Starting phenix.real_space_refine on Fri Mar 6 13:34:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aml_11822/03_2026/7aml_11822_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aml_11822/03_2026/7aml_11822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7aml_11822/03_2026/7aml_11822_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aml_11822/03_2026/7aml_11822_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7aml_11822/03_2026/7aml_11822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aml_11822/03_2026/7aml_11822.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 8 9.91 5 S 134 5.16 5 C 9986 2.51 5 N 2762 2.21 5 O 3128 1.98 5 H 15286 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 99 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31304 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 9267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 9267 Classifications: {'peptide': 596} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 565} Chain: "D" Number of atoms: 9267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 9267 Classifications: {'peptide': 596} Link IDs: {'PCIS': 2, 'PTRANS': 28, 'TRANS': 565} Chain: "B" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4719 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 17, 'TRANS': 286} Chain breaks: 2 Chain: "C" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1550 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "E" Number of atoms: 4719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4719 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 17, 'TRANS': 286} Chain breaks: 2 Chain: "F" Number of atoms: 1550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1550 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "A" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 102 Unusual residues: {' CA': 4, 'NAG': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "D" Number of atoms: 102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 102 Unusual residues: {' CA': 4, 'NAG': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.27, per 1000 atoms: 0.17 Number of scatterers: 31304 At special positions: 0 Unit cell: (180.36, 167.4, 101.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 8 19.99 S 134 16.00 O 3128 8.00 N 2762 7.00 C 9986 6.00 H 15286 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=57, symmetry=0 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 123 " distance=2.02 Simple disulfide: pdb=" SG CYS A 143 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 152 " - pdb=" SG CYS A 229 " distance=2.03 Simple disulfide: pdb=" SG CYS A 411 " - pdb=" SG CYS A 415 " distance=2.03 Simple disulfide: pdb=" SG CYS A 441 " - pdb=" SG CYS A 471 " distance=2.03 Simple disulfide: pdb=" SG CYS A 514 " - pdb=" SG CYS A 536 " distance=2.02 Simple disulfide: pdb=" SG CYS A 523 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS A 560 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS A 565 " - pdb=" SG CYS A 580 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 612 " distance=2.04 Simple disulfide: pdb=" SG CYS A 605 " - pdb=" SG CYS A 610 " distance=2.03 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 123 " distance=2.02 Simple disulfide: pdb=" SG CYS D 143 " - pdb=" SG CYS D 183 " distance=2.05 Simple disulfide: pdb=" SG CYS D 152 " - pdb=" SG CYS D 229 " distance=2.03 Simple disulfide: pdb=" SG CYS D 411 " - pdb=" SG CYS D 415 " distance=2.03 Simple disulfide: pdb=" SG CYS D 441 " - pdb=" SG CYS D 471 " distance=2.02 Simple disulfide: pdb=" SG CYS D 514 " - pdb=" SG CYS D 536 " distance=2.02 Simple disulfide: pdb=" SG CYS D 523 " - pdb=" SG CYS D 553 " distance=2.03 Simple disulfide: pdb=" SG CYS D 560 " - pdb=" SG CYS D 576 " distance=2.03 Simple disulfide: pdb=" SG CYS D 565 " - pdb=" SG CYS D 580 " distance=2.03 Simple disulfide: pdb=" SG CYS D 603 " - pdb=" SG CYS D 612 " distance=2.04 Simple disulfide: pdb=" SG CYS D 605 " - pdb=" SG CYS D 610 " distance=2.03 Simple disulfide: pdb=" SG CYS B 32 " - pdb=" SG CYS B 90 " distance=2.03 Simple disulfide: pdb=" SG CYS B 39 " - pdb=" SG CYS B 45 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 75 " distance=2.03 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 102 " distance=2.03 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 214 " distance=2.02 Simple disulfide: pdb=" SG CYS B 160 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 192 " distance=2.02 Simple disulfide: pdb=" SG CYS B 187 " - pdb=" SG CYS B 236 " distance=2.03 Simple disulfide: pdb=" SG CYS B 216 " - pdb=" SG CYS B 224 " distance=2.02 Simple disulfide: pdb=" SG CYS B 246 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 253 " - pdb=" SG CYS B 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 270 " - pdb=" SG CYS B 288 " distance=2.02 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 340 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 328 " distance=2.03 Simple disulfide: pdb=" SG CYS C 142 " - pdb=" SG CYS C 203 " distance=2.02 Simple disulfide: pdb=" SG CYS C 169 " - pdb=" SG CYS C 232 " distance=2.02 Simple disulfide: pdb=" SG CYS C 173 " - pdb=" SG CYS C 234 " distance=2.03 Simple disulfide: pdb=" SG CYS C 202 " - pdb=" SG CYS F 202 " distance=2.04 Simple disulfide: pdb=" SG CYS E 32 " - pdb=" SG CYS E 90 " distance=2.03 Simple disulfide: pdb=" SG CYS E 39 " - pdb=" SG CYS E 45 " distance=2.03 Simple disulfide: pdb=" SG CYS E 55 " - pdb=" SG CYS E 75 " distance=2.03 Simple disulfide: pdb=" SG CYS E 92 " - pdb=" SG CYS E 102 " distance=2.03 Simple disulfide: pdb=" SG CYS E 153 " - pdb=" SG CYS E 214 " distance=2.02 Simple disulfide: pdb=" SG CYS E 160 " - pdb=" SG CYS E 166 " distance=2.03 Simple disulfide: pdb=" SG CYS E 177 " - pdb=" SG CYS E 192 " distance=2.02 Simple disulfide: pdb=" SG CYS E 187 " - pdb=" SG CYS E 236 " distance=2.03 Simple disulfide: pdb=" SG CYS E 216 " - pdb=" SG CYS E 224 " distance=2.02 Simple disulfide: pdb=" SG CYS E 246 " - pdb=" SG CYS E 316 " distance=2.03 Simple disulfide: pdb=" SG CYS E 253 " - pdb=" SG CYS E 259 " distance=2.03 Simple disulfide: pdb=" SG CYS E 270 " - pdb=" SG CYS E 288 " distance=2.02 Simple disulfide: pdb=" SG CYS E 280 " - pdb=" SG CYS E 340 " distance=2.03 Simple disulfide: pdb=" SG CYS E 318 " - pdb=" SG CYS E 328 " distance=2.03 Simple disulfide: pdb=" SG CYS F 142 " - pdb=" SG CYS F 203 " distance=2.05 Simple disulfide: pdb=" SG CYS F 169 " - pdb=" SG CYS F 232 " distance=2.03 Simple disulfide: pdb=" SG CYS F 173 " - pdb=" SG CYS F 234 " distance=2.03 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 Links applied NAG-ASN " NAG A 705 " - " ASN A 259 " " NAG A 706 " - " ASN A 308 " " NAG A 707 " - " ASN A 346 " " NAG A 708 " - " ASN A 362 " " NAG A 709 " - " ASN A 378 " " NAG A 710 " - " ASN A 461 " " NAG A 711 " - " ASN A 572 " " NAG C 301 " - " ASN C 150 " " NAG D 705 " - " ASN D 259 " " NAG D 706 " - " ASN D 308 " " NAG D 707 " - " ASN D 346 " " NAG D 708 " - " ASN D 362 " " NAG D 709 " - " ASN D 378 " " NAG D 710 " - " ASN D 461 " " NAG D 711 " - " ASN D 572 " " NAG F 301 " - " ASN F 150 " Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 836.3 milliseconds 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3776 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 34 sheets defined 28.3% alpha, 18.