Starting phenix.real_space_refine on Mon Sep 23 13:02:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st9_25422/09_2024/7st9_25422_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st9_25422/09_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_25422/09_2024/7st9_25422.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st9_25422/09_2024/7st9_25422.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st9_25422/09_2024/7st9_25422_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7st9_25422/09_2024/7st9_25422_trim.cif" } 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. Time to flip 1 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 46553 Number of models: 1 Model: "" Number of chains: 26 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: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "C" 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: "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: 17.94, per 1000 atoms: 0.39 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.18 Conformation dependent library (CDL) restraints added in 2.7 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... Secondary structure from input PDB file: 137 helices and 18 sheets defined 54.9% alpha, 16.6% beta 4 base pairs and 29 stacking pairs defined. Time for finding SS restraints: 17.22 Creating SS restraints... Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 81 through 96 Processing helix chain 'A' and resid 114 through 131 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 163 through 174 removed outlier: 4.659A pdb=" N SER A 167 " --> pdb=" O MET A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 176 No H-bonds generated for 'chain 'A' and resid 175 through 176' Processing helix chain 'A' and resid 177 through 181 Processing helix chain 'A' and resid 194 through 211 Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 251 through 256 Processing helix chain 'A' and resid 269 through 284 Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 292 through 295 removed outlier: 3.937A pdb=" N ASN A 295 " --> pdb=" O ASN A 292 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 292 through 295' Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.917A pdb=" N TYR A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 324 Processing helix chain 'A' and resid 338 through 349 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 367 through 373 Processing helix chain 'A' and resid 374 through 384 removed outlier: 3.657A pdb=" N LEU A 378 " --> pdb=" O GLU A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 5.145A pdb=" N ASN A 388 " --> pdb=" O ASN A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 409 removed outlier: 3.687A pdb=" N ALA A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN A 409 " --> pdb=" O SER A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 431 removed outlier: 3.560A pdb=" N ASN A 417 " --> pdb=" O LEU A 413 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 431 " --> pdb=" O THR A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 472 Processing helix chain 'A' and resid 476 through 483 Processing helix chain 'A' and resid 483 through 509 Proline residue: A 489 - end of helix Processing helix chain 'A' and resid 565 through 591 removed outlier: 3.964A pdb=" N ARG A 586 " --> pdb=" O ASP A 582 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN A 587 " --> pdb=" O GLN A 583 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 588 " --> pdb=" O TYR A 584 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N MET A 589 " --> pdb=" O GLU A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 604 Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 19 through 23 Processing helix chain 'B' and resid 26 through 40 Processing helix chain 'B' and resid 54 through 68 Processing helix chain 'B' and resid 70 through 74 Processing helix chain 'B' and resid 85 through 99 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 119 Processing helix chain 'B' and resid 120 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 146 through 150 Processing helix chain 'B' and resid 151 through 156 Processing helix chain 'B' and resid 167 through 183 Processing helix chain 'B' and resid 187 through 199 Processing helix chain 'B' and resid 201 through 217 Processing helix chain 'B' and resid 220 through 228 removed outlier: 4.256A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 242 removed outlier: 3.646A pdb=" N ILE B 235 " --> pdb=" O PRO B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 256 Processing helix chain 'B' and resid 262 through 275 Processing helix chain 'B' and resid 281 through 302 removed outlier: 3.560A pdb=" N GLY B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 321 removed outlier: 3.512A pdb=" N LEU B 309 " --> pdb=" O THR B 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 13 Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 23 through 27 Processing helix chain 'C' and resid 30 through 44 Processing helix chain 'C' and resid 58 through 72 Processing helix chain 'C' and