Starting phenix.real_space_refine on Sat Mar 7 15:08:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nnl_49577/03_2026/9nnl_49577_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nnl_49577/03_2026/9nnl_49577.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nnl_49577/03_2026/9nnl_49577.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nnl_49577/03_2026/9nnl_49577.map" model { file = "/net/cci-nas-00/data/ceres_data/9nnl_49577/03_2026/9nnl_49577_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nnl_49577/03_2026/9nnl_49577_trim.cif" } resolution = 2.42 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= 0.007 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 14 5.49 5 Mg 2 5.21 5 S 150 5.16 5 C 14118 2.51 5 N 3832 2.21 5 O 4631 1.98 5 H 21452 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 44199 Number of models: 1 Model: "" Number of chains: 26 Chain: "B" Number of atoms: 6659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 6659 Classifications: {'peptide': 432} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain: "C" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1687 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "D" Number of atoms: 6659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 6659 Classifications: {'peptide': 432} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain: "F" Number of atoms: 6660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 6660 Classifications: {'peptide': 432} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain: "G" Number of atoms: 1687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1687 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 6659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 6659 Classifications: {'peptide': 432} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 411} Chain: "A" Number of atoms: 6732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6732 Classifications: {'peptide': 436} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain breaks: 1 Chain: "E" Number of atoms: 6731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 6731 Classifications: {'peptide': 436} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain breaks: 1 Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 38 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 62 Unusual residues: {'TA1': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "F" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "G" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "H" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 35 Classifications: {'water': 35} Link IDs: {None: 34} Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "E" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 46 Classifications: {'water': 46} Link IDs: {None: 45} Time building chain proxies: 8.51, per 1000 atoms: 0.19 Number of scatterers: 44199 At special positions: 0 Unit cell: (92.092, 143.52, 163.852, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 150 16.00 P 14 15.00 Mg 2 11.99 O 4631 8.00 N 3832 7.00 C 14118 6.00 H 21452 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 129 " distance=2.07 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 129 " distance=2.07 Simple disulfide: pdb=" SG CYS F 127 " - pdb=" SG CYS F 129 " distance=2.03 Simple disulfide: pdb=" SG CYS H 127 " - pdb=" SG CYS H 129 " distance=2.07 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.92 Conformation dependent library (CDL) restraints added in 2.2 seconds 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5192 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 18 sheets defined 50.9% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'B' and resid 10 through 29 removed outlier: 3.625A pdb=" N LYS B 19 " --> pdb=" O GLN B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 49 Processing helix chain 'B' and resid 70 through 78 Processing helix chain 'B' and resid 86 through 88 No H-bonds generated for 'chain 'B' and resid 86 through 88' Processing helix chain 'B' and resid 100 through 106 Processing helix chain 'B' and resid 109 through 125 removed outlier: 4.697A pdb=" N ASP B 114 " --> pdb=" O ALA B 110 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N SER B 115 " --> pdb=" O GLU B 111 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 Processing helix chain 'B' and resid 180 through 196 removed outlier: 3.536A pdb=" N HIS B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLN B 191 " --> pdb=" O LEU B 187 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU B 194 " --> pdb=" O HIS B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 214 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.593A pdb=" N THR B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 242 removed outlier: 3.909A pdb=" N ARG B 241 " --> pdb=" O THR B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 258 Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.992A pdb=" N ARG B 282 " --> pdb=" O GLN B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 294 removed outlier: 3.513A pdb=" N PHE B 294 " --> pdb=" O THR B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 299 removed outlier: 3.675A pdb=" N MET B 299 " --> pdb=" O ALA B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 322 through 337 Processing helix chain 'B' and resid 338 through 341 removed outlier: 3.556A pdb=" N PHE B 341 " --> pdb=" O SER B 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 338 through 341' Processing helix chain 'B' and resid 374 through 391 removed outlier: 3.534A pdb=" N PHE B 378 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU B 383 " --> pdb=" O LYS B 379 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG B 391 " --> pdb=" O ALA B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 404 through 425 removed outlier: 3.856A pdb=" N PHE B 408 " --> pdb=" O ASP B 404 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TYR B 425 " --> pdb=" O GLU B 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 3620 through 3635 Processing helix chain 'C' and resid 3666 through 3674 Processing helix chain 'D' and resid 10 through 29 removed outlier: 3.526A pdb=" N LYS D 19 " --> pdb=" O GLN D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 removed outlier: 4.646A pdb=" N ARG D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 70 through 78 Processing helix chain 'D' and resid 86 through 88 No H-bonds generated for 'chain 'D' and resid 86 through 88' Processing helix chain 'D' and resid 100 through 106 Processing helix chain 'D' and resid 107 through 125 removed outlier: 3.953A pdb=" N GLU D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU D 112 " --> pdb=" O GLU D 108 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N ASP D 114 " --> pdb=" O ALA D 110 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N SER D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL D 116 " --> pdb=" O LEU D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 159 Processing helix chain 'D' and resid 180 through 196 removed outlier: 3.617A pdb=" N HIS D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU D 194 " --> pdb=" O HIS D 190 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N THR D 196 " --> pdb=" O LEU D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 214 Processing helix chain 'D' and resid 221 through 242 removed outlier: 3.579A pdb=" N THR D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N CYS D 239 " --> pdb=" O GLY D 235 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N LEU D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG D 241 " --> pdb=" O THR D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 258 Processing helix chain 'D' and resid 278 through 282 Processing helix chain 'D' and resid 285 through 295 removed outlier: 3.604A pdb=" N PHE D 294 " --> pdb=" O