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 68 through 71 Processing helix chain 'A' and resid 89 through 96 removed outlier: 3.685A pdb=" N PHE A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER A 94 " --> pdb=" O TRP A 90 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 95 " --> pdb=" O SER A 91 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 96' Processing helix chain 'A' and resid 119 through 123 removed outlier: 4.082A pdb=" N CYS A 123 " --> pdb=" O LYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 182 removed outlier: 3.776A pdb=" N ILE A 182 " --> pdb=" O THR A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 315 Processing helix chain 'A' and resid 435 through 440 Processing helix chain 'A' and resid 441 through 443 No H-bonds generated for 'chain 'A' and resid 441 through 443' Processing helix chain 'A' and resid 469 through 471 No H-bonds generated for 'chain 'A' and resid 469 through 471' Processing helix chain 'A' and resid 519 through 525 removed outlier: 3.781A pdb=" N ALA A 525 " --> pdb=" O GLY A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 581 removed outlier: 4.176A pdb=" N CYS A 580 " --> pdb=" O CYS A 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 71 Processing helix chain 'D' and resid 89 through 96 removed outlier: 3.684A pdb=" N PHE D 93 " --> pdb=" O GLU D 89 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER D 94 " --> pdb=" O TRP D 90 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 96 " --> pdb=" O ASP D 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 89 through 96' Processing helix chain 'D' and resid 119 through 123 removed outlier: 4.082A pdb=" N CYS D 123 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 removed outlier: 3.901A pdb=" N SER D 181 " --> pdb=" O PHE D 177 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ILE D 182 " --> pdb=" O THR D 178 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N CYS D 183 " --> pdb=" O HIS D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 315 Processing helix chain 'D' and resid 435 through 440 Processing helix chain 'D' and resid 441 through 443 No H-bonds generated for 'chain 'D' and resid 441 through 443' Processing helix chain 'D' and resid 468 through 471 removed outlier: 3.577A pdb=" N CYS D 471 " --> pdb=" O ARG D 468 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 468 through 471' Processing helix chain 'D' and resid 519 through 525 removed outlier: 3.781A pdb=" N ALA D 525 " --> pdb=" O GLY D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 581 removed outlier: 4.184A pdb=" N CYS D 580 " --> pdb=" O CYS D 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 40 Processing helix chain 'B' and resid 42 through 56 Processing helix chain 'B' and resid 75 through 85 removed outlier: 3.853A pdb=" N ASP B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA B 81 " --> pdb=" O LEU B 77 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 90 Processing helix chain 'B' and resid 99 through 113 removed outlier: 3.806A pdb=" N HIS B 112 " --> pdb=" O GLY B 108 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU B 113 " --> pdb=" O ILE B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 136 removed outlier: 4.172A pdb=" N SER B 132 " --> pdb=" O ASN B 128 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N PHE B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 144 removed outlier: 3.592A pdb=" N SER B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU B 144 " --> pdb=" O ILE B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 152 through 161 Processing helix chain 'B' and resid 165 through 173 Processing helix chain 'B' and resid 174 through 179 Processing helix chain 'B' and resid 188 through 203 removed outlier: 3.738A pdb=" N LYS B 202 " --> pdb=" O GLN B 198 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 removed outlier: 4.395A pdb=" N GLY B 210 " --> pdb=" O LYS B 206 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N MET B 211 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU B 212 " --> pdb=" O SER B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 removed outlier: 3.533A pdb=" N GLU B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 238 Processing helix chain 'B' and resid 245 through 254 Processing helix chain 'B' and resid 258 through 271 removed outlier: 3.942A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR B 268 " --> pdb=" O ALA B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 294 removed outlier: 4.220A pdb=" N CYS B 288 " --> pdb=" O ASN B 284 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 289 " --> pdb=" O TYR B 285 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER B 293 " --> pdb=" O LEU B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 323 No H-bonds generated for 'chain 'B' and resid 321 through 323' Processing helix chain 'B' and resid 324 through 337 removed outlier: 3.727A pdb=" N CYS B 328 " --> pdb=" O SER B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 350 removed outlier: 3.690A pdb=" N ARG B 342 " --> pdb=" O ASN B 338 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE B 348 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY B 349 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 155 Processing helix chain 'C' and resid 173 through 177 Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'E' and resid 32 through 40 Processing helix chain 'E' and resid 42 through 56 Processing helix chain 'E' and resid 75 through 85 removed outlier: 3.853A pdb=" N ASP E 80 " --> pdb=" O ARG E 76 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ALA E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 90 Processing helix chain 'E' and resid 99 through 113 removed outlier: 3.807A pdb=" N HIS E 112 " --> pdb=" O GLY E 108 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 136 removed outlier: 4.171A pdb=" N SER E 132 " --> pdb=" O ASN E 128 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE E 135 " --> pdb=" O LEU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 144 removed outlier: 3.592A pdb=" N SER E 142 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLU E 144 " --> pdb=" O ILE E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 152 through 161 Processing helix chain 'E' and resid 165 through 173 Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'E' and resid 188 through 203 removed outlier: 3.739A pdb=" N LYS E 202 " --> pdb=" O GLN E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 204 through 214 removed outlier: 4.395A pdb=" N GLY E 210 " --> pdb=" O LYS E 206 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N MET E 211 " --> pdb=" O HIS E 207 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 