resid 74 through 78 removed outlier: 4.150A pdb=" N MET C 78 " --> pdb=" O ASN C 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 74 through 78' Processing helix chain 'C' and resid 89 through 102 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 118 through 122 Processing helix chain 'C' and resid 123 through 137 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 149 through 153 removed outlier: 3.552A pdb=" N LYS C 152 " --> pdb=" O TYR C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 154 through 161 Processing helix chain 'C' and resid 170 through 185 Processing helix chain 'C' and resid 190 through 202 removed outlier: 3.783A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 219 removed outlier: 3.500A pdb=" N VAL C 208 " --> pdb=" O ASP C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 237 Processing helix chain 'C' and resid 240 through 254 Processing helix chain 'C' and resid 255 through 271 removed outlier: 4.184A pdb=" N LYS C 270 " --> pdb=" O VAL C 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 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 292 through 312 removed outlier: 4.217A pdb=" N ARG C 296 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS C 312 " --> pdb=" O TYR C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 333 removed outlier: 3.711A pdb=" N ASN C 333 " --> pdb=" O ALA C 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 35 through 39 Processing helix chain 'D' and resid 42 through 56 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 70 through 83 Processing helix chain 'D' and resid 87 through 91 Processing helix chain 'D' and resid 102 through 116 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 122 through 129 Processing helix chain 'D' and resid 141 through 145 Processing helix chain 'D' and resid 146 through 152 Processing helix chain 'D' and resid 153 through 160 removed outlier: 3.515A pdb=" N GLU D 158 " --> pdb=" O ARG D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 176 Processing helix chain 'D' and resid 177 through 184 Processing helix chain 'D' and resid 197 through 208 Processing helix chain 'D' and resid 215 through 225 Processing helix chain 'D' and resid 227 through 246 Processing helix chain 'D' and resid 252 through 261 Processing helix chain 'D' and resid 264 through 278 Processing helix chain 'D' and resid 279 through 291 Processing helix chain 'D' and resid 292 through 294 No H-bonds generated for 'chain 'D' and resid 292 through 294' Processing helix chain 'D' and resid 296 through 310 Processing helix chain 'D' and resid 315 through 335 Processing helix chain 'D' and resid 338 through 353 Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.510A pdb=" N TYR E 8 " --> pdb=" O TRP E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 16 Processing helix chain 'E' and resid 19 through 30 Processing helix chain 'E' and resid 32 through 36 removed outlier: 3.786A pdb=" N ASP E 35 " --> pdb=" O GLN E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 61 Processing helix chain 'E' and resid 62 through 67 Processing helix chain 'E' and resid 97 through 103 removed outlier: 6.937A pdb=" N ASN E 103 " --> pdb=" O ASP E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 119 removed outlier: 3.686A pdb=" N VAL E 108 " --> pdb=" O ASN E 104 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LYS E 114 " --> pdb=" O GLN E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 147 through 161 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 178 through 184 Processing helix chain 'E' and resid 194 through 210 Processing helix chain 'E' and resid 216 through 227 Processing helix chain 'E' and resid 229 through 244 Processing helix chain 'E' and resid 257 through 273 Processing helix chain 'E' and resid 275 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 295 through 309 Processing helix chain 'E' and resid 314 through 335 Processing helix chain 'E' and resid 337 through 354 removed outlier: 4.404A pdb=" N HIS E 341 " --> pdb=" O LYS E 337 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 29 removed outlier: 3.611A pdb=" N THR F 22 " --> pdb=" O LEU F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 32 No H-bonds generated for 'chain 'F' and resid 30 through 32' Processing helix chain 'F' and resid 65 through 67 No H-bonds generated for 'chain 'F' and resid 65 through 67' Processing helix chain 'F' and resid 86 through 97 Processing helix chain 'F' and resid 141 through 145 removed outlier: 3.635A pdb=" N LEU F 145 " --> pdb=" O THR F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 173 Processing helix chain 'F' and resid 239 through 243 Processing helix chain 'F' and resid 245 through 252 removed outlier: 3.811A pdb=" N ILE F 251 " --> pdb=" O LYS F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 329 Processing helix chain 'G' and resid 9 through 27 Processing helix chain 'G' and resid 59 through 61 No H-bonds generated for 'chain 'G' and resid 59 through 61' Processing helix chain 'G' and resid 68 through 71 Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 98 through 106 Processing helix chain 'G' and resid 161 through 175 Processing helix chain 'G' and resid 188 through 205 Processing helix chain 'G' and resid 222 through 226 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 326 through 333 Processing helix chain 'G' and resid 334 through 339 Proline residue: G 337 - end of helix No H-bonds generated for 'chain 'G' and resid 334 through 339' Processing helix chain 'H' and resid 12 through 30 removed outlier: 3.628A pdb=" N TYR H 16 " --> pdb=" O ALA H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 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) Processing helix chain 'H' and resid 57 through 63 Processing helix chain 'H' and resid 75 through 77 No H-bonds generated for 'chain 'H' and resid 75 through 77' Processing helix chain 'H' and resid 97 through 114 Processing helix chain 'H' and resid 213 through 220 removed outlier: 3.552A pdb=" N ARG H 219 " --> pdb=" O ALA H 215 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE H 220 " --> pdb=" O GLN H 216 " (cutoff:3.500A) Processing helix chain 'H' and resid 242 through 252 Processing helix chain 'H' and resid 253 through 256 Processing helix chain 'H' and resid 412 through 425 Processing sheet with id=AA1, first strand: chain 'A' and resid 148 through 150 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) removed outlier: 6.378A pdb=" N LEU A 105 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N ILE A 223 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU A 107 " --> pdb=" O ILE A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 226 through 227 Processing sheet with id=AA3, first strand: chain 'B' and resid 75 through 78 removed outlier: 6.427A pdb=" N MET B 45 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N CYS B 144 " --> pdb=" O MET B 45 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ILE B 47 " --> pdb=" O CYS B 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 79 through 82 removed outlier: 6.378A pdb=" N LEU C 80 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU C 49 " --> pdb=" O VAL C 145 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ALA C 147 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N PHE C 51 " --> pdb=" O ALA C 147 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 188 through 189 removed outlier: 7.009A pdb=" N LYS C 188 " --> pdb=" O ILE C 227 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 92 through 95 removed outlier: 6.376A pdb=" N LEU D 93 " --> pdb=" O ILE D 138 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N MET D 61 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N CYS D 170 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N PHE D 63 " --> pdb=" O CYS D 170 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU D 62 " --> pdb=" O PHE D 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 69 through 76 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) removed outlier: 6.405A pdb=" N LEU E 39 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N CYS E 171 " --> pdb=" O LEU E 39 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU E 41 " --> pdb=" O CYS E 171 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LEU E 40 " --> pdb=" O ILE E 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 122 through 124 Processing sheet with id=AA9, first strand: chain 'E' and resid 212 through 213 removed outlier: 6.551A pdb=" N GLN E 212 " --> pdb=" O LEU E 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 69 through 72 removed outlier: 3.554A pdb=" N HIS H 291 " --> pdb=" O GLU F 131 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LEU H 281 " --> pdb=" O TRP H 296 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 79 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: 6.740A pdb=" N VAL F 255 " --> pdb=" O ILE F 157 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ILE F 157 " --> pdb=" O VAL F 255 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N PHE F 257 " --> pdb=" O GLU F 155 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU F 155 " --> pdb=" O PHE F 257 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N MET F 259 " --> pdb=" O SER F 153 " (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=AB3, first strand: chain 'F' and resid 232 through 238 removed outlier: 4.805A pdb=" N PHE F 192 " --> pdb=" O LEU F 207 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 78 through 82 removed outlier: 4.209A pdb=" N SER G 93 " --> pdb=" O ILE G 155 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 78 through 82 removed outlier: 6.999A pdb=" N ASP G 29 " --> pdb=" O MET G 44 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N MET G 44 " --> pdb=" O ASP G 29 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N GLN G 365 " --> pdb=" O ASN G 348 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N ASN G 348 " --> pdb=" O GLN G 365 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'G' and resid 282 through 289 Processing sheet with id=AB7, first strand: chain 'G' and resid 270 through 271 removed outlier: 6.120A pdb=" N VAL G 270 " --> pdb=" O LEU G 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 79 through 82 removed outlier: 4.029A pdb=" N LEU H 79 " --> pdb=" O ILE H 6 " (cutoff:3.500A) 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) Processing sheet with id=AB9, first strand: chain 'H' and resid 79 through 82 removed outlier: 4.029A pdb=" N LEU H 79 " --> pdb=" O ILE H 6 " (cutoff:3.500A) 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) removed outlier: 3.768A pdb=" N ASP H 301 " --> pdb=" O LYS H 234 " (cutoff:3.500A) 1280 hydrogen bonds defined for protein. 