Starting phenix.real_space_refine on Mon Jul 6 00:13:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aml_11822/07_2026/7aml_11822_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aml_11822/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7aml_11822/07_2026/7aml_11822.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aml_11822/07_2026/7aml_11822.map" model { file = "/net/cci-nas-00/data/ceres_data/7aml_11822/07_2026/7aml_11822_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aml_11822/07_2026/7aml_11822_trim.cif" } 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-6108/lib/python3.11/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, 98 Ad-hoc single atom residues: {' CA': 4} Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain breaks: 4 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, 98 Ad-hoc single atom residues: {' CA': 4} Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain breaks: 4 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: 5.41, 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: 2.77 Conformation dependent library (CDL) restraints added in 684.6 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: 0.77 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: 6.41 Time building geometry restraints manager: 3.92 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: 0.03 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: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.210 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.190 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 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:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5781 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/Z covalent geometry : bond 0.00560 / 0.28 (16330) covalent geometry : angle 0.83620 / 0.48 (22104) SS BOND : bond 0.00635 / 0.43 ( 57) SS BOND : angle 1.42044 / 0.89 ( 114) hydrogen bonds : bond 0.25498 / 16.46 ( 419) hydrogen bonds : angle 10.02961 / 6.72 ( 1155) link_NAG-ASN : bond 0.00711 / 0.46 ( 16) link_NAG-ASN : angle 4.82188 / 3.03 ( 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 : 1.089 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: 0.2892 time to fit residues: 85.9488 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 : 0.875 ------------------------------------------------------------------------------- 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... 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 = 0.4773 r_free = 0.4773 target = 0.223675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.187686 restraints weight = 78702.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.192675 restraints weight = 39146.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.195833 restraints weight = 25207.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.197728 restraints weight = 19103.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.198935 restraints weight = 16155.067| |-----------------------------------------------------------------------------| r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4503 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4503 r_free = 0.4503 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4502 r_free = 0.4502 target_work(ls_wunit_k1) = 0.196 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.4502 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5864 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16403 Z= 0.137 Angle : 0.613 12.096 22266 Z= 0.313 Chirality : 0.048 0.668 2486 Planarity : 0.004 0.045 2872 Dihedral : 7.343 63.427 2551 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.95 % Allowed : 6.35 % 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: -1.37 (0.24), residues: 408 sheet: -1.62 (0.25), residues: 362 loop : -2.39 (0.16), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 591 TYR 0.012 0.001 TYR D 564 PHE 0.017 0.001 PHE D 611 TRP 0.005 0.001 TRP D 538 HIS 0.012 0.001 HIS A 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (16330) covalent geometry : angle 0.58606 / 0.31 (22104) SS BOND : bond 0.00674 / 0.41 ( 57) SS BOND : angle 1.03841 / 0.63 ( 114) hydrogen bonds : bond 0.04343 / 2.94 ( 419) hydrogen bonds : angle 6.52603 / 4.51 ( 1155) link_NAG-ASN : bond 0.00573 / 0.39 ( 16) link_NAG-ASN : angle 3.65220 / 2.28 ( 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: 17 poor density : 147 time to evaluate : 0.890 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 190 TYR cc_start: 0.5902 (m-80) cc_final: 0.5668 (m-80) REVERT: C 186 ASN cc_start: 0.6425 (m-40) cc_final: 0.6215 (m-40) REVERT: E 315 PHE cc_start: 0.5415 (t80) cc_final: 0.4730 (t80) outliers start: 17 outliers final: 13 residues processed: 162 average time/residue: 0.2812 time to fit residues: 68.4189 Evaluate side-chains 148 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 135 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 53 optimal weight: 0.0970 chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 12 optimal weight: 20.0000 chunk 144 optimal weight: 1.9990 chunk 182 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 ASN ** B 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.217010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.185536 restraints weight = 77588.