230 removed outlier: 3.530A pdb=" N GLU E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 238 Processing helix chain 'E' and resid 245 through 254 Processing helix chain 'E' and resid 258 through 271 removed outlier: 3.941A pdb=" N PHE E 266 " --> pdb=" O ARG E 262 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE E 267 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR E 268 " --> pdb=" O ALA E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 284 through 294 removed outlier: 4.220A pdb=" N CYS E 288 " --> pdb=" O ASN E 284 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU E 289 " --> pdb=" O TYR E 285 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER E 293 " --> pdb=" O LEU E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 323 No H-bonds generated for 'chain 'E' and resid 321 through 323' Processing helix chain 'E' and resid 324 through 337 removed outlier: 3.726A pdb=" N CYS E 328 " --> pdb=" O SER E 324 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 350 removed outlier: 3.690A pdb=" N ARG E 342 " --> pdb=" O ASN E 338 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE E 348 " --> pdb=" O ALA E 344 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLY E 349 " --> pdb=" O ILE E 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 155 Processing helix chain 'F' and resid 173 through 177 Processing helix chain 'F' and resid 178 through 190 Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 34 removed outlier: 3.958A pdb=" N TYR A 30 " --> pdb=" O GLU A 130 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS A 132 " --> pdb=" O TYR A 30 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLU A 32 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N SER A 134 " --> pdb=" O GLU A 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE A 34 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 129 " --> pdb=" O VAL A 111 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL A 111 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 133 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N LYS A 110 " --> pdb=" O CYS A 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 46 removed outlier: 3.928A pdb=" N LEU A 45 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 163 removed outlier: 6.848A pdb=" N ILE A 162 " --> pdb=" O TYR A 249 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU A 238 " --> pdb=" O VAL A 231 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL A 240 " --> pdb=" O CYS A 229 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N LEU A 244 " --> pdb=" O LEU A 225 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR A 223 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY A 191 " --> pdb=" O VAL A 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 170 through 173 removed outlier: 6.863A pdb=" N LEU A 209 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 210 " --> pdb=" O ALA A 201 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 264 through 265 removed outlier: 6.935A pdb=" N GLU A 264 " --> pdb=" O ASN A 378 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N THR A 380 " --> pdb=" O GLU A 264 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE A 355 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 281 through 285 removed outlier: 3.517A pdb=" N LYS A 340 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 281 through 285 Processing sheet with id=AA8, first strand: chain 'A' and resid 302 through 305 removed outlier: 3.776A pdb=" N VAL A 302 " --> pdb=" O ASN A 362 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL A 361 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL A 373 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 409 through 410 removed outlier: 3.751A pdb=" N THR A 455 " --> pdb=" O ASN A 450 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASN A 450 " --> pdb=" O THR A 455 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 423 through 429 removed outlier: 3.718A pdb=" N THR A 491 " --> pdb=" O VAL A 478 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 537 through 538 Processing sheet with id=AB3, first strand: chain 'A' and resid 585 through 587 Processing sheet with id=AB4, first strand: chain 'A' and resid 589 through 591 Processing sheet with id=AB5, first strand: chain 'D' and resid 29 through 34 removed outlier: 3.959A pdb=" N TYR D 30 " --> pdb=" O GLU D 130 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LYS D 132 " --> pdb=" O TYR D 30 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU D 32 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER D 134 " --> pdb=" O GLU D 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 34 " --> pdb=" O SER D 134 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL D 129 " --> pdb=" O VAL D 111 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL D 111 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU D 133 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N LYS D 110 " --> pdb=" O CYS D 63 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 45 through 46 removed outlier: 3.876A pdb=" N LEU D 45 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 161 through 163 removed outlier: 6.848A pdb=" N ILE D 162 " --> pdb=" O TYR D 249 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU D 238 " --> pdb=" O VAL D 231 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL D 240 " --> pdb=" O CYS D 229 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU D 244 " --> pdb=" O LEU D 225 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N TYR D 223 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY D 191 " --> pdb=" O VAL D 228 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 170 through 173 removed outlier: 6.864A pdb=" N LEU D 209 " --> pdb=" O LEU D 171 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL D 210 " --> pdb=" O ALA D 201 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 264 through 265 removed outlier: 6.935A pdb=" N GLU D 264 " --> pdb=" O ASN D 378 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N THR D 380 " --> pdb=" O GLU D 264 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE D 355 " --> pdb=" O VAL D 379 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 281 through 285 removed outlier: 3.516A pdb=" N LYS D 340 " --> pdb=" O GLU D 319 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 281 through 285 Processing sheet with id=AC3, first strand: chain 'D' and resid 302 through 305 removed outlier: 3.775A pdb=" N VAL D 302 " --> pdb=" O ASN D 362 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL D 361 " --> pdb=" O VAL D 373 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL D 373 " --> pdb=" O VAL D 361 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 409 through 410 removed outlier: 3.620A pdb=" N THR D 455 " --> pdb=" O ASN D 450 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASN D 450 " --> pdb=" O THR D 455 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 423 through 429 removed outlier: 3.718A