THR D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 299 removed outlier: 3.640A pdb=" N MET D 299 " --> pdb=" O ALA D 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 296 through 299' Processing helix chain 'D' and resid 304 through 308 Processing helix chain 'D' and resid 322 through 337 removed outlier: 3.584A pdb=" N GLN D 334 " --> pdb=" O MET D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 341 removed outlier: 3.743A pdb=" N PHE D 341 " --> pdb=" O SER D 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 338 through 341' Processing helix chain 'D' and resid 373 through 392 removed outlier: 4.277A pdb=" N LEU D 377 " --> pdb=" O ALA D 373 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 404 through 425 removed outlier: 3.743A pdb=" N PHE D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N TYR D 425 " --> pdb=" O GLU D 421 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 29 removed outlier: 3.514A pdb=" N LYS F 19 " --> pdb=" O GLN F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 46 removed outlier: 3.541A pdb=" N GLU F 45 " --> pdb=" O ASP F 41 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ARG F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 41 through 46' Processing helix chain 'F' and resid 47 through 49 No H-bonds generated for 'chain 'F' and resid 47 through 49' Processing helix chain 'F' and resid 70 through 78 Processing helix chain 'F' and resid 86 through 88 No H-bonds generated for 'chain 'F' and resid 86 through 88' Processing helix chain 'F' and resid 100 through 106 Processing helix chain 'F' and resid 112 through 125 removed outlier: 3.545A pdb=" N VAL F 116 " --> pdb=" O LEU F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 159 removed outlier: 3.544A pdb=" N LEU F 150 " --> pdb=" O GLY F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 196 removed outlier: 3.748A pdb=" N GLN F 191 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLU F 194 " --> pdb=" O HIS F 190 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR F 196 " --> pdb=" O LEU F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 204 through 214 Processing helix chain 'F' and resid 221 through 242 removed outlier: 3.604A pdb=" N THR F 232 " --> pdb=" O LEU F 228 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR F 237 " --> pdb=" O MET F 233 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N CYS F 239 " --> pdb=" O GLY F 235 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LEU F 240 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG F 241 " --> pdb=" O THR F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 258 Processing helix chain 'F' and resid 278 through 282 removed outlier: 3.707A pdb=" N TYR F 281 " --> pdb=" O SER F 278 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG F 282 " --> pdb=" O GLN F 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 278 through 282' Processing helix chain 'F' and resid 285 through 294 Processing helix chain 'F' and resid 295 through 299 Processing helix chain 'F' and resid 304 through 308 Processing helix chain 'F' and resid 322 through 337 removed outlier: 3.615A pdb=" N GLN F 334 " --> pdb=" O MET F 330 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 341 removed outlier: 3.558A pdb=" N PHE F 341 " --> pdb=" O SER F 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 338 through 341' Processing helix chain 'F' and resid 374 through 391 removed outlier: 3.510A pdb=" N PHE F 378 " --> pdb=" O ILE F 374 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG F 391 " --> pdb=" O ALA F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 400 Processing helix chain 'F' and resid 404 through 428 removed outlier: 3.744A pdb=" N PHE F 408 " --> pdb=" O ASP F 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 3620 through 3635 Processing helix chain 'G' and resid 3666 through 3674 Processing helix chain 'H' and resid 10 through 29 Processing helix chain 'H' and resid 46 through 49 Processing helix chain 'H' and resid 70 through 78 Processing helix chain 'H' and resid 86 through 88 No H-bonds generated for 'chain 'H' and resid 86 through 88' Processing helix chain 'H' and resid 100 through 106 Processing helix chain 'H' and resid 108 through 125 removed outlier: 3.605A pdb=" N LEU H 112 " --> pdb=" O GLU H 108 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP H 114 " --> pdb=" O ALA H 110 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N SER H 115 " --> pdb=" O GLU H 111 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 159 removed outlier: 3.639A pdb=" N THR H 149 " --> pdb=" O SER H 145 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU H 150 " --> pdb=" O GLY H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 180 through 196 removed outlier: 3.687A pdb=" N GLN H 191 " --> pdb=" O LEU H 187 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU H 194 " --> pdb=" O HIS H 190 " (cutoff:3.500A) Processing helix chain 'H' and resid 204 through 213 Processing helix chain 'H' and resid 221 through 237 removed outlier: 3.508A pdb=" N THR H 232 " --> pdb=" O LEU H 228 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR H 237 " --> pdb=" O MET H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 241 Processing helix chain 'H' and resid 249 through 258 Processing helix chain 'H' and resid 277 through 282 removed outlier: 3.619A pdb=" N GLN H 280 " --> pdb=" O GLY H 277 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG H 282 " --> pdb=" O GLN H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 285 through 294 removed outlier: 3.513A pdb=" N PHE H 294 " --> pdb=" O THR H 290 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 299 Processing helix chain 'H' and resid 304 through 308 Processing helix chain 'H' and resid 322 through 337 removed outlier: 3.616A pdb=" N GLN H 334 " --> pdb=" O MET H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 341 Processing helix chain 'H' and resid 374 through 391 removed outlier: 3.560A pdb=" N PHE H 378 " --> pdb=" O ILE H 374 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG H 391 " --> pdb=" O ALA H 387 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 400 Processing helix chain 'H' and resid 404 through 427 removed outlier: 3.789A pdb=" N PHE H 408 " --> pdb=" O ASP H 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 28 removed outlier: 3.592A pdb=" N ALA A 19 " --> pdb=" O GLN A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 80 removed outlier: 4.848A pdb=" N ILE A 75 " --> pdb=" O GLU A 71 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 108 Processing helix chain 'A' and resid 110 through 113 Processing helix chain 'A' and resid 114 through 129 removed outlier: 4.094A pdb=" N CYS A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.242A pdb=" N THR A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP A 160 " --> pdb=" O ARG A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 198 removed outlier: 3.680A pdb=" N THR A 193 " --> pdb=" O LEU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.576A pdb=" N ILE A 209 " --> pdb=" O ASP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 3.728A pdb=" N LEU A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE A 234 " --> pdb=" O LEU A 230 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER A 241 " --> pdb=" O SER A 237 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 260 removed outlier: 3.656A pdb=" N PHE A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N GLN A 256 " --> pdb=" O LEU A 252 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N THR A 257 " --> pdb=" O THR A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.887A pdb=" N HIS A 283 " --> pdb=" O GLU A 279 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU A 284 " --> pdb=" O LYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 