Starting phenix.real_space_refine on Mon Mar 25 05:11:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st9_25422/03_2024/7st9_25422_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st9_25422/03_2024/7st9_25422.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st9_25422/03_2024/7st9_25422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st9_25422/03_2024/7st9_25422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st9_25422/03_2024/7st9_25422_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st9_25422/03_2024/7st9_25422_trim_updated.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.048 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: 7 Type Number sf(0) Gaussians P 49 5.49 5 Mg 4 5.21 5 S 122 5.16 5 C 14540 2.51 5 N 3969 2.21 5 O 4939 1.98 5 H 22930 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 46553 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 8507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 8507 Classifications: {'peptide': 522} Link IDs: {'PTRANS': 19, 'TRANS': 502} Chain breaks: 2 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 5028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5028 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 9, 'TRANS': 305} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 5167 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "D" Number of atoms: 5319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 5319 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 322} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5698 Classifications: {'peptide': 354} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 339} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 4624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 4624 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 4, 'TRANS': 288} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 5440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 5440 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 11, 'TRANS': 328} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 5057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 5057 Classifications: {'peptide': 316} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 304} Chain breaks: 5 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 804 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain breaks: 1 Chain: "I" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 303 Classifications: {'DNA': 11} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 10} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DA%5*END:plan2': 1, ' DA%5*END:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 60 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'peptide': 2, 'undetermined': 2} Link IDs: {'TRANS': 1, None: 2} Not linked: pdbres="THR C 402 " pdbres=" MG C 403 " Not linked: pdbres=" MG C 403 " pdbres="AGS C 404 " Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "B" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Classifications: {'water': 49} Link IDs: {None: 48} Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "D" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 109 Classifications: {'water': 109} Link IDs: {None: 108} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "F" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "J" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 20.07, per 1000 atoms: 0.43 Number of scatterers: 46553 At special positions: 0 Unit cell: (128.03, 134.638, 148.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 122 16.00 P 49 15.00 Mg 4 11.99 O 4939 8.00 N 3969 7.00 C 14540 6.00 H 22930 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 36.66 Conformation dependent library (CDL) restraints added in 4.2 seconds 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5360 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 128 helices and 16 sheets defined 46.7% alpha, 15.1% beta 4 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 26.65 Creating SS restraints... Processing helix chain 'A' and resid 66 through 69 No H-bonds generated for 'chain 'A' and resid 66 through 69' Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 82 through 95 Processing helix chain 'A' and resid 115 through 130 removed outlier: 3.715A pdb=" N ILE A 125 " --> pdb=" O GLU A 121 " (cutoff:3.500A) Proline residue: A 128 - end of helix Processing helix chain 'A' and resid 162 through 175 removed outlier: 4.334A pdb=" N PHE A 166 " --> pdb=" O MET A 163 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU A 170 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG A 174 " --> pdb=" O LYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 180 No H-bonds generated for 'chain 'A' and resid 178 through 180' Processing helix chain 'A' and resid 195 through 209 Processing helix chain 'A' and resid 239 through 242 No H-bonds generated for 'chain 'A' and resid 239 through 242' Processing helix chain 'A' and resid 246 through 249 No H-bonds generated for 'chain 'A' and resid 246 through 249' Processing helix chain 'A' and resid 252 through 255 No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 285 through 291 Processing helix chain 'A' and resid 293 through 305 removed outlier: 4.806A pdb=" N GLN A 298 " --> pdb=" O ASN A 295 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ASP A 302 " --> pdb=" O GLU A 299 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA A 305 " --> pdb=" O ASP A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 323 Processing helix chain 'A' and resid 339 through 348 Processing helix chain 'A' and resid 356 through 366 Processing helix chain 'A' and resid 368 through 372 Processing helix chain 'A' and resid 375 through 389 removed outlier: 5.253A pdb=" N ASN A 385 " --> pdb=" O