pdb=" N THR D 491 " --> pdb=" O VAL D 478 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 537 through 538 Processing sheet with id=AC7, first strand: chain 'D' and resid 585 through 587 Processing sheet with id=AC8, first strand: chain 'D' and resid 589 through 591 Processing sheet with id=AC9, first strand: chain 'B' and resid 303 through 304 removed outlier: 4.021A pdb=" N ASN B 303 " --> pdb=" O SER B 313 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER B 313 " --> pdb=" O ASN B 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 143 through 150 Processing sheet with id=AD2, first strand: chain 'C' and resid 202 through 208 removed outlier: 3.806A pdb=" N ALA C 233 " --> pdb=" O ARG C 204 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE C 206 " --> pdb=" O LYS C 231 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N LYS C 231 " --> pdb=" O ILE C 206 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N PHE C 208 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ALA C 229 " --> pdb=" O PHE C 208 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 212 through 215 Processing sheet with id=AD4, first strand: chain 'E' and resid 303 through 304 removed outlier: 4.022A pdb=" N ASN E 303 " --> pdb=" O SER E 313 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER E 313 " --> pdb=" O ASN E 303 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'F' and resid 144 through 150 Processing sheet with id=AD6, first strand: chain 'F' and resid 202 through 205 removed outlier: 3.512A pdb=" N CYS F 202 " --> pdb=" O VAL F 235 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 212 through 215 431 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.44 Time building geometry restraints manager: 3.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 15286 1.02 - 1.23: 24 1.23 - 1.43: 6850 1.43 - 1.63: 9302 1.63 - 1.84: 154 Bond restraints: 31616 Sorted by residual: bond pdb=" ND2 ASN A 452 " pdb="HD21 ASN A 452 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.62e+01 bond pdb=" ND2 ASN A 452 " pdb="HD22 ASN A 452 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" ND2 ASN A 185 " pdb="HD21 ASN A 185 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" ND2 ASN A 295 " pdb="HD21 ASN A 295 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.58e+01 bond pdb=" ND2 ASN A 295 " pdb="HD22 ASN A 295 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.57e+01 ... (remaining 31611 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 56275 2.53 - 5.06: 573 5.06 - 7.60: 71 7.60 - 10.13: 16 10.13 - 12.66: 3 Bond angle restraints: 56938 Sorted by residual: angle pdb=" N SER B 222 " pdb=" CA SER B 222 " pdb=" C SER B 222 " ideal model delta sigma weight residual 109.07 98.35 10.72 1.61e+00 3.86e-01 4.43e+01 angle pdb=" N SER E 222 " pdb=" CA SER E 222 " pdb=" C SER E 222 " ideal model delta sigma weight residual 109.07 98.92 10.15 1.61e+00 3.86e-01 3.97e+01 angle pdb=" N ASP D 562 " pdb=" CA ASP D 562 " pdb=" C ASP D 562 " ideal model delta sigma weight residual 111.02 118.01 -6.99 1.22e+00 6.72e-01 3.28e+01 angle pdb=" N SER A 142 " pdb=" CA SER A 142 " pdb=" C SER A 142 " ideal model delta sigma weight residual 109.76 101.15 8.61 1.59e+00 3.96e-01 2.93e+01 angle pdb=" N SER D 142 " pdb=" CA SER D 142 " pdb=" C SER D 142 " ideal model delta sigma weight residual 110.28 102.58 7.70 1.48e+00 4.57e-01 2.71e+01 ... (remaining 56933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 13704 16.43 - 32.85: 1191 32.85 - 49.28: 347 49.28 - 65.70: 117 65.70 - 82.13: 16 Dihedral angle restraints: 15375 sinusoidal: 8581 harmonic: 6794 Sorted by residual: dihedral pdb=" CB CYS B 187 " pdb=" SG CYS B 187 " pdb=" SG CYS B 236 " pdb=" CB CYS B 236 " ideal model delta sinusoidal sigma weight residual -86.00 -139.18 53.18 1 1.00e+01 1.00e-02 3.85e+01 dihedral pdb=" CB CYS E 187 " pdb=" SG CYS E 187 " pdb=" SG CYS E 236 " pdb=" CB CYS E 236 " ideal model delta sinusoidal sigma weight residual -86.00 -139.15 53.15 1 1.00e+01 1.00e-02 3.84e+01 dihedral pdb=" CB CYS C 169 " pdb=" SG CYS C 169 " pdb=" SG CYS C 232 " pdb=" CB CYS C 232 " ideal model delta sinusoidal sigma weight residual 93.00 145.04 -52.04 1 1.00e+01 1.00e-02 3.70e+01 ... (remaining 15372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.187: 2465 0.187 - 0.374: 19 0.374 - 0.560: 0 0.560 - 0.747: 0 0.747 - 0.934: 2 Chirality restraints: 2486 Sorted by residual: chirality pdb=" C1 NAG A 707 " pdb=" ND2 ASN A 346 " pdb=" C2 NAG A 707 " pdb=" O5 NAG A 707 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.18e+01 chirality pdb=" C1 NAG D 707 " pdb=" ND2 ASN D 346 " pdb=" C2 NAG D 707 " pdb=" O5 NAG D 707 " both_signs ideal model delta sigma weight residual False -2.40 -1.47 -0.93 2.00e-01 2.50e+01 2.17e+01 chirality pdb=" C1 NAG D 711 " pdb=" ND2 ASN D 572 " pdb=" C2 NAG D 711 " pdb=" O5 NAG D 711 " both_signs ideal model delta sigma weight residual False -2.40 -2.06 -0.34 2.00e-01 2.50e+01 2.91e+00 ... (remaining 2483 not shown) Planarity restraints: 4774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 185 " 0.001 2.00e-02 2.50e+03 1.94e-01 4.68e+02 pdb=" CG ASN A 185 " 0.061 2.00e-02 2.50e+03 pdb=" OD1 ASN A 185 " -0.123 2.00e-02 2.50e+03 pdb=" ND2 ASN A 185 " 0.319 2.00e-02 2.50e+03 pdb="HD21 ASN A 185 " -0.258 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS F 203 " 0.042 2.00e-02 2.50e+03 7.73e-02 5.97e+01 pdb=" N ARG F 204 " -0.133 2.00e-02 2.50e+03 pdb=" CA ARG F 204 " 0.035 2.00e-02 2.50e+03 pdb=" H ARG F 204 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE F 206 " -0.033 2.00e-02 2.50e+03 6.49e-02 4.21e+01 pdb=" N ALA F 207 " 0.112 2.00e-02 2.50e+03 pdb=" CA ALA F 207 " -0.032 2.00e-02 2.50e+03 pdb=" H ALA F 207 " -0.046 2.00e-02 2.50e+03 ... (remaining 4771 not shown) Histogram of nonbonded interaction distances: 1.52 - 2.13: 1009 2.13 - 2.75: 56840 2.75 - 3.37: 78737 3.37 - 3.98: 98238 3.98 - 4.60: 153003 Nonbonded interactions: 387827 Sorted by model distance: nonbonded pdb=" OE1 GLU A 482 " pdb=" H ASN A 485 " model vdw 1.516 2.450 nonbonded pdb=" OE1 GLU D 482 " pdb=" H ASN D 485 " model vdw 1.517 2.450 nonbonded pdb=" OE1 GLN A 416 " pdb=" H GLN A 416 " model vdw 1.539 2.450 nonbonded pdb=" OE1 GLN D 416 " pdb=" H GLN D 416 " model vdw 1.539 2.450 nonbonded pdb=" H GLU D 274 " pdb=" OD1 ASN D 346 " model vdw 1.554 2.450 ... (remaining 387822 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } 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=0.88 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 0.610 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 27.040 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5669 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 : 0.006 0.069 16403 Z= 0.279 Angle : 0.869 15.629 22266 Z= 0.488 Chirality : 0.058 0.934 2486 Planarity : 0.004 0.050 2872 Dihedral : 13.362 82.127 6396 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.84 % Allowed : 1.51 % Favored : 97.66 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.64 (0.16), residues: 1976 helix: -2.22 (0.23), residues: 396 sheet: -2.19 (0.24), residues: 370 loop : -2.66 (0.15), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 175 TYR 0.043 0.002 TYR E 110 PHE 0.036 0.002 PHE F 166 TRP 0.004 0.001 TRP E 107 HIS 0.004 0.001 HIS A 74 Details of bonding type rmsd covalent geometry : bond 0.00560 (16330) covalent geometry : angle 0.83620 (22104) SS BOND : bond 0.00635 ( 57) SS BOND : angle 1.42044 ( 114) hydrogen bonds : bond 0.25498 ( 419) hydrogen bonds : angle 10.02961 ( 1155) link_NAG-ASN : bond 0.00711 ( 16) link_NAG-ASN : angle 4.82188 ( 48) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 183 time to evaluate : 0.913 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: symmetry clash revert: symmetry clash REVERT: A 183 CYS cc_start: 0.1496 (OUTLIER) cc_final: 0.0985 (t) REVERT: A 565 CYS cc_start: 0.3962 (OUTLIER) cc_final: 0.3661 (p) outliers start: 15 outliers final: 9 residues processed: 198 average time/residue: 0.2862 time to fit residues: 84.1718 Evaluate side-chains 142 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 565 CYS Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 580 CYS Chi-restraints excluded: chain D residue 185 ASN Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain F residue 169 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 0.5980 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.0970 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 GLN A 452 ASN D 296 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.221639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.189829 restraints weight = 79198.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.192504 restraints weight = 41857.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.192653 restraints weight = 30244.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.192770 restraints weight = 29418.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.193095 restraints weight = 29072.348| |-----------------------------------------------------------------------------| r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4442 r_free = 0.4442 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4442 r_free = 0.4442 target_work(ls_wunit_k1) = 0.191 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16403 Z= 0.124 Angle : 0.609 12.193 22266 Z= 0.309 Chirality : 0.048 0.658 2486 Planarity : 0.004 0.043 2872 Dihedral : 7.375 63.491 2551 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.00 % Allowed : 6.30 % Favored : 92.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.17), residues: 1976 helix: -1.38 (0.24), residues: 408 sheet: -1.60 (0.25), residues: 374 loop : -2.39 (0.16), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 591 TYR 0.013 0.001 TYR B 110 PHE 0.017 0.001 PHE D 611 TRP 0.005 0.001 TRP D 538 HIS 0.013 0.001 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00279 (16330) covalent geometry : angle 0.58091 (22104) SS BOND : bond 0.00564 ( 57) SS BOND : angle 1.06140 ( 114) hydrogen bonds : bond 0.04287 ( 419) hydrogen bonds : angle 6.52843 ( 1155) link_NAG-ASN : bond 0.00627 ( 16) link_NAG-ASN : angle 3.70211 ( 48) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.141 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: symmetry clash revert: symmetry clash REVERT: A 183 CYS cc_start: -0.0072 (OUTLIER) cc_final: -0.0465 (t) REVERT: A 190 TYR cc_start: 0.6002 (m-80) cc_final: 0.5737 (m-80) REVERT: E 315 PHE cc_start: 0.5389 (t80) cc_final: 0.4731 (t80) outliers start: 18 outliers final: 13 residues processed: 162 average time/residue: 0.2821 time to fit residues: 67.6714 Evaluate side-chains 149 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 564 TYR Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain F residue 169 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 25 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 8 optimal weight: 10.0000 chunk 57 optimal weight: 0.5980 chunk 12 optimal weight: 0.0970 chunk 144 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 151 ASN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4713 r_free = 0.4713 target = 0.217605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.184203 restraints weight = 78082.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.184814 restraints weight = 42012.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.186484 restraints weight = 33442.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.187198 restraints weight = 29248.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.187417 restraints weight = 26492.913| |-----------------------------------------------------------------------------| r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4363 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4363 r_free = 0.4363 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4363 r_free = 0.4363 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4363 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6088 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16403 Z= 0.141 Angle : 0.577 11.241 22266 Z= 0.295 Chirality : 0.046 0.561 2486 Planarity : 0.004 0.049 2872 Dihedral : 6.868 64.387 2547 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.56 % Allowed : 8.14 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.75 (0.17), residues: 1976 helix: -1.00 (0.25), residues: 418 sheet: -1.37 (0.24), residues: 420 loop : -2.42 (0.16), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 591 TYR 0.019 0.001 TYR E 110 PHE 0.024 0.002 PHE C 214 TRP 0.004 0.001 TRP D 538 HIS 0.006 0.001 HIS F 148 Details of bonding type rmsd covalent geometry : bond 0.00328 (16330) covalent geometry : angle 0.55152 (22104) SS BOND : bond 0.00585 ( 57) SS BOND : angle 1.22467 ( 114) hydrogen bonds : bond 0.04347 ( 419) hydrogen bonds : angle 5.96063 ( 1155) link_NAG-ASN : bond 0.00546 ( 16) link_NAG-ASN : angle 3.25364 ( 48) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 0.757 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: symmetry clash revert: symmetry clash REVERT: A 183 CYS cc_start: -0.0137 (OUTLIER) cc_final: -0.0442 (t) REVERT: B 52 MET cc_start: 0.5783 (tpt) cc_final: 0.5470 (tpt) REVERT: E 315 PHE cc_start: 0.6136 (t80) cc_final: 0.5460 (t80) outliers start: 28 outliers final: 20 residues processed: 162 average time/residue: 0.3181 time to fit residues: 74.1359 Evaluate side-chains 143 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 564 TYR Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 187 CYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain F residue 169 CYS Chi-restraints excluded: chain F residue 203 CYS Chi-restraints excluded: chain F residue 211 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 77 optimal weight: 0.0970 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 108 optimal weight: 0.7980 chunk 150 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 178 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.216605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.183132 restraints weight = 77811.