296 removed outlier: 3.617A pdb=" N PHE A 296 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 306 through 310 Processing helix chain 'A' and resid 324 through 336 Processing helix chain 'A' and resid 383 through 401 removed outlier: 4.075A pdb=" N ALA A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LYS A 401 " --> pdb=" O LEU A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.795A pdb=" N TYR A 408 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 436 removed outlier: 4.057A pdb=" N SER A 419 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 29 Processing helix chain 'E' and resid 72 through 80 removed outlier: 3.520A pdb=" N VAL E 78 " --> pdb=" O VAL E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 108 Processing helix chain 'E' and resid 110 through 113 Processing helix chain 'E' and resid 114 through 129 removed outlier: 4.050A pdb=" N CYS E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 161 removed outlier: 4.063A pdb=" N THR E 150 " --> pdb=" O GLY E 146 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N VAL E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP E 160 " --> pdb=" O ARG E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 198 removed outlier: 3.709A pdb=" N THR E 193 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 217 Processing helix chain 'E' and resid 223 through 244 removed outlier: 3.649A pdb=" N LEU E 227 " --> pdb=" O THR E 223 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N SER E 241 " --> pdb=" O SER E 237 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N LEU E 242 " --> pdb=" O ILE E 238 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 260 removed outlier: 4.030A pdb=" N GLN E 256 " --> pdb=" O LEU E 252 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 282 removed outlier: 3.645A pdb=" N TYR E 282 " --> pdb=" O ALA E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 296 removed outlier: 3.687A pdb=" N PHE E 296 " --> pdb=" O THR E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 301 Processing helix chain 'E' and resid 306 through 310 Processing helix chain 'E' and resid 324 through 336 Processing helix chain 'E' and resid 383 through 400 removed outlier: 3.996A pdb=" N ALA E 387 " --> pdb=" O ALA E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 410 removed outlier: 3.854A pdb=" N TYR E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) Processing helix chain 'E' and resid 415 through 435 removed outlier: 3.909A pdb=" N SER E 419 " --> pdb=" O GLU E 415 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 90 through 92 removed outlier: 8.171A pdb=" N VAL B 91 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU B 65 " --> pdb=" O VAL B 91 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N ILE B 64 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N HIS B 6 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N VAL B 66 " --> pdb=" O HIS B 6 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N GLN B 8 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N SER B 138 " --> pdb=" O ALA B 9 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N PHE B 133 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N PHE B 167 " --> pdb=" O PHE B 133 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU B 135 " --> pdb=" O PHE B 167 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N VAL B 169 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N HIS B 137 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N ASP B 203 " --> pdb=" O PRO B 268 " (cutoff:3.500A) removed outlier: 11.733A pdb=" N PHE B 270 " --> pdb=" O ASP B 203 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N PHE B 265 " --> pdb=" O SER B 371 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N SER B 371 " --> pdb=" O PHE B 265 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 3648 through 3652 Processing sheet with id=AA4, first strand: chain 'C' and resid 3677 through 3681 Processing sheet with id=AA5, first strand: chain 'D' and resid 90 through 92 removed outlier: 8.112A pdb=" N VAL D 91 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N LEU D 65 " --> pdb=" O VAL D 91 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ILE D 64 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N HIS D 6 " --> pdb=" O ILE D 64 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N VAL D 66 " --> pdb=" O HIS D 6 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLN D 8 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N SER D 138 " --> pdb=" O ALA D 9 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE D 133 " --> pdb=" O ASN D 165 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N PHE D 167 " --> pdb=" O PHE D 133 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU D 135 " --> pdb=" O PHE D 167 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL D 169 " --> pdb=" O LEU D 135 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N HIS D 137 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N MET D 164 " --> pdb=" O GLU D 198 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N TYR D 200 " --> pdb=" O MET D 164 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR D 166 " --> pdb=" O TYR D 200 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ILE D 202 " --> pdb=" O THR D 166 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N SER D 168 " --> pdb=" O ILE D 202 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N THR D 199 " --> pdb=" O PHE D 266 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N CYS D 201 " --> pdb=" O PRO D 268 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N PHE D 270 " --> pdb=" O CYS D 201 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N PHE D 265 " --> pdb=" O SER D 371 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N SER D 371 " --> pdb=" O PHE D 265 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 51 through 54 Processing sheet with id=AA7, first strand: chain 'F' and resid 90 through 92 removed outlier: 8.125A pdb=" N VAL F 91 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N LEU F 65 " --> pdb=" O VAL F 91 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N ILE F 64 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N HIS F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N VAL F 66 " --> pdb=" O HIS F 6 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N GLN F 8 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLU F 3 " --> pdb=" O LEU F 130 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N SER F 138 " --> pdb=" O ALA F 9 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N GLN F 131 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ASN F 165 " --> pdb=" O GLN F 131 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N PHE F 133 " --> pdb=" O ASN F 165 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N PHE F 167 " --> pdb=" O PHE F 133 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N LEU F 135 " --> pdb=" O PHE F 167 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N VAL F 169 " --> pdb=" O LEU F 135 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N HIS F 137 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N MET F 164 " --> pdb=" O GLU F 198 " (cutoff:3.500A) removed outlier: 8.286A pdb=" N TYR F 200 " --> pdb=" O MET F 164 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N THR F 166 " --> pdb=" O TYR F 200 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N ILE F 202 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N SER F 168 " --> pdb=" O ILE F 202 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR F 199 " --> pdb=" O PHE F 266 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N CYS F 201 " --> pdb=" O PRO F 268 " (cutoff:3.500A) removed outlier: 10.374A pdb=" N PHE F 270 " --> pdb=" O CYS F 201 " (cutoff:3.500A) removed outlier: 13.870A pdb=" N ASP F 203 " --> pdb=" O PHE F 270 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N PHE F 265 " --> pdb=" O SER F 371 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N SER F 371 " --> pdb=" O PHE F 265 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 51 through 54 Processing sheet with id=AA9, first strand: chain 'G' and resid 3648 through 3653 Processing sheet with id=AB1, first strand: chain 'G' and resid 3677 through 3681 Processing sheet with id=AB2, first strand: chain 'H' and resid 90 through 92 removed outlier: 8.163A pdb=" N VAL H 91 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N LEU H 65 " --> pdb=" O VAL H 91 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL H 5 " --> pdb=" O GLN H 134 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N THR H 136 " --> pdb=" O VAL H 5 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE H 7 " --> pdb=" O THR H 136 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N SER H 138 " --> pdb=" O ILE H 7 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N ALA H 9 " --> pdb=" O SER H 138 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N PHE H 133 " --> pdb=" O ASN H 165 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N PHE H 167 " --> pdb=" O PHE H 133 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU H 135 " --> pdb=" O PHE H 167 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL H 169 " --> pdb=" O LEU H 135 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N HIS H 137 " --> pdb=" O VAL H 169 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N MET H 164 " --> pdb=" O GLU H 198 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N TYR H 200 " --> pdb=" O MET H 164 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N THR H 166 " --> pdb=" O TYR H 200 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N ILE H 202 " --> pdb=" O THR H 166 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER H 168 " --> pdb=" O ILE H 202 " (cutoff:3.500A) removed outlier: 8.435A pdb=" N ASP H 203 " --> pdb=" O PRO H 268 " (cutoff:3.500A) removed outlier: 11.941A pdb=" N PHE H 270 " --> pdb=" O ASP H 203 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N PHE H 265 " --> pdb=" O SER H 371 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N SER H 371 " --> pdb=" O PHE H 265 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 51 through 54 removed outlier: 4.300A pdb=" N LYS H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 65 through 68 removed outlier: 5.786A pdb=" N GLU A 3 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N GLY A 134 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N GLN A 133 " --> pdb=" O SER A 165 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N LEU A 167 " --> pdb=" O GLN A 133 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N PHE A 135 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N PHE A 169 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N VAL A 137 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N ILE A 171 " --> pdb=" O VAL A 137 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LYS A 166 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.301A pdb=" N PHE A 202 " --> pdb=" O LYS A 166 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU A 168 " --> pdb=" O PHE A 202 " (cutoff:3.500A) removed outlier: 8.141A pdb=" N VAL A 204 " --> pdb=" O GLU A 168 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N SER A 170 " --> pdb=" O VAL A 204 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 53 through 55 Processing sheet with id=AB6, first strand: chain 'A' and resid 269 through 272 Processing sheet with id=AB7, first strand: chain 'E' and resid 65 through 68 removed outlier: 8.296A pdb=" N VAL E 66 " --> pdb=" O CYS E 4 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N SER E 6 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N VAL E 68 " --> pdb=" O SER E 6 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N HIS E 8 " --> pdb=" O VAL E 68 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N GLU E 3 " --> pdb=" O LEU E 132 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY E 134 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N GLN E 133 " --> pdb=" O SER E 165 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N LEU E 167 " --> pdb=" O GLN E 133 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N PHE E 135 " --> pdb=" O LEU E 167 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N PHE E 169 " --> pdb=" O PHE E 135 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N VAL E 137 " --> pdb=" O PHE E 169 " (cutoff:3.500A) removed outlier: 7.626A pdb=" N ILE E 171 " --> pdb=" O VAL E 137 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LYS E 166 " --> pdb=" O CYS E 200 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N PHE E 202 " --> pdb=" O LYS E 166 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N GLU E 168 " --> pdb=" O PHE E 202 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL E 204 " --> pdb=" O GLU E 168 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N SER E 170 " --> pdb=" O VAL E 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 53 through 55 Processing sheet with id=AB9, first strand: chain 'E' and resid 269 through 272 1056 hydrogen bonds defined for protein. 3003 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: 11.87 Time building geometry restraints manager: 5.42 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: 21380 1.02 - 1.22: 171 1.22 - 1.42: 9684 1.42 - 1.62: 12975 1.62 - 1.82: 244 Bond restraints: 44454 Sorted by residual: bond pdb=" C MET B 267 " pdb=" O MET B 267 " ideal model delta sigma weight residual 1.240 1.148 0.092 1.14e-02 7.69e+03 6.55e+01 bond pdb=" C SER F 126 " pdb=" O SER F 126 " ideal model delta sigma weight residual 1.237 1.154 0.083 1.16e-02 7.43e+03 5.06e+01 bond pdb=" C PHE B 266 " pdb=" O PHE B 266 " ideal model delta sigma weight residual 1.234 1.151 0.083 1.26e-02 6.30e+03 4.39e+01 bond pdb=" C MET F 267 " pdb=" O MET F 267 " ideal model delta sigma weight residual 1.240 1.170 0.070 1.14e-02 7.69e+03 3.78e+01 bond pdb=" C ASP G3632 " pdb=" O ASP G3632 " ideal model delta sigma weight residual 1.236 1.161 0.075 1.22e-02 6.72e+03 3.76e+01 ... (remaining 44449 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 79230 2.38 - 4.76: 652 4.76 - 7.14: 76 7.14 - 9.51: 9 9.51 - 11.89: 5 Bond angle restraints: 79972 Sorted by residual: angle pdb=" N GLN A 233 " pdb=" CA GLN A 233 " pdb=" C GLN A 233 " ideal model delta sigma weight residual 112.90 101.80 11.10 1.31e+00 5.83e-01 7.18e+01 angle pdb=" N SER A 439 " pdb=" CA SER A 439 " pdb=" C SER A 439 " ideal model delta sigma weight residual 113.23 104.19 9.04 1.24e+00 6.50e-01 5.31e+01 angle pdb=" N THR A 56 " pdb=" CA THR A 56 " pdb=" C THR A 56 " ideal model delta sigma weight residual 112.59 104.38 8.21 1.22e+00 6.72e-01 4.53e+01 angle pdb=" N HIS G3609 " pdb=" CA HIS G3609 " pdb=" C HIS G3609 " ideal model delta sigma weight residual 109.14 99.39 9.75 1.49e+00 4.50e-01 4.28e+01 angle pdb=" N ASP F 128 " pdb=" CA ASP F 128 " pdb=" C ASP F 128 " ideal model delta sigma weight residual 112.92 104.96 7.96 1.23e+00 6.61e-01 4.19e+01 ... (remaining 79967 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.82: 20467 33.82 - 67.64: 852 67.64 - 101.46: 47 101.46 - 135.28: 1 135.28 - 169.09: 4 Dihedral angle restraints: 21371 sinusoidal: 11822 harmonic: 9549 Sorted by residual: dihedral pdb=" C5' GTP E 501 " pdb=" O5' GTP E 501 " pdb=" PA GTP E 501 " pdb=" O3A GTP E 501 " ideal model delta sinusoidal sigma weight residual 69.27 -121.64 -169.09 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O5' GTP E 501 " pdb=" O3A GTP E 501 " pdb=" PA GTP E 501 " pdb=" PB GTP E 501 " ideal model delta sinusoidal sigma