3636 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: 17.59 Time building geometry restraints manager: 11.36 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: 0.00 - 1.32: 82262 1.32 - 2.64: 1932 2.64 - 3.96: 157 3.96 - 5.29: 13 5.29 - 6.61: 7 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: 2184 2.19 - 2.79: 93692 2.79 - 3.39: 131591 3.39 - 4.00: 176426 4.00 - 4.60: 271103 Nonbonded interactions: 674996 Sorted by model distance: nonbonded pdb=" OD2 ASP H 390 " pdb=" HG SER H 392 " model vdw 1.584 2.450 nonbonded pdb=" O GLU A 230 " pdb=" HZ3 LYS B 149 " model vdw 1.585 2.450 nonbonded pdb=" O ARG B 16 " pdb="HE22 GLN B 18 " model vdw 1.593 2.450 nonbonded pdb=" HG SER A 325 " pdb=" OE1 GLN B 35 " model vdw 1.605 2.450 nonbonded pdb=" OD1 ASN D 96 " pdb=" HG SER D 98 " model vdw 1.617 2.450 ... (remaining 674991 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.410 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: 0.660 Extract box with map and model: 1.380 Check model and map are aligned: 0.270 Set scattering table: 0.350 Process input model: 93.770 Find NCS groups from input model: 0.590 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:10.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 110.220 ------------------------------------------------------------------------------- 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= 0.142 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 : 2.783 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: 2.7813 time to fit residues: 1145.0767 Evaluate side-chains 202 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 198 time to evaluate : 2.781 ------------------------------------------------------------------------------- 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: 3.9990 chunk 117 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 143 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 163 optimal weight: 2.9990 chunk 254 optimal weight: 9.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN A 369 ASN A 411 ASN C 333 ASN E 336 ASN H 203 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 23660 Z= 0.324 Angle : 0.559 6.415 32131 Z= 0.303 Chirality : 0.042 0.168 3702 Planarity : 0.004 0.046 3954 Dihedral : 12.051 135.701 3458 Min Nonbonded Distance : 1.568 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.66 % Allowed : 18.51 % 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: 2.16 (0.17), residues: 2762 helix: 2.27 (0.15), residues: 1325 sheet: 0.71 (0.21), residues: 589 loop : 0.76 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 339 HIS 0.006 0.001 HIS G 259 PHE 0.018 0.001 PHE E 305 TYR 0.014 0.001 TYR A 584 ARG 0.018 0.001 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 236 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 194 time to evaluate : 2.791 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: D 145 MET cc_start: 0.8270 (mtp) cc_final: 0.7933 (mtp) outliers start: 42 outliers final: 14 residues processed: 232 average time/residue: 2.7080 time to fit residues: 719.8073 Evaluate side-chains 198 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 184 time to evaluate : 2.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 GLU 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 252 THR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain E residue 90 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 355 HIS 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: 0.4980 chunk 70 optimal weight: 3.9990 chunk 254 optimal weight: 0.2980 chunk 275 optimal weight: 10.0000 chunk 226 optimal weight: 0.2980 chunk 252 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN E 336 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 23660 Z= 0.155 Angle : 0.482 6.083 32131 Z= 0.260 Chirality : 0.039 0.165 3702 Planarity : 0.003 0.042 3954 Dihedral : 11.938 131.761 3456 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.51 % Allowed : 18.19 % Favored : 80.30 % 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: 2.21 (0.17), residues: 2762 helix: 2.41 (0.15), residues: 1326 sheet: 0.68 (0.21), residues: 587 loop : 0.64 (0.23), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 324 HIS 0.004 0.001 HIS G 295 PHE 0.010 0.001 PHE G 152 TYR 0.012 0.001 TYR A 584 ARG 0.008 0.000 ARG A 578 *********************** 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 225 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 