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.185214 restraints weight = 39465.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.185257 restraints weight = 28631.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.185441 restraints weight = 28061.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.185743 restraints weight = 26756.012| |-----------------------------------------------------------------------------| r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4348 r_free = 0.4348 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4348 r_free = 0.4348 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16403 Z= 0.128 Angle : 0.553 10.680 22266 Z= 0.280 Chirality : 0.045 0.555 2486 Planarity : 0.004 0.047 2872 Dihedral : 6.456 59.626 2540 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.67 % Allowed : 9.87 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.62 (0.18), residues: 1976 helix: -0.78 (0.25), residues: 416 sheet: -1.50 (0.23), residues: 458 loop : -2.28 (0.17), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 527 TYR 0.019 0.001 TYR B 106 PHE 0.020 0.001 PHE F 214 TRP 0.004 0.001 TRP D 538 HIS 0.005 0.001 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00302 (16330) covalent geometry : angle 0.52870 (22104) SS BOND : bond 0.00483 ( 57) SS BOND : angle 1.14346 ( 114) hydrogen bonds : bond 0.03703 ( 419) hydrogen bonds : angle 5.64319 ( 1155) link_NAG-ASN : bond 0.00498 ( 16) link_NAG-ASN : angle 3.14222 ( 48) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 1.043 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: symmetry clash revert: symmetry clash REVERT: A 183 CYS cc_start: -0.0131 (OUTLIER) cc_final: -0.0486 (t) REVERT: B 52 MET cc_start: 0.5745 (tpt) cc_final: 0.5437 (tpt) REVERT: E 93 LYS cc_start: 0.7674 (mtmt) cc_final: 0.7459 (mttp) outliers start: 30 outliers final: 21 residues processed: 156 average time/residue: 0.3044 time to fit residues: 70.5681 Evaluate side-chains 140 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 183 CYS Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 479 ILE Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain F residue 169 CYS Chi-restraints excluded: chain F residue 203 CYS Chi-restraints excluded: chain F residue 211 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 101 optimal weight: 0.0010 chunk 65 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 134 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 28 optimal weight: 4.9990 chunk 190 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 overall best weight: 1.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4675 r_free = 0.4675 target = 0.213884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.178806 restraints weight = 77514.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.180166 restraints weight = 38507.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.181245 restraints weight = 32305.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.182088 restraints weight = 26850.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.182487 restraints weight = 25795.469| |-----------------------------------------------------------------------------| r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4307 r_free = 0.4307 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4307 r_free = 0.4307 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6242 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 16403 Z= 0.154 Angle : 0.581 10.598 22266 Z= 0.296 Chirality : 0.045 0.537 2486 Planarity : 0.004 0.055 2872 Dihedral : 6.409 57.943 2540 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 1.67 % Allowed : 10.76 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.18), residues: 1976 helix: -0.95 (0.24), residues: 432 sheet: -1.37 (0.23), residues: 470 loop : -2.35 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 527 TYR 0.014 0.002 TYR C 168 PHE 0.027 0.002 PHE C 214 TRP 0.004 0.001 TRP A 538 HIS 0.004 0.001 HIS D 337 Details of bonding type rmsd covalent geometry : bond 0.00357 (16330) covalent geometry : angle 0.55721 (22104) SS BOND : bond 0.00556 ( 57) SS BOND : angle 1.30371 ( 114) hydrogen bonds : bond 0.04196 ( 419) hydrogen bonds : angle 5.56312 ( 1155) link_NAG-ASN : bond 0.00461 ( 16) link_NAG-ASN : angle 3.10834 ( 48) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.871 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: A 122 MET cc_start: 0.8188 (tpp) cc_final: 0.7956 (tpp) REVERT: B 52 MET cc_start: 0.5818 (tpt) cc_final: 0.5531 (tpt) REVERT: E 93 LYS cc_start: 0.7440 (mtmt) cc_final: 0.7239 (mttp) outliers start: 30 outliers final: 23 residues processed: 155 average time/residue: 0.3014 time to fit residues: 68.6403 Evaluate side-chains 148 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 125 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 CYS Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 479 ILE Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 566 ASP Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain B residue 174 ILE Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain F residue 169 CYS Chi-restraints excluded: chain F residue 203 CYS Chi-restraints excluded: chain F residue 211 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 141 optimal weight: 2.9990 chunk 165 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 76 optimal weight: 0.2980 chunk 95 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN E 221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.214729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.179995 restraints weight = 76928.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.181094 restraints weight = 47149.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.182995 restraints weight = 33725.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.183250 restraints weight = 26862.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.183561 restraints weight = 25553.409| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4330 r_free = 0.4330 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4330 r_free = 0.4330 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6151 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16403 Z= 0.117 Angle : 0.533 10.212 22266 Z= 0.269 Chirality : 0.044 0.501 2486 Planarity : 0.004 0.047 2872 Dihedral : 6.099 58.385 2539 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.17 % Allowed : 12.37 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.18), residues: 1976 helix: -0.65 (0.25), residues: 432 sheet: -1.26 (0.24), residues: 466 loop : -2.27 (0.17), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 527 TYR 0.020 0.001 TYR B 106 PHE 0.018 0.001 PHE C 214 TRP 0.006 0.001 TRP A 538 HIS 0.005 0.001 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00273 (16330) covalent geometry : angle 0.51106 (22104) SS BOND : bond 0.00475 ( 57) SS BOND : angle 1.07475 ( 114) hydrogen bonds : bond 0.03558 ( 419) hydrogen bonds : angle 5.31553 ( 1155) link_NAG-ASN : bond 0.00474 ( 16) link_NAG-ASN : angle 2.91971 ( 48) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.908 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: B 52 MET cc_start: 0.5573 (tpt) cc_final: 0.5293 (tpt) outliers start: 21 outliers final: 16 residues processed: 146 average time/residue: 0.3159 time to fit residues: 67.4758 Evaluate side-chains 139 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain F residue 169 CYS Chi-restraints excluded: chain F residue 203 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 11 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 chunk 144 optimal weight: 0.0770 chunk 81 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 113 optimal weight: 0.6980 chunk 2 optimal weight: 10.0000 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.213946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.180615 restraints weight = 77176.