weight residual -85.88 72.23 -158.10 1 2.00e+01 2.50e-03 4.63e+01 dihedral pdb=" C8 GTP A 501 " pdb=" C1' GTP A 501 " pdb=" N9 GTP A 501 " pdb=" O4' GTP A 501 " ideal model delta sinusoidal sigma weight residual 104.59 -52.46 157.06 1 2.00e+01 2.50e-03 4.61e+01 ... (remaining 21368 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3050 0.070 - 0.140: 334 0.140 - 0.209: 21 0.209 - 0.279: 5 0.279 - 0.349: 2 Chirality restraints: 3412 Sorted by residual: chirality pdb=" CA CYS H 129 " pdb=" N CYS H 129 " pdb=" C CYS H 129 " pdb=" CB CYS H 129 " both_signs ideal model delta sigma weight residual False 2.51 2.86 -0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" CA GLU A 3 " pdb=" N GLU A 3 " pdb=" C GLU A 3 " pdb=" CB GLU A 3 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA CYS D 129 " pdb=" N CYS D 129 " pdb=" C CYS D 129 " pdb=" CB CYS D 129 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 3409 not shown) Planarity restraints: 6741 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 2 " 0.152 9.50e-02 1.11e+02 1.97e-01 8.21e+02 pdb=" NE ARG A 2 " 0.153 2.00e-02 2.50e+03 pdb=" CZ ARG A 2 " 0.032 2.00e-02 2.50e+03 pdb=" NH1 ARG A 2 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG A 2 " -0.047 2.00e-02 2.50e+03 pdb="HH11 ARG A 2 " -0.380 2.00e-02 2.50e+03 pdb="HH12 ARG A 2 " 0.376 2.00e-02 2.50e+03 pdb="HH21 ARG A 2 " -0.033 2.00e-02 2.50e+03 pdb="HH22 ARG A 2 " -0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN F 280 " -0.053 2.00e-02 2.50e+03 5.57e-02 4.65e+01 pdb=" CD GLN F 280 " 0.006 2.00e-02 2.50e+03 pdb=" OE1 GLN F 280 " 0.049 2.00e-02 2.50e+03 pdb=" NE2 GLN F 280 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN F 280 " 0.081 2.00e-02 2.50e+03 pdb="HE22 GLN F 280 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B 280 " 0.040 2.00e-02 2.50e+03 4.55e-02 3.11e+01 pdb=" CD GLN B 280 " 0.003 2.00e-02 2.50e+03 pdb=" OE1 GLN B 280 " -0.043 2.00e-02 2.50e+03 pdb=" NE2 GLN B 280 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN B 280 " -0.068 2.00e-02 2.50e+03 pdb="HE22 GLN B 280 " 0.066 2.00e-02 2.50e+03 ... (remaining 6738 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 3016 2.21 - 2.81: 90586 2.81 - 3.40: 121222 3.40 - 4.00: 169252 4.00 - 4.60: 260865 Nonbonded interactions: 644941 Sorted by model distance: nonbonded pdb=" HG SER D 322 " pdb=" HB2 GLU D 325 " model vdw 1.612 2.270 nonbonded pdb=" OE1 GLU C3655 " pdb=" H GLU C3655 " model vdw 1.810 2.450 nonbonded pdb=" OE1 GLU G3655 " pdb=" H GLU G3655 " model vdw 1.840 2.450 nonbonded pdb=" HB2 ARG D 306 " pdb=" HE ARG D 306 " model vdw 1.859 2.270 nonbonded pdb=" H SER D 145 " pdb=" HG SER D 145 " model vdw 1.860 2.100 ... (remaining 644936 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 138 or (resid 139 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 140 through 502)) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 1 through 263 or (resid 264 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 265 through 502)) selection = (chain 'D' and (resid 1 through 389 or (resid 390 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) \ or resid 391 through 502)) selection = (chain 'F' and (resid 1 through 263 or (resid 264 and (name N or name CA or name \ C or name O or name CB or name CG or name ND1 or name CD2 or name CE1 or name N \ E2 or name H or name HA or name HB2 or name HB3 or name HD1 or name HD2 or name \ HE1)) or resid 265 through 389 or (resid 390 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name NE or name CZ or name NH1 or na \ me NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name HD2 or \ name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) or re \ sid 391 through 502)) selection = (chain 'H' and (resid 1 through 389 or (resid 390 and (name N or name CA or name \ C or name O or name CB or name CG or name CD or name NE or name CZ or name NH1 \ or name NH2 or name HA or name HB2 or name HB3 or name HG2 or name HG3 or name H \ D2 or name HD3 or name HE or name HH11 or name HH12 or name HH21 or name HH22)) \ or resid 391 through 502)) } ncs_group { reference = chain 'C' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.060 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: 0.290 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 42.730 Find NCS groups from input model: 0.770 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:7.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 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 0.092 23006 Z= 0.375 Angle : 0.726 11.104 31272 Z= 0.434 Chirality : 0.046 0.349 3412 Planarity : 0.005 0.064 4070 Dihedral : 17.038 169.094 8808 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.00 % Allowed : 16.27 % Favored : 82.74 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 3.08 % 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: -0.11 (0.16), residues: 2788 helix: 0.56 (0.15), residues: 1202 sheet: -0.11 (0.23), residues: 474 loop : -0.63 (0.18), residues: 1112 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 282 TYR 0.021 0.001 TYR B 281 PHE 0.021 0.001 PHE A 244 TRP 0.014 0.002 TRP A 21 HIS 0.009 0.001 HIS E 61 Details of bonding type rmsd covalent geometry : bond 0.00550 (23002) covalent geometry : angle 0.71898 (31264) SS BOND : bond 0.03272 ( 4) SS BOND : angle 6.51830 ( 8) hydrogen bonds : bond 0.15157 ( 1056) hydrogen bonds : angle 6.54982 ( 3003) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 MET cc_start: 0.9110 (mtp) cc_final: 0.8737 (mtp) REVERT: B 300 MET cc_start: 0.9042 (mtt) cc_final: 0.8731 (mtt) REVERT: B 324 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.7228 (tptm) REVERT: D 432 GLU cc_start: 0.5444 (OUTLIER) cc_final: 0.4843 (mp0) REVERT: F 324 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.7509 (mptm) REVERT: H 330 MET cc_start: 0.9084 (mmp) cc_final: 0.8679 (mmp) REVERT: E 203 MET cc_start: 0.8628 (mtm) cc_final: 0.8321 (mtp) REVERT: E 425 MET cc_start: 0.8705 (mmm) cc_final: 0.8396 (mmm) outliers start: 24 outliers final: 14 residues processed: 152 average time/residue: 1.6509 time to fit residues: 283.8849 Evaluate side-chains 136 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain C residue 3690 PHE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 333 VAL Chi-restraints excluded: chain D residue 432 GLU Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 324 LYS Chi-restraints excluded: chain G residue 3690 PHE Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 379 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 0.4980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 ASN F 57 ASN A 35 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.064385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.049128 restraints weight = 151357.359| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.46 r_work: 0.2927 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.0743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23006 Z= 0.141 Angle : 0.545 7.150 31272 Z= 0.282 Chirality : 0.041 0.166 3412 Planarity : 0.004 0.063 4070 Dihedral : 9.693 169.361 3575 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.16 % Allowed : 16.22 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.60 (0.16), residues: 2788 helix: 1.38 (0.16), residues: 1154 sheet: -0.11 (0.23), residues: 474 loop : -0.29 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 221 TYR 0.017 0.001 TYR A 282 PHE 0.017 0.001 PHE A 52 TRP 0.012 0.001 TRP A 21 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00304 (23002) covalent geometry : angle 0.54444 (31264) SS BOND : bond 0.00729 ( 4) SS BOND : angle 1.63563 ( 8) hydrogen bonds : bond 0.05064 ( 1056) hydrogen bonds : angle 4.96341 ( 3003) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 120 time to evaluate : 1.194 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 