187 time to evaluate : 2.800 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: D 145 MET cc_start: 0.8267 (mtp) cc_final: 0.7951 (mtp) REVERT: H 202 MET cc_start: 0.4319 (tpt) cc_final: 0.4040 (tpt) outliers start: 38 outliers final: 17 residues processed: 215 average time/residue: 2.5548 time to fit residues: 629.3430 Evaluate side-chains 192 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 175 time to evaluate : 2.792 ------------------------------------------------------------------------------- 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 108 SER Chi-restraints excluded: chain B residue 164 SER Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain E residue 6 ASP Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain E residue 354 ASP 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 154 CYS Chi-restraints excluded: chain H residue 392 SER Chi-restraints excluded: chain H residue 440 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 251 optimal weight: 8.9990 chunk 191 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 255 optimal weight: 10.0000 chunk 270 optimal weight: 2.9990 chunk 133 optimal weight: 2.9990 chunk 242 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 336 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 23660 Z= 0.335 Angle : 0.539 7.083 32131 Z= 0.291 Chirality : 0.042 0.172 3702 Planarity : 0.004 0.042 3954 Dihedral : 12.269 136.816 3455 Min Nonbonded Distance : 1.580 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.55 % Allowed : 17.76 % Favored : 80.70 % 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: 1.97 (0.16), residues: 2762 helix: 2.14 (0.14), residues: 1334 sheet: 0.65 (0.21), residues: 584 loop : 0.57 (0.23), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 324 HIS 0.006 0.001 HIS E 341 PHE 0.019 0.001 PHE G 152 TYR 0.013 0.001 TYR E 135 ARG 0.008 0.000 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 219 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 180 time to evaluate : 2.823 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: 0.8252 (mtp) cc_final: 0.7882 (mtp) outliers start: 39 outliers final: 21 residues processed: 213 average time/residue: 2.6304 time to fit residues: 640.1968 Evaluate side-chains 191 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 2.812 ------------------------------------------------------------------------------- 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 108 SER 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 C residue 105 GLN Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 29 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 322 ILE Chi-restraints excluded: chain H residue 154 CYS Chi-restraints excluded: chain H residue 203 HIS Chi-restraints excluded: chain H residue 440 PHE 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: 0.6980 chunk 201 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 chunk 230 optimal weight: 0.8980 chunk 187 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 138 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 57 ASN E 336 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23660 Z= 0.232 Angle : 0.503 6.227 32131 Z= 0.273 Chirality : 0.040 0.166 3702 Planarity : 0.004 0.048 3954 Dihedral : 12.265 133.540 3455 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.35 % Allowed : 17.76 % Favored : 80.90 % 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: 1.99 (0.16), residues: 2762 helix: 2.19 (0.14), residues: 1332 sheet: 0.61 (0.21), residues: 586 loop : 0.57 (0.23), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 129 HIS 0.005 0.001 HIS G 295 PHE 0.015 0.001 PHE G 152 TYR 0.010 0.001 TYR E 135 ARG 0.007 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 210 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 176 time to evaluate : 2.809 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: 0.8262 (mtp) cc_final: 0.7922 (mtp) REVERT: H 440 PHE cc_start: 0.7801 (OUTLIER) cc_final: 0.6931 (t80) outliers start: 34 outliers final: 20 residues processed: 205 average time/residue: 2.7466 time to fit residues: 652.8110 Evaluate side-chains 191 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 2.813 ------------------------------------------------------------------------------- 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 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 C residue 105 GLN Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 352 CYS Chi-restraints excluded: chain F residue 29 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 322 ILE Chi-restraints excluded: chain G residue 355 HIS Chi-restraints excluded: chain H residue 154 CYS Chi-restraints excluded: chain H residue 203 HIS Chi-restraints excluded: chain H residue 392 SER 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: 0.9980 chunk 243 optimal weight: 0.0070 chunk 53 optimal weight: 3.9990 chunk 158 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 270 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 chunk 125 