 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8674 (tm-30) REVERT: A 125 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: B 122 ASP cc_start: 0.8049 (t0) cc_final: 0.7295 (t0) REVERT: C 225 PHE cc_start: 0.8702 (m-80) cc_final: 0.8455 (m-80) REVERT: D 59 GLU cc_start: 0.8681 (tp30) cc_final: 0.8189 (tp30) REVERT: D 197 GLU cc_start: 0.8692 (mm-30) cc_final: 0.8290 (mm-30) REVERT: E 27 GLN cc_start: 0.8364 (OUTLIER) cc_final: 0.7733 (tt0) REVERT: E 28 TYR cc_start: 0.8401 (m-80) cc_final: 0.7642 (m-10) REVERT: E 54 MET cc_start: 0.8855 (tpt) cc_final: 0.8357 (tpt) REVERT: E 79 GLU cc_start: 0.8253 (mp0) cc_final: 0.7969 (pm20) REVERT: G 67 GLU cc_start: 0.8951 (tp30) cc_final: 0.8691 (tp30) REVERT: G 89 ASN cc_start: 0.8657 (t0) cc_final: 0.8387 (t0) REVERT: G 133 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.7903 (mm-30) REVERT: H 9 ASP cc_start: 0.8516 (t0) cc_final: 0.7947 (t0) REVERT: H 14 LEU cc_start: 0.8815 (mt) cc_final: 0.8593 (tt) REVERT: H 32 GLN cc_start: 0.9246 (tt0) cc_final: 0.8849 (tm-30) REVERT: H 37 ARG cc_start: 0.8605 (ptp-110) cc_final: 0.8147 (mtm180) outliers start: 24 outliers final: 19 residues processed: 176 average time/residue: 0.2814 time to fit residues: 69.3531 Evaluate side-chains 177 residues out of total 1262 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 154 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 88 GLU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain B residue 157 ILE 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 281 ILE Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 27 GLN Chi-restraints excluded: chain E residue 86 ILE Chi-restraints excluded: chain E residue 165 LEU Chi-restraints excluded: chain G residue 84 SER Chi-restraints excluded: chain G residue 94 SER Chi-restraints excluded: chain G residue 133 GLU Chi-restraints excluded: chain G residue 202 THR Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 63 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 157 random chunks: chunk 132 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 124 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 128 optimal weight: 0.9980 chunk 15 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3316 r_free = 0.3316 target = 0.078274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.055660 restraints weight = 29978.975| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 2.42 r_work: 0.2686 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 12968 Z= 0.272 Angle : 0.609 9.534 17663 Z= 0.293 Chirality : 0.041 0.270 2159 Planarity : 0.004 0.040 2125 Dihedral : 9.525 173.409 2674 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.41 % Favored : 94.47 % Rotamer: Outliers : 2.38 % Allowed : 15.15 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.06 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.23), residues: 1590 helix: 2.25 (0.19), residues: 830 sheet: -0.64 (0.56), residues: 110 loop : -0.58 (0.26), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 168 HIS 0.003 0.001 HIS C 17 PHE 0.013 0.001 PHE G 218 TYR 0.016 0.001 TYR C 237 ARG 0.009 0.000 ARG B 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2707.99 seconds wall clock time: 48 minutes 51.90 seconds (2931.90 seconds total)