MET cc_start: 0.9416 (mtp) cc_final: 0.9021 (mtp) REVERT: B 257 MET cc_start: 0.9278 (mmm) cc_final: 0.8996 (mmm) REVERT: B 300 MET cc_start: 0.9173 (mtt) cc_final: 0.8837 (mtt) REVERT: B 324 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.6979 (tptm) REVERT: F 298 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8627 (t0) REVERT: F 362 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8660 (tttp) REVERT: H 330 MET cc_start: 0.9395 (mmp) cc_final: 0.9068 (mmp) REVERT: E 49 PHE cc_start: 0.6741 (OUTLIER) cc_final: 0.5447 (p90) REVERT: E 203 MET cc_start: 0.9177 (mtm) cc_final: 0.8965 (mtp) REVERT: E 282 TYR cc_start: 0.7795 (t80) cc_final: 0.7415 (t80) outliers start: 28 outliers final: 12 residues processed: 141 average time/residue: 1.4442 time to fit residues: 234.2856 Evaluate side-chains 134 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain C residue 3690 PHE Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 297 LYS Chi-restraints excluded: chain F residue 298 ASN Chi-restraints excluded: chain F residue 362 LYS Chi-restraints excluded: chain F residue 363 MET Chi-restraints excluded: chain F residue 388 MET Chi-restraints excluded: chain G residue 3690 PHE Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 253 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 128 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 126 optimal weight: 4.9990 chunk 100 optimal weight: 0.0980 chunk 99 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 230 optimal weight: 2.9990 chunk 43 optimal weight: 0.2980 chunk 10 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 35 GLN E 301 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.065427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.050254 restraints weight = 152762.339| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.48 r_work: 0.2897 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 23006 Z= 0.114 Angle : 0.509 6.715 31272 Z= 0.258 Chirality : 0.040 0.148 3412 Planarity : 0.004 0.062 4070 Dihedral : 9.149 165.712 3558 Min Nonbonded Distance : 1.781 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.12 % Allowed : 15.44 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.72 (0.16), residues: 2788 helix: 1.61 (0.15), residues: 1180 sheet: -0.19 (0.23), residues: 484 loop : -0.34 (0.19), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 282 TYR 0.006 0.001 TYR F 59 PHE 0.013 0.001 PHE A 52 TRP 0.013 0.001 TRP A 21 HIS 0.004 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00250 (23002) covalent geometry : angle 0.50863 (31264) SS BOND : bond 0.00648 ( 4) SS BOND : angle 1.58875 ( 8) hydrogen bonds : bond 0.04272 ( 1056) hydrogen bonds : angle 4.61887 ( 3003) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 121 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 MET cc_start: 0.9343 (mtp) cc_final: 0.8966 (mtp) REVERT: B 257 MET cc_start: 0.9270 (mmm) cc_final: 0.9044 (mmm) REVERT: B 300 MET cc_start: 0.9129 (mtt) cc_final: 0.8803 (mtt) REVERT: B 324 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.6920 (tptm) REVERT: F 324 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.6986 (mptm) REVERT: H 330 MET cc_start: 0.9340 (mmp) cc_final: 0.9048 (mmp) REVERT: E 49 PHE cc_start: 0.6480 (OUTLIER) cc_final: 0.5139 (p90) REVERT: E 282 TYR cc_start: 0.7870 (t80) cc_final: 0.7455 (t80) outliers start: 27 outliers final: 14 residues processed: 145 average time/residue: 1.4514 time to fit residues: 241.3865 Evaluate side-chains 135 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 118 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain C residue 3690 PHE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 239 CYS Chi-restraints excluded: chain F residue 297 LYS Chi-restraints excluded: chain F residue 324 LYS Chi-restraints excluded: chain G residue 3690 PHE Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 253 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 109 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 247 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN F 57 ASN E 176 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.063356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.048170 restraints weight = 152290.994| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.46 r_work: 0.2889 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23006 Z= 0.192 Angle : 0.540 6.730 31272 Z= 0.275 Chirality : 0.042 0.150 3412 Planarity : 0.004 0.064 4070 Dihedral : 9.120 166.191 3558 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.20 % Allowed : 15.73 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.70 (0.16), residues: 2788 helix: 1.58 (0.15), residues: 1176 sheet: -0.19 (0.23), residues: 484 loop : -0.35 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 84 TYR 0.008 0.001 TYR H 425 PHE 0.013 0.001 PHE A 52 TRP 0.012 0.001 TRP A 21 HIS 0.005 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00436 (23002) covalent geometry : angle 0.53907 (31264) SS BOND : bond 0.00602 ( 4) SS BOND : angle 1.49598 ( 8) hydrogen bonds : bond 0.04648 ( 1056) hydrogen bonds : angle 4.66116 ( 3003) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 118 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 233 MET cc_start: 0.9353 (mtp) cc_final: 0.9003 (mtp) REVERT: B 300 MET cc_start: 0.9171 (mtt) cc_final: 0.8860 (mtt) REVERT: B 324 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.6982 (tptm) REVERT: F 324 LYS cc_start: 0.8532 (OUTLIER) cc_final: 0.7017 (mptm) REVERT: H 330 MET cc_start: 0.9363 (mmp) cc_final: 0.9099 (mmp) REVERT: A 84 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8441 (ptp90) REVERT: E 49 PHE cc_start: 0.6606 (OUTLIER) cc_final: 0.5240 (p90) REVERT: E 282 TYR cc_start: 0.7920 (t80) cc_final: 0.7483 (t80) outliers start: 29 outliers final: 18 residues processed: 140 average time/residue: 1.4823 time to fit residues: 238.5562 Evaluate side-chains 137 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain C residue 3690 PHE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 239 CYS Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 324 LYS Chi-restraints excluded: chain G residue 3690 PHE Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 253 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 259 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 265 optimal weight: 0.6980 chunk 165 optimal weight: 0.6980 chunk 217 optimal weight: 1.9990 chunk 263 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 212 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.064042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.048462 restraints weight = 150729.261| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.52 r_work: 0.2884 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23006 Z= 0.144 Angle : 0.520 6.696 31272 Z= 0.263 Chirality : 0.041 0.147 3412 Planarity : 0.004 0.063 4070 Dihedral : 8.969 165.600 3558 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.29 % Allowed : 15.85 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.78 (0.16), residues: 2788 helix: 1.68 (0.15), residues: 1176 sheet: -0.19 (0.23), residues: 484 loop : -0.31 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 221 TYR 0.006 0.001 TYR E 319 PHE 0.011 0.001 PHE A 52 TRP 0.012 0.001 TRP A 21 HIS 0.004 0.001 HIS A 266 Details of bonding type rmsd covalent geometry : bond 0.00323 (23002) covalent geometry : angle 0.51992 (31264) SS BOND : bond 0.00595 ( 4) SS BOND : angle 1.46796 ( 8) hydrogen bonds : bond 0.04346 ( 1056) hydrogen bonds : angle 4.56706 ( 3003) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 MET cc_start: 0.9292 (mtp) cc_final: 0.8949 (mtp) REVERT: B 257 MET cc_start: 0.9260 (mmm) cc_final: 0.8950 (mmm) REVERT: B 299 MET cc_start: 0.7862 (mtp) cc_final: 0.7579 (mtp) REVERT: B 300 