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.185159 restraints weight = 48571.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.185532 restraints weight = 41359.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.186721 restraints weight = 32558.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.186663 restraints weight = 29721.983| |-----------------------------------------------------------------------------| r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4370 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4370 r_free = 0.4370 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4370 r_free = 0.4370 target_work(ls_wunit_k1) = 0.184 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (7 function evaluations) r_final: 0.4370 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6167 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 16403 Z= 0.157 Angle : 0.604 11.295 22266 Z= 0.310 Chirality : 0.047 0.599 2486 Planarity : 0.005 0.061 2872 Dihedral : 6.934 68.204 2546 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.56 % Allowed : 8.36 % Favored : 90.08 % 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: -2.82 (0.17), residues: 1976 helix: -1.04 (0.25), residues: 416 sheet: -1.38 (0.24), residues: 420 loop : -2.47 (0.16), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 591 TYR 0.018 0.002 TYR E 110 PHE 0.025 0.002 PHE C 214 TRP 0.004 0.001 TRP D 538 HIS 0.005 0.001 HIS A 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.16 (16330) covalent geometry : angle 0.57514 / 0.30 (22104) SS BOND : bond 0.00650 / 0.42 ( 57) SS BOND : angle 1.54663 / 0.88 ( 114) hydrogen bonds : bond 0.04540 / 2.97 ( 419) hydrogen bonds : angle 6.03313 / 4.19 ( 1155) link_NAG-ASN : bond 0.00552 / 0.36 ( 16) link_NAG-ASN : angle 3.33914 / 2.05 ( 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 167 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.960 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 MET cc_start: 0.5584 (tpt) cc_final: 0.5235 (tpt) outliers start: 28 outliers final: 18 residues processed: 160 average time/residue: 0.3078 time to fit residues: 72.0868 Evaluate side-chains 140 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.849 ------------------------------------------------------------------------------- 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 231 VAL Chi-restraints excluded: chain A residue 302 VAL Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 302 VAL 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 187 CYS Chi-restraints excluded: chain B residue 320 SER Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 187 CYS 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: 2.9990 chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 108 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 chunk 19 optimal weight: 7.9990 chunk 178 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 144 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 151 ASN E 151 ASN ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.216384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.182237 restraints weight = 77796.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.184088 restraints weight = 40456.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.184469 restraints weight = 31736.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.185156 restraints weight = 27698.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.185563 restraints weight = 26302.357| |-----------------------------------------------------------------------------| r_work (final): 0.4345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4345 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4345 r_free = 0.4345 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 = 0.4345 r_free = 0.4345 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4345 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6224 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16403 Z= 0.132 Angle : 0.553 10.584 22266 Z= 0.280 Chirality : 0.045 0.545 2486 Planarity : 0.004 0.048 2872 Dihedral : 6.370 58.957 2539 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.39 % Allowed : 10.26 % Favored : 88.35 % 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: -0.75 (0.25), residues: 414 sheet: -1.52 (0.23), residues: 458 loop : -2.29 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 527 TYR 0.026 0.001 TYR B 106 PHE 0.022 0.001 PHE F 214 TRP 0.005 0.001 TRP A 538 HIS 0.006 0.001 HIS A 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (16330) covalent geometry : angle 0.52897 / 0.27 (22104) SS BOND : bond 0.00575 / 0.39 ( 57) SS BOND : angle 1.12740 / 0.65 ( 114) hydrogen bonds : bond 0.03663 / 2.39 ( 419) hydrogen bonds : angle 5.59510 / 3.90 ( 1155) link_NAG-ASN : bond 0.00508 / 0.32 ( 16) link_NAG-ASN : angle 3.15768 / 1.93 ( 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 156 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.843 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: symmetry clash revert: symmetry clash REVERT: B 52 MET cc_start: 0.5806 (tpt) cc_final: 0.5493 (tpt) REVERT: E 106 TYR cc_start: 0.8365 (t80) cc_final: 0.8137 (t80) outliers start: 25 outliers final: 16 residues processed: 152 average time/residue: 0.2794 time to fit residues: 63.3420 Evaluate side-chains 132 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 572 ASN Chi-restraints excluded: chain D residue 159 ASN 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 101 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 190 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 147 optimal weight: 2.