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.180371 restraints weight = 48544.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.181692 restraints weight = 37866.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.182945 restraints weight = 31293.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.182987 restraints weight = 26183.216| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4328 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4328 r_free = 0.4328 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4328 r_free = 0.4328 target_work(ls_wunit_k1) = 0.181 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4328 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6155 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16403 Z= 0.124 Angle : 0.546 10.949 22266 Z= 0.277 Chirality : 0.043 0.489 2486 Planarity : 0.004 0.054 2872 Dihedral : 6.089 57.696 2539 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 1.17 % Allowed : 13.10 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.18), residues: 1976 helix: -0.59 (0.25), residues: 432 sheet: -1.19 (0.24), residues: 470 loop : -2.24 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 527 TYR 0.010 0.001 TYR C 180 PHE 0.019 0.001 PHE C 214 TRP 0.005 0.001 TRP A 538 HIS 0.004 0.001 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00290 (16330) covalent geometry : angle 0.52115 (22104) SS BOND : bond 0.00510 ( 57) SS BOND : angle 1.46780 ( 114) hydrogen bonds : bond 0.03702 ( 419) hydrogen bonds : angle 5.25552 ( 1155) link_NAG-ASN : bond 0.00446 ( 16) link_NAG-ASN : angle 2.85422 ( 48) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 125 time to evaluate : 0.921 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: B 52 MET cc_start: 0.5542 (tpt) cc_final: 0.5245 (tpt) outliers start: 21 outliers final: 19 residues processed: 143 average time/residue: 0.3230 time to fit residues: 67.4270 Evaluate side-chains 140 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain B residue 92 CYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 221 GLN Chi-restraints excluded: chain F residue 169 CYS Chi-restraints excluded: chain F residue 203 CYS Chi-restraints excluded: chain F residue 211 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 194 optimal weight: 0.0370 chunk 161 optimal weight: 7.9990 chunk 136 optimal weight: 0.4980 chunk 105 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 148 optimal weight: 0.2980 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.9662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN E 221 GLN F 222 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.213295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.178510 restraints weight = 77024.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.178981 restraints weight = 44190.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.179970 restraints weight = 33533.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.181177 restraints weight = 29805.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.181437 restraints weight = 25227.526| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4303 r_free = 0.4303 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4303 r_free = 0.4303 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6230 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16403 Z= 0.131 Angle : 0.551 9.811 22266 Z= 0.280 Chirality : 0.044 0.480 2486 Planarity : 0.004 0.047 2872 Dihedral : 6.185 59.830 2539 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.51 % Allowed : 12.82 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.18), residues: 1976 helix: -0.57 (0.25), residues: 432 sheet: -1.18 (0.24), residues: 470 loop : -2.24 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 527 TYR 0.019 0.001 TYR B 106 PHE 0.020 0.001 PHE F 214 TRP 0.005 0.001 TRP B 107 HIS 0.004 0.001 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00305 (16330) covalent geometry : angle 0.53042 (22104) SS BOND : bond 0.00649 ( 57) SS BOND : angle 1.25554 ( 114) hydrogen bonds : bond 0.03739 ( 419) hydrogen bonds : angle 5.26681 ( 1155) link_NAG-ASN : bond 0.00435 ( 16) link_NAG-ASN : angle 2.78706 ( 48) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 0.799 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: symmetry clash REVERT: B 52 MET cc_start: 0.5721 (tpt) cc_final: 0.5427 (tpt) REVERT: B 122 SER cc_start: 0.5530 (m) cc_final: 0.4681 (p) outliers start: 27 outliers final: 18 residues processed: 150 average time/residue: 0.3353 time to fit residues: 72.3458 Evaluate side-chains 137 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ASN Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 259 ASN Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 302 VAL Chi-restraints excluded: chain D residue 460 VAL Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain F residue 169 CYS Chi-restraints excluded: chain F residue 203 CYS Chi-restraints excluded: chain F residue 211 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 179 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 23 optimal weight: 0.0570 chunk 64 optimal weight: 8.9990 chunk 146 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 19 optimal weight: 6.9990 chunk 186 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 chunk 156 optimal weight: 1.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4766 r_free = 0.4766 target = 0.219745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.186953 restraints weight = 81189.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.187702 restraints weight = 51264.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.187774 restraints weight = 35212.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.188588 restraints weight = 32876.