MET cc_start: 0.9139 (mtt) cc_final: 0.8858 (mtt) REVERT: B 324 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.6959 (tptm) REVERT: F 324 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.6967 (mptm) REVERT: H 330 MET cc_start: 0.9317 (mmp) cc_final: 0.9056 (mmp) REVERT: E 49 PHE cc_start: 0.6776 (OUTLIER) cc_final: 0.5399 (p90) REVERT: E 282 TYR cc_start: 0.7979 (t80) cc_final: 0.7544 (t80) outliers start: 31 outliers final: 22 residues processed: 146 average time/residue: 1.3872 time to fit residues: 234.2032 Evaluate side-chains 142 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 117 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain C residue 3690 PHE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 239 CYS Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 297 LYS Chi-restraints excluded: chain F residue 324 LYS Chi-restraints excluded: chain F residue 363 MET Chi-restraints excluded: chain G residue 3690 PHE Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 253 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 245 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 274 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 254 optimal weight: 3.9990 chunk 201 optimal weight: 2.9990 chunk 240 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.063498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.048276 restraints weight = 154569.445| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 2.49 r_work: 0.2854 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23006 Z= 0.186 Angle : 0.535 6.810 31272 Z= 0.272 Chirality : 0.041 0.149 3412 Planarity : 0.004 0.062 4070 Dihedral : 8.924 164.752 3558 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.54 % Allowed : 15.73 % Favored : 82.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.73 (0.16), residues: 2788 helix: 1.62 (0.15), residues: 1176 sheet: -0.18 (0.23), residues: 484 loop : -0.33 (0.18), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 264 TYR 0.007 0.001 TYR H 425 PHE 0.012 0.001 PHE A 141 TRP 0.012 0.001 TRP A 21 HIS 0.005 0.001 HIS F 396 Details of bonding type rmsd covalent geometry : bond 0.00421 (23002) covalent geometry : angle 0.53466 (31264) SS BOND : bond 0.00593 ( 4) SS BOND : angle 1.45977 ( 8) hydrogen bonds : bond 0.04601 ( 1056) hydrogen bonds : angle 4.60396 ( 3003) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 119 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 233 MET cc_start: 0.9266 (mtp) cc_final: 0.8928 (mtp) REVERT: B 257 MET cc_start: 0.9324 (mmm) cc_final: 0.9083 (mmm) REVERT: B 300 MET cc_start: 0.9174 (mtt) cc_final: 0.8903 (mtt) REVERT: B 324 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.6974 (tptm) REVERT: F 324 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.6987 (mptm) REVERT: H 330 MET cc_start: 0.9335 (mmp) cc_final: 0.9087 (mmp) REVERT: E 49 PHE cc_start: 0.6734 (OUTLIER) cc_final: 0.5446 (p90) REVERT: E 282 TYR cc_start: 0.8018 (t80) cc_final: 0.7561 (t80) outliers start: 37 outliers final: 23 residues processed: 149 average time/residue: 1.1026 time to fit residues: 190.7514 Evaluate side-chains 143 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 117 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain C residue 3690 PHE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 239 CYS Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 297 LYS Chi-restraints excluded: chain F residue 324 LYS Chi-restraints excluded: chain G residue 3690 PHE Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 253 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 111 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 205 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.063493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.047939 restraints weight = 150488.053| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.54 r_work: 0.2853 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23006 Z= 0.162 Angle : 0.526 6.867 31272 Z= 0.267 Chirality : 0.041 0.147 3412 Planarity : 0.004 0.061 4070 Dihedral : 8.837 164.695 3558 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.41 % Allowed : 15.77 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.88 (0.16), residues: 2788 helix: 1.74 (0.15), residues: 1164 sheet: -0.12 (0.24), residues: 474 loop : -0.23 (0.18), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 84 TYR 0.007 0.001 TYR E 319 PHE 0.010 0.001 PHE E 149 TRP 0.012 0.001 TRP A 21 HIS 0.006 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00367 (23002) covalent geometry : angle 0.52576 (31264) SS BOND : bond 0.00618 ( 4) SS BOND : angle 1.53533 ( 8) hydrogen bonds : bond 0.04420 ( 1056) hydrogen bonds : angle 4.54757 ( 3003) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 233 MET cc_start: 0.9258 (mtp) cc_final: 0.8926 (mtp) REVERT: B 257 MET cc_start: 0.9325 (mmm) cc_final: 0.9074 (mmm) REVERT: B 300 MET cc_start: 0.9171 (mtt) cc_final: 0.8922 (mtt) REVERT: B 324 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.6966 (tptm) REVERT: F 324 LYS cc_start: 0.8555 (OUTLIER) cc_final: 0.6998 (mptm) REVERT: H 330 MET cc_start: 0.9316 (mmp) cc_final: 0.8958 (mmp) REVERT: E 49 PHE cc_start: 0.6886 (OUTLIER) cc_final: 0.5696 (p90) REVERT: E 282 TYR cc_start: 0.8037 (t80) cc_final: 0.7587 (t80) outliers start: 34 outliers final: 24 residues processed: 148 average time/residue: 0.9886 time to fit residues: 168.9865 Evaluate side-chains 146 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain C residue 3690 PHE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 239 CYS Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 297 LYS Chi-restraints excluded: chain F residue 324 LYS Chi-restraints excluded: chain F residue 363 MET Chi-restraints excluded: chain G residue 3690 PHE Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 253 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 142 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 209 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 199 optimal weight: 0.8980 chunk 95 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 chunk 273 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN ** F 57 ASN ** 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 = 0.3300 r_free = 0.3300 target = 0.063430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.047871 restraints weight = 151543.061| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.54 r_work: 0.2856 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2741 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23006 Z= 0.164 Angle : 0.528 7.576 31272 Z= 0.267 Chirality : 0.041 0.148 3412 Planarity : 0.004 0.060 4070 Dihedral : 8.745 163.488 3557 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.33 % Allowed : 16.06 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.91 (0.16), residues: 2788 helix: 1.75 (0.15), residues: 1164 sheet: 0.01 (0.24), residues: 458 loop : -0.25 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 84 TYR 0.007 0.001 TYR E 319 PHE 0.011 0.001 PHE E 149 TRP 0.012 0.001 TRP A 21 HIS 0.006 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00370 (23002) covalent geometry : angle 0.52765 (31264) SS BOND : bond 0.00587 ( 4) SS BOND : angle 1.45879 ( 8) hydrogen bonds : bond 0.04396 ( 1056) hydrogen bonds : angle 4.52356 ( 3003) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 MET cc_start: 0.9240 (mtp) cc_final: 0.8913 (mtp) REVERT: B 257 MET cc_start: 0.9333 (mmm) cc_final: 0.9094 (mmm) REVERT: B 300 MET cc_start: 0.9178 (mtt) cc_final: 0.8920 (mtt) REVERT: B 324 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.6970 (tptm) REVERT: F 324 LYS cc_start: 0.8559 (OUTLIER) cc_final: 0.6995 (mptm) REVERT: G 3658 LYS cc_start: 0.8524 (mmtm) cc_final: 0.8227 (mmmt) REVERT: H 330 MET cc_start: 0.9320 (mmp) cc_final: 