LEU A 381 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N THR A 386 " --> pdb=" O GLU A 382 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N PHE A 387 " --> pdb=" O ASN A 383 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASN A 388 " --> pdb=" O TYR A 384 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS A 389 " --> pdb=" O ASN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 409 removed outlier: 3.579A pdb=" N ASN A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 431 removed outlier: 3.716A pdb=" N ILE A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 471 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 484 through 508 Proline residue: A 489 - end of helix Processing helix chain 'A' and resid 565 through 585 Processing helix chain 'A' and resid 587 through 590 No H-bonds generated for 'chain 'A' and resid 587 through 590' Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'B' and resid 11 through 14 No H-bonds generated for 'chain 'B' and resid 11 through 14' Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' Processing helix chain 'B' and resid 27 through 39 Processing helix chain 'B' and resid 55 through 74 removed outlier: 6.957A pdb=" N ARG B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N SER B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ALA B 72 " --> pdb=" O GLY B 68 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N ASP B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 98 removed outlier: 4.240A pdb=" N ILE B 93 " --> pdb=" O VAL B 89 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N LYS B 94 " --> pdb=" O ARG B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 118 No H-bonds generated for 'chain 'B' and resid 116 through 118' Processing helix chain 'B' and resid 121 through 134 removed outlier: 3.666A pdb=" N ARG B 128 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARG B 129 " --> pdb=" O GLN B 125 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR B 130 " --> pdb=" O ALA B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 152 through 157 removed outlier: 4.068A pdb=" N ARG B 157 " --> pdb=" O PRO B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 182 Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 202 through 216 Processing helix chain 'B' and resid 221 through 225 Processing helix chain 'B' and resid 232 through 241 Processing helix chain 'B' and resid 245 through 255 Processing helix chain 'B' and resid 263 through 276 removed outlier: 3.766A pdb=" N ASN B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 300 Processing helix chain 'B' and resid 306 through 320 Processing helix chain 'C' and resid 10 through 12 No H-bonds generated for 'chain 'C' and resid 10 through 12' Processing helix chain 'C' and resid 15 through 18 No H-bonds generated for 'chain 'C' and resid 15 through 18' Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 31 through 43 Processing helix chain 'C' and resid 59 through 71 Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 90 through 101 removed outlier: 3.952A pdb=" N ILE C 97 " --> pdb=" O VAL C 93 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LYS C 98 " --> pdb=" O ARG C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing helix chain 'C' and resid 124 through 136 removed outlier: 3.547A pdb=" N ARG C 131 " --> pdb=" O GLN C 127 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG C 132 " --> pdb=" O ASN C 128 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 155 through 159 Processing helix chain 'C' and resid 171 through 184 Processing helix chain 'C' and resid 191 through 201 Processing helix chain 'C' and resid 205 through 218 Processing helix chain 'C' and resid 229 through 236 Processing helix chain 'C' and resid 241 through 253 Processing helix chain 'C' and resid 256 through 270 removed outlier: 4.184A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 287 removed outlier: 3.937A pdb=" N ASP C 287 " --> pdb=" O LYS C 283 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 312 removed outlier: 3.641A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 331 Processing helix chain 'D' and resid 27 through 30 No H-bonds generated for 'chain 'D' and resid 27 through 30' Processing helix chain 'D' and resid 43 through 55 removed outlier: 4.509A pdb=" N VAL D 48 " --> pdb=" O HIS D 44 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 71 through 82 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 103 through 114 removed outlier: 4.001A pdb=" N VAL D 110 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 142 through 144 No H-bonds generated for 'chain 'D' and resid 142 through 144' Processing helix chain 'D' and resid 147 through 159 removed outlier: 3.592A pdb=" N LEU D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ARG D 154 " --> pdb=" O GLN D 150 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ARG D 155 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N THR D 156 " --> pdb=" O ALA D 152 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 175 No H-bonds generated for 'chain 'D' and resid 173 through 175' Processing helix chain 'D' and resid 178 through 183 Processing helix chain 'D' and resid 198 through 207 Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 228 through 245 Processing helix chain 'D' and resid 253 through 260 Processing helix chain 'D' and resid 265 through 277 Processing helix chain 'D' and resid 280 through 292 removed outlier: 3.772A pdb=" N LYS D 292 " --> pdb=" O ASN D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 297 through 309 Processing helix chain 'D' and resid 316 through 334 Processing helix chain 'D' and resid 339 through 352 Processing helix chain 'E' and resid 4 through 7 No H-bonds generated for 'chain 