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4657 r_free = 0.4657 target = 0.212098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.178608 restraints weight = 77257.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.177806 restraints weight = 50699.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.179207 restraints weight = 38143.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.180460 restraints weight = 30176.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.180422 restraints weight = 28000.390| |-----------------------------------------------------------------------------| r_work (final): 0.4304 ------------------------------------------------------------------------------- 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: 2 | |-----------------------------------------------------------------------------| |-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: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.113 16403 Z= 0.187 Angle : 0.623 10.918 22266 Z= 0.320 Chirality : 0.046 0.552 2486 Planarity : 0.005 0.059 2872 Dihedral : 6.621 58.537 2539 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 1.56 % Allowed : 12.04 % Favored : 86.40 % 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: -2.89 (0.17), residues: 1976 helix: -1.23 (0.23), residues: 432 sheet: -1.43 (0.23), residues: 470 loop : -2.50 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 170 TYR 0.015 0.002 TYR B 124 PHE 0.031 0.002 PHE C 214 TRP 0.004 0.001 TRP B 107 HIS 0.006 0.001 HIS D 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (16330) covalent geometry : angle 0.59827 / 0.31 (22104) SS BOND : bond 0.00737 / 0.46 ( 57) SS BOND : angle 1.41248 / 0.84 ( 114) hydrogen bonds : bond 0.04690 / 3.08 ( 419) hydrogen bonds : angle 5.76660 / 4.01 ( 1155) link_NAG-ASN : bond 0.00430 / 0.27 ( 16) link_NAG-ASN : angle 3.22731 / 1.94 ( 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 149 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.5520 (tpt) cc_final: 0.5220 (tpt) outliers start: 28 outliers final: 21 residues processed: 144 average time/residue: 0.2885 time to fit residues: 62.4137 Evaluate side-chains 138 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 138 ASP 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 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 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 Chi-restraints excluded: chain F residue 216 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: 6.9990 chunk 84 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 76 optimal weight: 0.0980 chunk 95 optimal weight: 1.9990 chunk 170 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4661 r_free = 0.4661 target = 0.212557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.176640 restraints weight = 76808.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.179179 restraints weight = 40187.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.180544 restraints weight = 29228.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.180790 restraints weight = 27275.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.180986 restraints weight = 24976.215| |-----------------------------------------------------------------------------| r_work (final): 0.4297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4299 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4299 r_free = 0.4299 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4299 r_free = 0.4299 target_work(ls_wunit_k1) = 0.178 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (21 function evaluations) r_final: 0.4299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16403 Z= 0.149 Angle : 0.568 10.664 22266 Z= 0.289 Chirality : 0.045 0.521 2486 Planarity : 0.004 0.047 2872 Dihedral : 6.365 57.865 2539 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.45 % Allowed : 12.71 % Favored : 85.84 % 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: -2.77 (0.17), residues: 1976 helix: -1.04 (0.24), residues: 432 sheet: -1.40 (0.23), residues: 482 loop : -2.44 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 527 TYR 0.015 0.002 TYR B 106 PHE 0.023 0.001 PHE F 214 TRP 0.006 0.001 TRP A 538 HIS 0.005 0.001 HIS A 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (16330) covalent geometry : angle 0.54474 / 0.28 (22104) SS BOND : bond 0.00578 / 0.37 ( 57) SS BOND : angle 1.17470 / 0.70 ( 114) hydrogen bonds : bond 0.03984 / 2.61 ( 419) hydrogen bonds : angle 5.53456 / 3.86 ( 1155) link_NAG-ASN : bond 0.00473 / 0.29 ( 16) link_NAG-ASN : angle 3.10212 / 1.86 ( 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: 26 poor density : 127 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.5838 (tpt) cc_final: 0.5535 (tpt) REVERT: E 333 GLU cc_start: 0.5126 (OUTLIER) cc_final: 0.3996 (tm-30) outliers start: 26 outliers final: 19 residues processed: 146 average time/residue: 0.2852 time to fit residues: 61.6836 Evaluate side-chains 139 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.902 ------------------------------------------------------------------------------- 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 479 ILE Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain D residue 159 ASN 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 174 ILE Chi-restraints excluded: chain B residue 247 LEU 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 333 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 11 optimal weight: 8.9990 chunk 148 optimal weight: 1.9990 chunk 151 optimal weight: 0.3980 chunk 144 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 113 optimal weight: 0.0980 chunk 2 optimal weight: 9.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.4659 r_free = 0.4659 target = 0.212335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.178971 restraints weight = 76867.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.178487 restraints weight = 54673.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.179704 restraints weight = 40969.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.180884 restraints weight = 33419.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.181111 restraints weight = 29621.336| |-----------------------------------------------------------------------------| r_work (final): 0.4302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4301 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4301 r_free = 0.4301 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4301 r_free = 0.4301 target_work(ls_wunit_k1) = 0.179 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4301 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6299 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16403 Z= 0.139 Angle : 0.554 10.278 22266 Z= 0.282 Chirality : 0.044 0.500 2486 Planarity : 0.004 0.049 2872 Dihedral : 6.227 59.462 2539 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.11 % Allowed : 13.38 % 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: -2.68 (0.17), residues: 1976 helix: -0.93 (0.24), residues: 434 sheet: -1.37 (0.24), residues: 458 loop : -2.37 (0.17), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 527 TYR 0.011 0.001 TYR F 158 PHE 0.022 0.001 PHE C 214 TRP 0.005 0.001 TRP A 538 HIS 0.005 0.001 HIS A 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 (16330) covalent geometry : angle 0.53214 / 0.28 (22104) SS BOND : bond 0.00572 / 0.38 ( 57) SS BOND : angle 1.19188 / 0.70 ( 114) hydrogen bonds : bond 0.03934 / 2.59 ( 419) hydrogen bonds : angle 5.37836 / 3.75 ( 1155) link_NAG-ASN : bond 0.00442 / 0.26 ( 16) link_NAG-ASN : angle 2.96396 / 1.76 ( 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 147 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 52 MET cc_start: 0.5475 (tpt) cc_final: 0.5167 (tpt) REVERT: E 284 ASN cc_start: 0.6914 (m110) cc_final: 0.6660 (p0) outliers start: 20 outliers final: 16 residues processed: 145 average time/residue: 0.2846 time to fit residues: 61.3176 Evaluate side-chains 137 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 121 time to evaluate : 0.827 ------------------------------------------------------------------------------- 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 572 ASN Chi-restraints excluded: chain D residue 159 ASN Chi-restraints excluded: chain D residue 259 ASN Chi-restraints excluded: chain D residue 478 VAL Chi-restraints excluded: chain D residue 572 ASN Chi-restraints excluded: chain D residue 607 GLU 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 276 SER 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: 0.9990 chunk 161 optimal weight: 0.8980 chunk 136 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 144 optimal weight: 0.0970 chunk 74 optimal weight: 10.0000 chunk 148 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 66 optimal weight: 0.0670 chunk 76 optimal weight: 0.3980 chunk 72 optimal weight: 0.4980 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.214633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.180098 restraints weight = 76768.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.181823 restraints weight = 39342.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.182879 restraints weight = 31170.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.183950 restraints weight = 25686.