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.188787 restraints weight = 30413.859| |-----------------------------------------------------------------------------| r_work (final): 0.4422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4422 r_free = 0.4422 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4422 r_free = 0.4422 target_work(ls_wunit_k1) = 0.186 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.4422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6252 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 16403 Z= 0.103 Angle : 0.520 9.353 22266 Z= 0.261 Chirality : 0.043 0.456 2486 Planarity : 0.004 0.046 2872 Dihedral : 5.941 59.777 2539 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.89 % Allowed : 13.60 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.18), residues: 1976 helix: -0.35 (0.25), residues: 434 sheet: -1.16 (0.24), residues: 454 loop : -2.14 (0.17), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 527 TYR 0.014 0.001 TYR B 106 PHE 0.015 0.001 PHE C 214 TRP 0.006 0.001 TRP A 538 HIS 0.004 0.001 HIS D 600 Details of bonding type rmsd covalent geometry : bond 0.00244 (16330) covalent geometry : angle 0.50028 (22104) SS BOND : bond 0.00495 ( 57) SS BOND : angle 1.15933 ( 114) hydrogen bonds : bond 0.03326 ( 419) hydrogen bonds : angle 5.07054 ( 1155) link_NAG-ASN : bond 0.00450 ( 16) link_NAG-ASN : angle 2.65454 ( 48) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 0.895 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: symmetry clash REVERT: D 230 MET cc_start: 0.6833 (mpp) cc_final: 0.5933 (mtm) REVERT: B 52 MET cc_start: 0.5668 (tpt) cc_final: 0.5373 (tpt) outliers start: 16 outliers final: 10 residues processed: 133 average time/residue: 0.3048 time to fit residues: 59.5783 Evaluate side-chains 126 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 116 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain F residue 169 CYS Chi-restraints excluded: chain F residue 203 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 11 optimal weight: 10.0000 chunk 109 optimal weight: 3.9990 chunk 193 optimal weight: 0.2980 chunk 183 optimal weight: 1.9990 chunk 3 optimal weight: 0.4980 chunk 99 optimal weight: 2.9990 chunk 176 optimal weight: 0.5980 chunk 166 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 150 optimal weight: 0.4980 chunk 188 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.220034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.186918 restraints weight = 81261.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.187645 restraints weight = 47275.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.188277 restraints weight = 37775.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.189099 restraints weight = 31852.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.189265 restraints weight = 29318.052| |-----------------------------------------------------------------------------| r_work (final): 0.4428 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4428 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4428 r_free = 0.4428 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4428 r_free = 0.4428 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4428 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.4799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 16403 Z= 0.102 Angle : 0.521 12.308 22266 Z= 0.262 Chirality : 0.043 0.443 2486 Planarity : 0.004 0.046 2872 Dihedral : 5.810 59.274 2539 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.72 % Allowed : 13.88 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.18), residues: 1976 helix: -0.29 (0.25), residues: 434 sheet: -1.11 (0.24), residues: 458 loop : -2.07 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 527 TYR 0.014 0.001 TYR C 180 PHE 0.014 0.001 PHE C 214 TRP 0.005 0.000 TRP A 538 HIS 0.006 0.001 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00245 (16330) covalent geometry : angle 0.50407 (22104) SS BOND : bond 0.00529 ( 57) SS BOND : angle 1.02572 ( 114) hydrogen bonds : bond 0.03258 ( 419) hydrogen bonds : angle 4.97253 ( 1155) link_NAG-ASN : bond 0.00450 ( 16) link_NAG-ASN : angle 2.54949 ( 48) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3952 Ramachandran restraints generated. 1976 Oldfield, 0 Emsley, 1976 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.831 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: B 52 MET cc_start: 0.5661 (tpt) cc_final: 0.5368 (tpt) outliers start: 13 outliers final: 12 residues processed: 131 average time/residue: 0.3086 time to fit residues: 59.0228 Evaluate side-chains 130 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 118 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 562 ASP Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain D residue 228 VAL Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain D residue 603 CYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain C residue 211 ASP Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain F residue 169 CYS Chi-restraints excluded: chain F residue 203 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 128 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 190 optimal weight: 0.8980 chunk 98 optimal weight: 0.2980 chunk 178 optimal weight: 0.9980 chunk 179 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 151 ASN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4748 r_free = 0.4748 target = 0.217837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.183846 restraints weight = 80966.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.184436 restraints weight = 47444.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.185327 restraints weight = 37742.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.186129 restraints weight = 31878.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.186340 restraints weight = 29397.590| |-----------------------------------------------------------------------------| r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4378 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4378 r_free = 0.4378 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4378 r_free = 0.4378 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.4378 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6329 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16403 Z= 0.139 Angle : 0.558 9.442 22266 Z= 0.283 Chirality : 0.043 0.432 2486 Planarity : 0.004 0.045 2872 Dihedral : 6.019 56.685 2539 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.11 % Allowed : 13.71 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.26 (0.18), residues: 1976 helix: -0.52 (0.25), residues: 434 sheet: -1.12 (0.24), residues: 454 loop : -2.13 (0.17), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 527 TYR 0.013 0.001 TYR B 106 PHE 0.025 0.001 PHE C 214 TRP 0.003 0.001 TRP A 538 HIS 0.006 0.001 HIS A 600 Details of bonding type rmsd covalent geometry : bond 0.00326 (16330) covalent geometry : angle 0.54094 (22104) SS BOND : bond 0.00687 ( 57) SS BOND : angle 1.17180 ( 114) hydrogen bonds : bond 0.03870 ( 419) hydrogen bonds : angle 5.16927 ( 1155) link_NAG-ASN : bond 0.00375 ( 16) link_NAG-ASN : angle 2.49509 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5178.58 seconds wall clock time: 88 minutes 58.00 seconds (5338.00 seconds total)