'E' and resid 4 through 7' Processing helix chain 'E' and resid 13 through 15 No H-bonds generated for 'chain 'E' and resid 13 through 15' Processing helix chain 'E' and resid 20 through 29 Processing helix chain 'E' and resid 33 through 35 No H-bonds generated for 'chain 'E' and resid 33 through 35' Processing helix chain 'E' and resid 49 through 60 Processing helix chain 'E' and resid 63 through 66 Processing helix chain 'E' and resid 98 through 118 removed outlier: 6.937A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ARG E 106 " --> pdb=" O ASN E 103 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU E 111 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU E 112 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU E 113 " --> pdb=" O GLN E 110 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS E 114 " --> pdb=" O GLU E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 145 No H-bonds generated for 'chain 'E' and resid 143 through 145' Processing helix chain 'E' and resid 148 through 160 removed outlier: 3.708A pdb=" N ARG E 155 " --> pdb=" O GLN E 151 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ARG E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR E 157 " --> pdb=" O ALA E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 184 Processing helix chain 'E' and resid 195 through 209 Processing helix chain 'E' and resid 217 through 226 Processing helix chain 'E' and resid 230 through 243 Processing helix chain 'E' and resid 258 through 272 Processing helix chain 'E' and resid 276 through 292 removed outlier: 3.665A pdb=" N HIS E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 309 Processing helix chain 'E' and resid 315 through 334 Processing helix chain 'E' and resid 339 through 353 Processing helix chain 'F' and resid 19 through 31 Proline residue: F 30 - end of helix Processing helix chain 'F' and resid 64 through 66 No H-bonds generated for 'chain 'F' and resid 64 through 66' Processing helix chain 'F' and resid 86 through 96 Processing helix chain 'F' and resid 142 through 144 No H-bonds generated for 'chain 'F' and resid 142 through 144' Processing helix chain 'F' and resid 160 through 172 Processing helix chain 'F' and resid 239 through 251 removed outlier: 4.405A pdb=" N LYS F 244 " --> pdb=" O THR F 240 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ILE F 245 " --> pdb=" O SER F 241 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ARG F 246 " --> pdb=" O PHE F 242 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N LYS F 247 " --> pdb=" O ASP F 243 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N SER F 248 " --> pdb=" O LYS F 244 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ILE F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 318 through 328 Processing helix chain 'G' and resid 10 through 26 Processing helix chain 'G' and resid 58 through 60 No H-bonds generated for 'chain 'G' and resid 58 through 60' Processing helix chain 'G' and resid 68 through 70 No H-bonds generated for 'chain 'G' and resid 68 through 70' Processing helix chain 'G' and resid 75 through 77 No H-bonds generated for 'chain 'G' and resid 75 through 77' Processing helix chain 'G' and resid 98 through 104 Processing helix chain 'G' and resid 162 through 174 Processing helix chain 'G' and resid 189 through 204 Processing helix chain 'G' and resid 223 through 225 No H-bonds generated for 'chain 'G' and resid 223 through 225' Processing helix chain 'G' and resid 234 through 243 removed outlier: 4.126A pdb=" N ASN G 243 " --> pdb=" O ASN G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 327 through 334 removed outlier: 4.129A pdb=" N THR G 334 " --> pdb=" O LYS G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 336 through 338 No H-bonds generated for 'chain 'G' and resid 336 through 338' Processing helix chain 'H' and resid 13 through 29 Processing helix chain 'H' and resid 51 through 56 removed outlier: 3.826A pdb=" N SER H 55 " --> pdb=" O SER H 51 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASN H 56 " --> pdb=" O LEU H 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 51 through 56' Processing helix chain 'H' and resid 58 through 62 Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 97 through 113 Processing helix chain 'H' and resid 214 through 219 removed outlier: 3.552A pdb=" N ARG H 219 " --> pdb=" O ALA H 215 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 250 Processing helix chain 'H' and resid 252 through 255 Processing helix chain 'H' and resid 412 through 424 Processing sheet with id= A, first strand: chain 'A' and resid 260 through 264 removed outlier: 6.377A pdb=" N ILE A 104 " --> pdb=" O LYS A 261 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N ILE A 263 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU A 106 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU A 219 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 7.724A pdb=" N LEU A 107 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N ILE A 221 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N GLY A 109 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE A 223 " --> pdb=" O GLY A 109 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE A 184 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N CYS A 222 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ILE A 186 " --> pdb=" O CYS A 222 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR A 224 " --> pdb=" O ILE A 186 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 159 through 162 removed outlier: 6.296A pdb=" N LYS B 109 " --> pdb=" O ARG B 139 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ALA B 141 " --> pdb=" O LYS B 109 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL B 111 " --> pdb=" O