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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 53 ASN ** H 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2565 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= 0.182 Angle : 0.488 6.487 32131 Z= 0.264 Chirality : 0.039 0.173 3702 Planarity : 0.004 0.079 3954 Dihedral : 12.276 131.430 3455 Min Nonbonded Distance : 1.736 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.19 % Allowed : 17.99 % Favored : 80.82 % 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: 2.06 (0.16), residues: 2762 helix: 2.28 (0.15), residues: 1339 sheet: 0.56 (0.21), residues: 586 loop : 0.60 (0.23), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 129 HIS 0.005 0.001 HIS G 295 PHE 0.012 0.001 PHE G 152 TYR 0.008 0.001 TYR E 135 ARG 0.015 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 206 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 176 time to evaluate : 2.841 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: 0.8268 (mtp) cc_final: 0.7936 (mtp) REVERT: H 440 PHE cc_start: 0.7799 (OUTLIER) cc_final: 0.6924 (t80) outliers start: 30 outliers final: 17 residues processed: 200 average time/residue: 2.6498 time to fit residues: 605.9734 Evaluate side-chains 189 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 171 time to evaluate : 2.789 ------------------------------------------------------------------------------- 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 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 C residue 105 GLN Chi-restraints excluded: chain D residue 127 GLU Chi-restraints excluded: chain E residue 6 ASP 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 154 CYS Chi-restraints excluded: chain H residue 392 SER 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: 9.9990 chunk 30 optimal weight: 2.9990 chunk 154 optimal weight: 2.9990 chunk 197 optimal weight: 0.4980 chunk 153 optimal weight: 0.7980 chunk 228 optimal weight: 0.7980 chunk 151 optimal weight: 0.0020 chunk 269 optimal weight: 0.0770 chunk 168 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 overall best weight: 0.4346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 57 ASN E 45 ASN E 74 GLN H 151 ASN H 203 HIS H 221 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23660 Z= 0.134 Angle : 0.469 6.946 32131 Z= 0.254 Chirality : 0.039 0.181 3702 Planarity : 0.003 0.096 3954 Dihedral : 12.213 131.930 3455 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.95 % Allowed : 18.27 % Favored : 80.78 % 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: 2.48 (0.15), residues: 1334 sheet: 0.54 (0.21), residues: 585 loop : 0.66 (0.23), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 129 HIS 0.006 0.001 HIS B 232 PHE 0.008 0.001 PHE D 290 TYR 0.009 0.001 TYR A 235 ARG 0.013 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 202 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 178 time to evaluate : 2.828 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: 0.8275 (mtp) cc_final: 0.7954 (mtp) REVERT: H 440 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.6909 (t80) outliers start: 24 outliers final: 11 residues processed: 198 average time/residue: 2.5856 time to fit residues: 587.5906 Evaluate side-chains 181 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 169 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 SER 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 E residue 352 CYS 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 1 MET Chi-restraints excluded: chain H residue 392 SER Chi-restraints excluded: chain H residue 440 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 166 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 161 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 74 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 23660 Z= 0.320 Angle : 0.530 6.601 32131 Z= 0.286 Chirality : 0.041 0.195 3702 Planarity : 0.004 0.051 3954 Dihedral : 12.466 135.108 3455 Min Nonbonded Distance : 1.626 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.03 % Allowed : 18.07 % Favored : 80.90 % 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: 2.01 (0.16), residues: 2762 helix: 2.23 (0.14), residues: 1334 sheet: 0.55 (0.21), residues: 587 loop : 0.60 (0.23), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 129 HIS 0.005 0.001 HIS E 341 PHE 0.018 0.001 PHE G 152 TYR 0.014 0.001 TYR D 160 ARG 0.011 0.000 ARG A 575 *********************** 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 197 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 171 time to evaluate : 2.807 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: 0.8269 (mtp) cc_final: 0.7903 (mtp) REVERT: H 440 PHE cc_start: 0.7811 (OUTLIER) cc_final: 0.6935 (t80) outliers start: 26 outliers final: 11 residues processed: 194 average time/residue: 2.7506 time to fit residues: 606.9991 Evaluate side-chains 178 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 166 time to evaluate : 2.792 ------------------------------------------------------------------------------- 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 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 C residue 105 GLN Chi-restraints excluded: chain F residue 29 THR 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 440 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 245 optimal weight: 2.9990 chunk 258 optimal weight: 2.9990 chunk 235 optimal weight: 0.0370 chunk 251 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 109 optimal weight: 0.6980 chunk 197 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 227 optimal weight: 0.6980 chunk 237 optimal weight: 5.9990 chunk 250 optimal weight: 1.