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.184248 restraints weight = 24026.228| |-----------------------------------------------------------------------------| r_work (final): 0.4342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4340 r_free = 0.4340 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4340 r_free = 0.4340 target_work(ls_wunit_k1) = 0.182 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 0.4766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16403 Z= 0.091 Angle : 0.513 9.677 22266 Z= 0.257 Chirality : 0.043 0.465 2486 Planarity : 0.004 0.047 2872 Dihedral : 5.888 59.854 2539 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.67 % Allowed : 13.82 % 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: -2.38 (0.18), residues: 1976 helix: -0.66 (0.24), residues: 460 sheet: -1.18 (0.24), residues: 454 loop : -2.22 (0.17), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 527 TYR 0.017 0.001 TYR C 180 PHE 0.011 0.001 PHE C 214 TRP 0.007 0.000 TRP A 538 HIS 0.006 0.001 HIS D 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.09 (16330) covalent geometry : angle 0.49419 / 0.25 (22104) SS BOND : bond 0.00537 / 0.29 ( 57) SS BOND : angle 0.88725 / 0.52 ( 114) hydrogen bonds : bond 0.03101 / 2.00 ( 419) hydrogen bonds : angle 5.03855 / 3.51 ( 1155) link_NAG-ASN : bond 0.00510 / 0.30 ( 16) link_NAG-ASN : angle 2.78231 / 1.66 ( 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 142 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 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: symmetry clash revert: symmetry clash REVERT: B 52 MET cc_start: 0.5740 (tpt) cc_final: 0.5438 (tpt) REVERT: B 122 SER cc_start: 0.5916 (m) cc_final: 0.4929 (p) outliers start: 12 outliers final: 9 residues processed: 141 average time/residue: 0.2809 time to fit residues: 58.7790 Evaluate side-chains 134 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 125 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 572 ASN 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 E residue 276 SER Chi-restraints excluded: chain F residue 169 CYS Chi-restraints excluded: chain F residue 203 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 179 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 153 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 146 optimal weight: 1.9990 chunk 149 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 186 optimal weight: 0.8980 chunk 180 optimal weight: 0.7980 chunk 156 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.218858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.185328 restraints weight = 81189.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.186519 restraints weight = 45201.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.186785 restraints weight = 33865.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.186919 restraints weight = 30833.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.188733 restraints weight = 29028.943| |-----------------------------------------------------------------------------| r_work (final): 0.4407 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4409 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4409 r_free = 0.4409 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4409 r_free = 0.4409 target_work(ls_wunit_k1) = 0.185 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.4409 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6325 moved from start: 0.4938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16403 Z= 0.114 Angle : 0.523 9.475 22266 Z= 0.264 Chirality : 0.043 0.460 2486 Planarity : 0.004 0.045 2872 Dihedral : 5.884 58.713 2539 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.72 % Allowed : 14.33 % Favored : 84.95 % 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: -0.66 (0.24), residues: 458 sheet: -1.16 (0.24), residues: 458 loop : -2.21 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 527 TYR 0.015 0.001 TYR B 106 PHE 0.018 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/Z covalent geometry : bond 0.00266 / 0.11 (16330) covalent geometry : angle 0.50490 / 0.26 (22104) SS BOND : bond 0.00634 / 0.35 ( 57) SS BOND : angle 0.96465 / 0.56 ( 114) hydrogen bonds : bond 0.03494 / 2.28 ( 419) hydrogen bonds : angle 5.06928 / 3.52 ( 1155) link_NAG-ASN : bond 0.00447 / 0.26 ( 16) link_NAG-ASN : angle 2.73294 / 1.62 ( 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 140 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 127 time to evaluate : 0.837 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: D 230 MET cc_start: 0.6884 (mpp) cc_final: 0.6019 (mtm) REVERT: B 52 MET cc_start: 0.5721 (tpt) cc_final: 0.5421 (tpt) REVERT: B 122 SER cc_start: 0.5605 (m) cc_final: 0.4633 (p) outliers start: 13 outliers final: 10 residues processed: 138 average time/residue: 0.2841 time to fit residues: 57.8451 Evaluate side-chains 133 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 ASN 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 186 ASN Chi-restraints excluded: chain E residue 87 LEU Chi-restraints excluded: chain E residue 276 SER 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: 2.9990 chunk 109 optimal weight: 0.9990 chunk 193 optimal weight: 0.2980 chunk 183 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 chunk 176 optimal weight: 0.0970 chunk 166 optimal weight: 0.0980 chunk 24 optimal weight: 0.0270 chunk 150 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 overall best weight: 0.3038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4777 r_free = 0.4777 target = 0.220935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.188007 restraints weight = 81547.