ALA B 141 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ALA B 143 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU B 113 " --> pdb=" O ALA B 143 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 162 through 166 removed outlier: 6.489A pdb=" N LYS C 112 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N CYS C 144 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE C 114 " --> pdb=" O CYS C 144 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N LEU C 146 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N LEU C 116 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 185 through 189 removed outlier: 6.458A pdb=" N LYS D 135 " --> pdb=" O ARG D 165 " (cutoff:3.500A) removed outlier: 7.865A pdb=" N CYS D 167 " --> pdb=" O LYS D 135 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE D 137 " --> pdb=" O CYS D 167 " (cutoff:3.500A) removed outlier: 7.845A pdb=" N ILE D 169 " --> pdb=" O ILE D 137 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU D 139 " --> pdb=" O ILE D 169 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 186 through 190 removed outlier: 6.495A pdb=" N LYS E 136 " --> pdb=" O ARG E 166 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N ILE E 168 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL E 138 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL E 170 " --> pdb=" O VAL E 138 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ILE E 140 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 69 through 76 Processing sheet with id= G, first strand: chain 'E' and resid 122 through 124 Processing sheet with id= H, first strand: chain 'F' and resid 69 through 72 Processing sheet with id= I, first strand: chain 'F' and resid 80 through 85 removed outlier: 6.896A pdb=" N ASP F 36 " --> pdb=" O GLU F 51 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N GLU F 51 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL F 305 " --> pdb=" O LEU F 61 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL F 264 " --> pdb=" O ASP F 260 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS F 216 " --> pdb=" O ILE F 157 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LYS F 159 " --> pdb=" O LEU F 214 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N LEU F 214 " --> pdb=" O LYS F 159 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'F' and resid 232 through 238 Processing sheet with id= K, first strand: chain 'G' and resid 64 through 66 removed outlier: 6.691A pdb=" N GLU G 139 " --> pdb=" O LYS G 114 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N PHE G 116 " --> pdb=" O VAL G 137 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL G 137 " --> pdb=" O PHE G 116 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ILE G 118 " --> pdb=" O ILE G 135 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE G 135 " --> pdb=" O ILE G 118 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N VAL G 120 " --> pdb=" O ARG G 133 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ARG G 133 " --> pdb=" O VAL G 120 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'G' and resid 295 through 297 removed outlier: 6.323A pdb=" N ASN G 348 " --> pdb=" O GLN G 365 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLN G 365 " --> pdb=" O ASN G 348 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N MET G 44 " --> pdb=" O ASP G 29 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ASP G 29 " --> pdb=" O MET G 44 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 320 through 325 Processing sheet with id= N, first strand: chain 'H' and resid 80 through 82 removed outlier: 5.784A pdb=" N LEU H 3 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LEU H 123 " --> pdb=" O LEU H 3 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ASN H 96 " --> pdb=" O PRO H 208 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN H 463 " --> pdb=" O THR H 71 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU H 427 " --> pdb=" O SER H 443 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 158 through 161 Processing sheet with id= P, first strand: chain 'H' and resid 405 through 411 1057 hydrogen bonds defined for protein. 2988 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 9 hydrogen bonds 18 hydrogen bond angles 0 basepair planarities 4 basepair parallelities 29 stacking parallelities Total time for adding SS restraints: 19.26 Time building geometry restraints manager: 38.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 22875 1.06 - 1.28: 3884 1.28 - 1.50: 9860 1.50 - 1.73: 9786 1.73 - 1.95: 185 Bond restraints: 46590 Sorted by residual: bond pdb=" N VAL A 588 " pdb=" CA VAL A 588 " ideal model delta sigma weight residual 1.462 1.500 -0.038 1.18e-02 7.18e+03 1.06e+01 bond pdb=" N ASN A 592 " pdb=" CA ASN A 592 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.27e-02 6.20e+03 9.46e+00 bond pdb=" N GLN A 583 " pdb=" CA GLN A 583 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.21e-02 6.83e+03 9.27e+00 bond pdb=" N TYR A 584 " pdb=" CA TYR A 584 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.29e-02 6.01e+03 8.67e+00 bond pdb=" N MET A 590 " pdb=" CA MET A 590 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.19e-02 7.06e+03 8.23e+00 ... (remaining 46585 not shown) Histogram of bond angle deviations from ideal: 98.48 - 106.09: 593 106.09 - 113.69: 56632 113.69 - 121.30: 18178 121.30 - 128.91: 8836 128.91 - 136.52: 132 Bond angle restraints: 84371 Sorted by residual: angle pdb=" O3' DA I 0 " pdb=" P DC I 1 " pdb=" O5' DC I 1 " ideal model delta sigma weight residual 104.00 98.67 5.33 1.50e+00 4.44e-01 1.26e+01 angle pdb=" CA LEU A 595 " pdb=" C LEU A 595 " pdb=" O LEU A 595 " ideal model delta sigma weight residual 121.49 117.44 4.05 1.16e+00 7.43e-01 