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 247 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 23660 Z= 0.139 Angle : 0.481 7.013 32131 Z= 0.259 Chirality : 0.039 0.191 3702 Planarity : 0.004 0.062 3954 Dihedral : 12.320 133.135 3454 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.59 % Allowed : 18.63 % Favored : 80.78 % 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: 2.19 (0.17), residues: 2762 helix: 2.43 (0.15), residues: 1333 sheet: 0.53 (0.21), residues: 587 loop : 0.66 (0.23), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 129 HIS 0.007 0.001 HIS B 232 PHE 0.011 0.001 PHE H 205 TYR 0.010 0.001 TYR A 584 ARG 0.009 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 190 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 175 time to evaluate : 2.817 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: 0.8268 (mtp) cc_final: 0.7948 (mtp) REVERT: H 440 PHE cc_start: 0.7776 (OUTLIER) cc_final: 0.6890 (t80) outliers start: 15 outliers final: 9 residues processed: 188 average time/residue: 2.7440 time to fit residues: 588.5741 Evaluate side-chains 180 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 170 time to evaluate : 2.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 LYS Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain E residue 273 GLU 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 1 MET 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 165 optimal weight: 0.6980 chunk 265 optimal weight: 2.9990 chunk 162 optimal weight: 0.6980 chunk 126 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 278 optimal weight: 6.9990 chunk 256 optimal weight: 9.9990 chunk 222 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 136 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 23660 Z= 0.179 Angle : 0.490 6.964 32131 Z= 0.263 Chirality : 0.039 0.196 3702 Planarity : 0.004 0.056 3954 Dihedral : 12.347 133.764 3454 Min Nonbonded Distance : 1.715 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.55 % Allowed : 18.79 % Favored : 80.66 % 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: 2.19 (0.17), residues: 2762 helix: 2.43 (0.14), residues: 1334 sheet: 0.56 (0.21), residues: 580 loop : 0.63 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 129 HIS 0.004 0.001 HIS B 232 PHE 0.015 0.001 PHE H 205 TYR 0.010 0.001 TYR A 584 ARG 0.011 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 188 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 174 time to evaluate : 2.907 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: 0.8264 (mtp) cc_final: 0.7912 (mtp) REVERT: H 440 PHE cc_start: 0.7783 (OUTLIER) cc_final: 0.6907 (t80) outliers start: 14 outliers final: 7 residues processed: 185 average time/residue: 2.7862 time to fit residues: 593.6692 Evaluate side-chains 178 residues out of total 2539 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 170 time to evaluate : 2.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 248 SER Chi-restraints excluded: chain B residue 297 MET Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain E residue 273 GLU Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 224 SER Chi-restraints excluded: chain G residue 355 HIS 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: 2.9990 chunk 68 optimal weight: 0.3980 chunk 204 optimal weight: 0.0670 chunk 32 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 228 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.098125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.067527 restraints weight = 111532.705| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.43 r_work: 0.2825 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2703 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23660 Z= 0.173 Angle : 0.489 7.257 32131 Z= 0.262 Chirality : 0.040 0.204 3702 Planarity : 0.004 0.062 3954 Dihedral : 12.343 134.821 3454 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.48 % Allowed : 18.99 % Favored : 80.54 % 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: 2.20 (0.17), residues: 2762 helix: 2.44 (0.14), residues: 1334 sheet: 0.57 (0.21), residues: 580 loop : 0.63 (0.23), residues: 848 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP H 129 HIS 0.005 0.001 HIS B 232 PHE 0.016 0.001 PHE H 205 TYR 0.011 0.001 TYR A 584 ARG 0.010 0.000 ARG A 578 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13434.04 seconds wall clock time: 228 minutes 19.90 seconds (13699.90 seconds total)