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.189682 restraints weight = 47378.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.189681 restraints weight = 33328.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.190695 restraints weight = 32042.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.190839 restraints weight = 30633.219| |-----------------------------------------------------------------------------| r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4447 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4447 r_free = 0.4447 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4447 r_free = 0.4447 target_work(ls_wunit_k1) = 0.188 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.4447 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6255 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 16403 Z= 0.088 Angle : 0.497 8.940 22266 Z= 0.248 Chirality : 0.042 0.437 2486 Planarity : 0.003 0.046 2872 Dihedral : 5.559 56.440 2539 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.61 % Allowed : 14.44 % Favored : 84.95 % 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: -2.03 (0.18), residues: 1976 helix: -0.22 (0.25), residues: 448 sheet: -1.00 (0.24), residues: 454 loop : -2.05 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 527 TYR 0.020 0.001 TYR B 106 PHE 0.009 0.001 PHE C 214 TRP 0.007 0.001 TRP A 538 HIS 0.005 0.001 HIS A 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.09 (16330) covalent geometry : angle 0.48084 / 0.24 (22104) SS BOND : bond 0.00467 / 0.26 ( 57) SS BOND : angle 0.81181 / 0.46 ( 114) hydrogen bonds : bond 0.02939 / 1.87 ( 419) hydrogen bonds : angle 4.85405 / 3.37 ( 1155) link_NAG-ASN : bond 0.00497 / 0.29 ( 16) link_NAG-ASN : angle 2.58455 / 1.54 ( 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: 11 poor density : 123 time to evaluate : 0.815 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: symmetry clash revert: symmetry clash REVERT: B 52 MET cc_start: 0.5674 (tpt) cc_final: 0.5371 (tpt) outliers start: 11 outliers final: 10 residues processed: 133 average time/residue: 0.2899 time to fit residues: 56.7548 Evaluate side-chains 128 residues out of total 1794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 118 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 ASN Chi-restraints excluded: chain A residue 603 CYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 128 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 190 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 178 optimal weight: 0.6980 chunk 179 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 158 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.220711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.187294 restraints weight = 81717.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.188834 restraints weight = 46908.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.189272 restraints weight = 36923.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.190119 restraints weight = 31025.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.190129 restraints weight = 27620.858| |-----------------------------------------------------------------------------| r_work (final): 0.4449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4437 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4437 r_free = 0.4437 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4437 r_free = 0.4437 target_work(ls_wunit_k1) = 0.187 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 0 (3 function evaluations) r_final: 0.4437 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6276 moved from start: 0.5018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.225 16403 Z= 0.138 Angle : 0.715 59.198 22266 Z= 0.397 Chirality : 0.043 0.437 2486 Planarity : 0.003 0.046 2872 Dihedral : 5.559 56.336 2539 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.72 % Allowed : 14.49 % Favored : 84.78 % 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: -2.02 (0.18), residues: 1976 helix: -0.21 (0.25), residues: 448 sheet: -0.99 (0.24), residues: 454 loop : -2.04 (0.17), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 527 TYR 0.016 0.001 TYR B 106 PHE 0.010 0.001 PHE C 214 TRP 0.007 0.001 TRP A 538 HIS 0.005 0.001 HIS A 600 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (16330) covalent geometry : angle 0.70436 / 0.40 (22104) SS BOND : bond 0.00515 / 0.28 ( 57) SS BOND : angle 0.85188 / 0.48 ( 114) hydrogen bonds : bond 0.03008 / 1.93 ( 419) hydrogen bonds : angle 4.86266 / 3.37 ( 1155) link_NAG-ASN : bond 0.00485 / 0.28 ( 16) link_NAG-ASN : angle 2.58218 / 1.53 ( 48) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4920.06 seconds wall clock time: 84 minutes 38.97 seconds (5078.97 seconds total)