1.22e+01 angle pdb=" CA ALA A 591 " pdb=" C ALA A 591 " pdb=" O ALA A 591 " ideal model delta sigma weight residual 120.75 117.15 3.60 1.12e+00 7.97e-01 1.03e+01 angle pdb=" CA ASN A 592 " pdb=" C ASN A 592 " pdb=" O ASN A 592 " ideal model delta sigma weight residual 121.11 117.49 3.62 1.17e+00 7.31e-01 9.59e+00 angle pdb=" N MET A 589 " pdb=" CA MET A 589 " pdb=" C MET A 589 " ideal model delta sigma weight residual 111.36 108.25 3.11 1.09e+00 8.42e-01 8.12e+00 ... (remaining 84366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.06: 20423 28.06 - 56.13: 1050 56.13 - 84.19: 105 84.19 - 112.26: 18 112.26 - 140.32: 1 Dihedral angle restraints: 21597 sinusoidal: 12152 harmonic: 9445 Sorted by residual: dihedral pdb=" C5' ADP E 401 " pdb=" O5' ADP E 401 " pdb=" PA ADP E 401 " pdb=" O2A ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 25.83 -85.83 1 2.00e+01 2.50e-03 2.23e+01 dihedral pdb=" O1A AGS D 402 " pdb=" O3A AGS D 402 " pdb=" PA AGS D 402 " pdb=" PB AGS D 402 " ideal model delta sinusoidal sigma weight residual -67.73 72.59 -140.32 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" O1A AGS C 404 " pdb=" O3A AGS C 404 " pdb=" PA AGS C 404 " pdb=" PB AGS C 404 " ideal model delta sinusoidal sigma weight residual -67.73 38.90 -106.63 1 3.00e+01 1.11e-03 1.37e+01 ... (remaining 21594 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 2767 0.035 - 0.071: 627 0.071 - 0.106: 190 0.106 - 0.142: 112 0.142 - 0.177: 6 Chirality restraints: 3702 Sorted by residual: chirality pdb=" CA LEU A 595 " pdb=" N LEU A 595 " pdb=" C LEU A 595 " pdb=" CB LEU A 595 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.86e-01 chirality pdb=" CA ARG B 157 " pdb=" N ARG B 157 " pdb=" C ARG B 157 " pdb=" CB ARG B 157 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CB VAL C 37 " pdb=" CA VAL C 37 " pdb=" CG1 VAL C 37 " pdb=" CG2 VAL C 37 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.99e-01 ... (remaining 3699 not shown) Planarity restraints: 6661 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 202 " 0.142 9.50e-02 1.11e+02 4.77e-02 2.74e+00 pdb=" NE ARG D 202 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG D 202 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG D 202 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG D 202 " 0.000 2.00e-02 2.50e+03 pdb="HH11 ARG D 202 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG D 202 " 0.000 2.00e-02 2.50e+03 pdb="HH21 ARG D 202 " -0.000 2.00e-02 2.50e+03 pdb="HH22 ARG D 202 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 443 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO A 444 " -0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 444 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 444 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 488 " -0.019 5.00e-02 4.00e+02 2.90e-02 1.34e+00 pdb=" N PRO A 489 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 489 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 489 " -0.016 5.00e-02 4.00e+02 ... (remaining 6658 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 2239 2.19 - 2.79: 93875 2.79 - 3.39: 131765 3.39 - 4.00: 176728 4.00 - 4.60: 271415 Nonbonded interactions: 676022 Sorted by model distance: nonbonded pdb=" OD2 ASP H 390 " pdb=" HG SER H 392 " model vdw 1.584 1.850 nonbonded pdb=" O GLU A 230 " pdb=" HZ3 LYS B 149 " model vdw 1.585 1.850 nonbonded pdb=" O ARG B 16 " pdb="HE22 GLN B 18 " model vdw 1.593 1.850 nonbonded pdb=" HG SER A 325 " pdb=" OE1 GLN B 35 " model vdw 1.605 1.850 nonbonded pdb=" OD1 ASN D 96 " pdb=" HG SER D 98 " model vdw 1.617 1.850 ... (remaining 676017 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 3.040 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: 0.740 Extract box with map and model: 14.420 Check model and map are aligned: 0.690 Set scattering table: 0.380 Process input model: 167.280 Find NCS groups from input model: 1.220 Set up NCS constraints: 0.120 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:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 199.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 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 : 0.002 0.039 23660 Z= 0.147 Angle : 0.458 5.789 32131 Z= 0.253 Chirality : 0.039 0.177 3702 Planarity : 0.003 0.062 3954 Dihedral : 17.016 140.322 9021 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 0.71 % Allowed : 15.54 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.56 (0.17), residues: 2762 helix: 2.74 (0.15), residues: 1278 sheet: 0.83 (0.21), residues: 590 loop : 0.87 (0.23), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 324 HIS 0.005 0.001 HIS H 74 PHE 0.008 0.001 PHE G 152 TYR 0.009 0.001 TYR D 64 ARG 0.008 0.000 ARG D 202 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 367 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 349 time to evaluate : 3.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 MET cc_start: 0.8154 (mtp) cc_final: 0.7732 (mtp) outliers start: 18 outliers final: 4 residues processed: 364 average time/residue: 3.4260 time to fit residues: 1408.4869 Evaluate side-chains 202 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 198 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain D residue 37 ASP Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 352 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 236 optimal weight: 4.9990 chunk 212 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 219 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 133 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 254 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 411 ASN C 333 ASN E 336 ASN H 203 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23660 Z= 0.290 Angle : 0.518 6.134 32131 Z= 0.276 Chirality : 0.041 0.157 3702 Planarity : 0.004 0.058 3954 Dihedral : 12.024 143.110 3458 Min Nonbonded Distance : 1.623 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 1.63 % Allowed : 18.55 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.26 (0.17), residues: 2762 helix: 2.34 (0.15), residues: 1310 sheet: 0.87 (0.21), residues: 584 loop : 0.78 (0.23), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 339 HIS 0.007 0.001 HIS G 259 PHE 0.018 0.001 PHE E 305 TYR 0.013 0.001 TYR A 584 ARG 0.008 0.000 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 200 time to evaluate : 3.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 MET cc_start: 0.8264 (mtp) cc_final: 0.7941 (mtp) outliers start: 41 outliers final: 15 residues processed: 235 average time/residue: 3.2656 time to fit residues: 873.5621 Evaluate side-chains 199 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 184 time to evaluate : 3.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain E residue 90 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 355 HIS Chi-restraints excluded: chain H residue 158 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 141 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 254 optimal weight: 10.0000 chunk 275 optimal weight: 8.9990 chunk 226 optimal weight: 1.9990 chunk 252 optimal weight: 2.9990 chunk 86 optimal weight: 3.9990 chunk 204 optimal weight: 4.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN E 336 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23660 Z= 0.280 Angle : 0.503 6.273 32131 Z= 0.270 Chirality : 0.041 0.160 3702 Planarity : 0.004 0.051 3954 Dihedral : 12.175 142.629 3456 Min Nonbonded Distance : 1.572 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.82 % Allowed : 18.07 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.07 (0.17), residues: 2762 helix: 2.15 (0.15), residues: 1306 sheet: 0.91 (0.21), residues: 583 loop : 0.64 (0.22), residues: 873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 324 HIS 0.005 0.001 HIS E 341 PHE 0.018 0.001 PHE G 152 TYR 0.012 0.001 TYR E 135 ARG 0.005 0.000 ARG F 151 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 183 time to evaluate : 3.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 MET cc_start: 0.7451 (mtt) cc_final: 0.7206 (mtm) REVERT: D 145 MET cc_start: 0.8268 (mtp) cc_final: 0.7911 (mtp) outliers start: 46 outliers final: 22 residues processed: 220 average time/residue: 3.3702 time to fit residues: 842.1196 Evaluate side-chains 196 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 174 time to evaluate : 3.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 355 HIS Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 154 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 121 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 255 optimal weight: 4.9990 chunk 270 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 ASN C 184 HIS D 57 ASN E 336 ASN H 221 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 23660 Z= 0.386 Angle : 0.544 7.039 32131 Z= 0.294 Chirality : 0.043 0.203 3702 Planarity : 0.004 0.051 3954 Dihedral : 12.409 143.848 3455 Min Nonbonded Distance : 1.599 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 2.02 % Allowed : 17.52 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.16), residues: 2762 helix: 1.91 (0.14), residues: 1305 sheet: 0.82 (0.21), residues: 583 loop : 0.49 (0.22), residues: 874 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 324 HIS 0.006 0.001 HIS E 341 PHE 0.021 0.001 PHE G 152 TYR 0.014 0.001 TYR E 135 ARG 0.009 0.001 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 232 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 181 time to evaluate : 3.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 MET cc_start: 0.8270 (mtp) cc_final: 0.7999 (mtp) REVERT: E 172 ASP cc_start: 0.7250 (OUTLIER) cc_final: 0.6952 (p0) REVERT: F 310 MET cc_start: 0.8117 (ptm) cc_final: 0.7867 (ptm) outliers start: 51 outliers final: 28 residues processed: 222 average time/residue: 3.3769 time to fit residues: 852.0675 Evaluate side-chains 199 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 170 time to evaluate : 3.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 172 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 29 THR Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 203 SER Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 276 ASP Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 355 HIS Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 154 CYS Chi-restraints excluded: chain H residue 203 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 225 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 111 optimal weight: 0.0010 chunk 230 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 138 optimal weight: 0.2980 chunk 242 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.2592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN E 45 ASN E 74 GLN E 336 ASN H 151 ASN H 221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23660 Z= 0.183 Angle : 0.482 6.201 32131 Z= 0.261 Chirality : 0.039 0.169 3702 Planarity : 0.004 0.053 3954 Dihedral : 12.318 140.110 3455 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.39 % Allowed : 18.27 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.00 (0.17), residues: 2762 helix: 2.15 (0.15), residues: 1297 sheet: 0.83 (0.21), residues: 583 loop : 0.57 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 324 HIS 0.006 0.001 HIS B 232 PHE 0.012 0.001 PHE G 152 TYR 0.009 0.001 TYR E 135 ARG 0.008 0.000 ARG A 578 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 174 time to evaluate : 4.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 MET cc_start: 0.8249 (mtp) cc_final: 0.7988 (mtp) REVERT: F 310 MET cc_start: 0.8063 (ptm) cc_final: 0.7821 (ptm) outliers start: 35 outliers final: 23 residues processed: 204 average time/residue: 3.2880 time to fit residues: 763.3519 Evaluate side-chains 189 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 166 time to evaluate : 3.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 306 GLN Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain E residue 354 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 355 HIS Chi-restraints excluded: chain H residue 203 HIS Chi-restraints excluded: chain H residue 440 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 91 optimal weight: 1.9990 chunk 243 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 270 optimal weight: 0.0470 chunk 224 optimal weight: 2.9990 chunk 125 optimal weight: 0.0570 chunk 22 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN E 336 ASN H 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23660 Z= 0.171 Angle : 0.473 5.882 32131 Z= 0.255 Chirality : 0.039 0.169 3702 Planarity : 0.003 0.058 3954 Dihedral : 12.307 140.305 3455 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.35 % Allowed : 18.15 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.09 (0.17), residues: 2762 helix: 2.25 (0.15), residues: 1297 sheet: 0.84 (0.21), residues: 583 loop : 0.59 (0.22), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 324 HIS 0.006 0.001 HIS B 232 PHE 0.011 0.001 PHE G 152 TYR 0.008 0.001 TYR E 135 ARG 0.009 0.000 ARG A 578 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 204 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 170 time to evaluate : 3.675 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 MET cc_start: 0.8251 (mtp) cc_final: 0.7995 (mtp) REVERT: F 310 MET cc_start: 0.8052 (ptm) cc_final: 0.7801 (ptm) outliers start: 34 outliers final: 20 residues processed: 198 average time/residue: 3.3306 time to fit residues: 751.9207 Evaluate side-chains 186 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 166 time to evaluate : 3.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain E residue 354 ASP Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 355 HIS Chi-restraints excluded: chain H residue 203 HIS Chi-restraints excluded: chain H residue 440 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 261 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 153 optimal weight: 1.9990 chunk 228 optimal weight: 0.0980 chunk 151 optimal weight: 1.9990 chunk 269 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 chunk 164 optimal weight: 2.9990 chunk 124 optimal weight: 1.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN E 336 ASN H 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23660 Z= 0.248 Angle : 0.493 6.114 32131 Z= 0.264 Chirality : 0.040 0.173 3702 Planarity : 0.004 0.086 3954 Dihedral : 12.354 142.590 3453 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.51 % Allowed : 17.99 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.00 (0.16), residues: 2762 helix: 2.16 (0.15), residues: 1299 sheet: 0.79 (0.21), residues: 588 loop : 0.58 (0.22), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 129 HIS 0.006 0.001 HIS G 295 PHE 0.014 0.001 PHE G 152 TYR 0.010 0.001 TYR E 135 ARG 0.015 0.000 ARG A 578 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 206 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 168 time to evaluate : 3.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 MET cc_start: 0.8255 (mtp) cc_final: 0.7997 (mtp) outliers start: 38 outliers final: 24 residues processed: 201 average time/residue: 3.2540 time to fit residues: 755.0028 Evaluate side-chains 189 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 3.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 533 ILE Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 260 ARG Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 355 HIS Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 154 CYS Chi-restraints excluded: chain H residue 203 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 171 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 212 optimal weight: 3.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 ASN H 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23660 Z= 0.216 Angle : 0.483 6.455 32131 Z= 0.260 Chirality : 0.039 0.183 3702 Planarity : 0.004 0.062 3954 Dihedral : 12.333 143.876 3453 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.23 % Allowed : 18.15 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.05 (0.17), residues: 2762 helix: 2.22 (0.15), residues: 1291 sheet: 0.79 (0.21), residues: 588 loop : 0.60 (0.22), residues: 883 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 129 HIS 0.006 0.001 HIS G 295 PHE 0.013 0.001 PHE G 152 TYR 0.009 0.001 TYR E 135 ARG 0.009 0.000 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 202 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 171 time to evaluate : 3.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 MET cc_start: 0.8248 (mtp) cc_final: 0.7993 (mtp) outliers start: 31 outliers final: 21 residues processed: 196 average time/residue: 3.3143 time to fit residues: 739.6587 Evaluate side-chains 187 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 166 time to evaluate : 3.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 260 ARG Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 355 HIS Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 154 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 245 optimal weight: 3.9990 chunk 258 optimal weight: 5.9990 chunk 235 optimal weight: 3.9990 chunk 251 optimal weight: 8.9990 chunk 151 optimal weight: 1.9990 chunk 109 optimal weight: 0.2980 chunk 197 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 227 optimal weight: 0.8980 chunk 237 optimal weight: 4.9990 chunk 250 optimal weight: 5.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN E 336 ASN H 221 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23660 Z= 0.272 Angle : 0.503 6.735 32131 Z= 0.269 Chirality : 0.040 0.184 3702 Planarity : 0.004 0.062 3954 Dihedral : 12.395 143.380 3453 Min Nonbonded Distance : 1.660 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.11 % Allowed : 18.31 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.96 (0.16), residues: 2762 helix: 2.13 (0.15), residues: 1293 sheet: 0.76 (0.21), residues: 589 loop : 0.57 (0.22), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 129 HIS 0.005 0.001 HIS G 295 PHE 0.016 0.001 PHE G 152 TYR 0.014 0.001 TYR G 85 ARG 0.010 0.000 ARG A 578 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 199 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 171 time to evaluate : 3.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 MET cc_start: 0.8262 (mtp) cc_final: 0.8007 (mtp) outliers start: 28 outliers final: 24 residues processed: 193 average time/residue: 3.2558 time to fit residues: 717.1565 Evaluate side-chains 190 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 3.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 537 ASP Chi-restraints excluded: chain A residue 568 ASP Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 201 GLU Chi-restraints excluded: chain G residue 260 ARG Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 355 HIS Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 154 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 165 optimal weight: 1.9990 chunk 265 optimal weight: 4.9990 chunk 162 optimal weight: 1.9990 chunk 126 optimal weight: 0.0070 chunk 184 optimal weight: 2.9990 chunk 278 optimal weight: 6.9990 chunk 256 optimal weight: 10.0000 chunk 222 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 171 optimal weight: 2.9990 chunk 136 optimal weight: 0.9980 overall best weight: 1.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 ASN H 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23660 Z= 0.168 Angle : 0.477 7.248 32131 Z= 0.255 Chirality : 0.039 0.191 3702 Planarity : 0.003 0.070 3954 Dihedral : 12.344 147.121 3453 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.03 % Allowed : 18.47 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.13 (0.17), residues: 2762 helix: 2.30 (0.15), residues: 1291 sheet: 0.79 (0.22), residues: 585 loop : 0.64 (0.22), residues: 886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 129 HIS 0.007 0.001 HIS B 232 PHE 0.017 0.001 PHE H 205 TYR 0.011 0.001 TYR A 501 ARG 0.015 0.000 ARG A 578 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5524 Ramachandran restraints generated. 2762 Oldfield, 0 Emsley, 2762 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 116 is missing expected H atoms. Skipping. Residue LEU 509 is missing expected H atoms. Skipping. Residue SER 547 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue THR 56 is missing expected H atoms. Skipping. Residue SER 9 is missing expected H atoms. Skipping. Residue THR 60 is missing expected H atoms. Skipping. Residue MET 1 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 187 is missing expected H atoms. Skipping. Residue LEU 221 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 269 is missing expected H atoms. Skipping. Residue SER 448 is missing expected H atoms. Skipping. Residue LYS 457 is missing expected H atoms. Skipping. Evaluate side-chains 196 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 170 time to evaluate : 3.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 145 MET cc_start: 0.8247 (mtp) cc_final: 0.7885 (mtp) REVERT: G 260 ARG cc_start: 0.7004 (OUTLIER) cc_final: 0.6599 (ptm-80) REVERT: H 440 PHE cc_start: 0.7827 (OUTLIER) cc_final: 0.6958 (t80) outliers start: 26 outliers final: 16 residues processed: 192 average time/residue: 3.3305 time to fit residues: 726.4623 Evaluate side-chains 186 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 3.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain B residue 303 VAL Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 14 SER Chi-restraints excluded: chain F residue 22 THR Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 260 ARG Chi-restraints excluded: chain G residue 322 ILE Chi-restraints excluded: chain G residue 355 HIS Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 154 CYS Chi-restraints excluded: chain H residue 440 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 176 optimal weight: 3.9990 chunk 236 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 204 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 222 optimal weight: 0.3980 chunk 93 optimal weight: 2.9990 chunk 228 optimal weight: 0.0770 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 ASN H 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.097343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.065067 restraints weight = 111973.499| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.36 r_work: 0.2805 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 23660 Z= 0.152 Angle : 0.471 7.970 32131 Z= 0.251 Chirality : 0.039 0.203 3702 Planarity : 0.004 0.090 3954 Dihedral : 12.312 152.403 3453 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.79 % Allowed : 18.83 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.23 (0.17), residues: 2762 helix: 2.40 (0.15), residues: 1291 sheet: 0.79 (0.22), residues: 586 loop : 0.69 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 129 HIS 0.006 0.001 HIS B 232 PHE 0.026 0.001 PHE H 205 TYR 0.019 0.001 TYR G 85 ARG 0.021 0.000 ARG A 578 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16314.84 seconds wall clock time: 285 minutes 48.20 seconds (17148.20 seconds total)