0.8973 (mmp) REVERT: E 49 PHE cc_start: 0.6722 (OUTLIER) cc_final: 0.5557 (p90) REVERT: E 282 TYR cc_start: 0.8059 (t80) cc_final: 0.7606 (t80) outliers start: 32 outliers final: 24 residues processed: 146 average time/residue: 0.8023 time to fit residues: 136.3993 Evaluate side-chains 145 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain C residue 3690 PHE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 239 CYS Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 297 LYS Chi-restraints excluded: chain F residue 324 LYS Chi-restraints excluded: chain G residue 3690 PHE Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 253 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 19 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 130 optimal weight: 0.9980 chunk 209 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.063597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.048061 restraints weight = 151264.719| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 2.52 r_work: 0.2871 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 23006 Z= 0.145 Angle : 0.521 8.295 31272 Z= 0.263 Chirality : 0.041 0.146 3412 Planarity : 0.004 0.060 4070 Dihedral : 8.595 161.249 3557 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.29 % Allowed : 16.14 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 0.96 (0.16), residues: 2788 helix: 1.81 (0.15), residues: 1164 sheet: 0.01 (0.24), residues: 458 loop : -0.23 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 84 TYR 0.006 0.001 TYR E 319 PHE 0.010 0.001 PHE E 149 TRP 0.012 0.001 TRP A 21 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00327 (23002) covalent geometry : angle 0.52063 (31264) SS BOND : bond 0.00571 ( 4) SS BOND : angle 1.52838 ( 8) hydrogen bonds : bond 0.04242 ( 1056) hydrogen bonds : angle 4.47354 ( 3003) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 119 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 MET cc_start: 0.9225 (mtp) cc_final: 0.8899 (mtp) REVERT: B 257 MET cc_start: 0.9330 (mmm) cc_final: 0.9092 (mmm) REVERT: B 300 MET cc_start: 0.9172 (mtt) cc_final: 0.8929 (mtt) REVERT: B 324 LYS cc_start: 0.8633 (OUTLIER) cc_final: 0.6969 (tptm) REVERT: F 324 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.6997 (mptm) REVERT: G 3658 LYS cc_start: 0.8545 (mmtm) cc_final: 0.8245 (mmmt) REVERT: H 330 MET cc_start: 0.9318 (mmp) cc_final: 0.8975 (mmp) REVERT: E 49 PHE cc_start: 0.6628 (OUTLIER) cc_final: 0.5482 (p90) REVERT: E 282 TYR cc_start: 0.8068 (t80) cc_final: 0.7607 (t80) outliers start: 31 outliers final: 23 residues processed: 148 average time/residue: 0.8041 time to fit residues: 138.5628 Evaluate side-chains 144 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 118 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain C residue 3690 PHE Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 239 CYS Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 297 LYS Chi-restraints excluded: chain F residue 324 LYS Chi-restraints excluded: chain G residue 3690 PHE Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 213 CYS Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 170 SER Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 253 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 76 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 138 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 227 optimal weight: 0.4980 chunk 218 optimal weight: 0.1980 chunk 124 optimal weight: 0.1980 chunk 272 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 375 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.064174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.048990 restraints weight = 153785.234| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.51 r_work: 0.2879 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 23006 Z= 0.123 Angle : 0.512 8.996 31272 Z= 0.257 Chirality : 0.040 0.145 3412 Planarity : 0.004 0.061 4070 Dihedral : 8.391 156.251 3557 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.95 % Allowed : 16.60 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 1.04 (0.16), residues: 2788 helix: 1.87 (0.15), residues: 1168 sheet: 0.03 (0.24), residues: 458 loop : -0.17 (0.18), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 84 TYR 0.006 0.001 TYR E 319 PHE 0.010 0.001 PHE E 149 TRP 0.012 0.001 TRP A 21 HIS 0.007 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00276 (23002) covalent geometry : angle 0.51159 (31264) SS BOND : bond 0.00608 ( 4) SS BOND : angle 1.46121 ( 8) hydrogen bonds : bond 0.04035 ( 1056) hydrogen bonds : angle 4.40621 ( 3003) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5576 Ramachandran restraints generated. 2788 Oldfield, 0 Emsley, 2788 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 233 MET cc_start: 0.9203 (mtp) cc_final: 0.8876 (mtp) REVERT: B 257 MET cc_start: 0.9319 (mmm) cc_final: 0.9083 (mmm) REVERT: B 300 MET cc_start: 0.9164 (mtt) cc_final: 0.8924 (mtt) REVERT: B 324 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.6952 (tptm) REVERT: F 293 MET cc_start: 0.9005 (mtp) cc_final: 0.8669 (mtp) REVERT: F 324 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.6981 (mptm) REVERT: G 3658 LYS cc_start: 0.8533 (mmtm) cc_final: 0.8233 (mmmt) REVERT: H 1 MET cc_start: 0.6858 (ptt) cc_final: 0.6011 (pp-130) REVERT: H 330 MET cc_start: 0.9294 (mmp) cc_final: 0.8950 (mmp) REVERT: A 1 MET cc_start: 0.6708 (ppp) cc_final: 0.5814 (ppp) REVERT: E 49 PHE cc_start: 0.6565 (OUTLIER) cc_final: 0.5561 (p90) REVERT: E 282 TYR cc_start: 0.8077 (t80) cc_final: 0.7614 (t80) outliers start: 23 outliers final: 19 residues processed: 140 average time/residue: 0.7898 time to fit residues: 128.5138 Evaluate side-chains 140 residues out of total 2410 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 324 LYS Chi-restraints excluded: chain C residue 3690 PHE Chi-restraints excluded: chain D residue 166 THR Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 239 CYS Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 297 LYS Chi-restraints excluded: chain F residue 324 LYS Chi-restraints excluded: chain G residue 3690 PHE Chi-restraints excluded: chain H residue 168 SER Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 379 SER Chi-restraints excluded: chain A residue 435 VAL Chi-restraints excluded: chain E residue 49 PHE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 241 SER Chi-restraints excluded: chain E residue 253 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 263 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 165 optimal weight: 0.0970 chunk 262 optimal weight: 0.3980 chunk 117 optimal weight: 0.0170 chunk 160 optimal weight: 1.9990 chunk 264 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 overall best weight: 0.3816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 ASN D 375 GLN ** F 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3617 HIS A 91 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.065721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.050686 restraints weight = 153554.055| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.49 r_work: 0.2933 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 23006 Z= 0.090 Angle : 0.494 9.187 31272 Z= 0.245 Chirality : 0.040 0.146 3412 Planarity : 0.004 0.060 4070 Dihedral : 7.924 144.154 3557 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.71 % Allowed : 16.76 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % 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: 1.24 (0.16), residues: 2788 helix: 2.10 (0.16), residues: 1164 sheet: 0.05 (0.24), residues: 458 loop : -0.11 (0.19), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 79 TYR 0.005 0.001 TYR B 208 PHE 0.008 0.001 PHE E 149 TRP 0.011 0.001 TRP E 21 HIS 0.005 0.001 HIS A 88 Details of bonding type rmsd covalent geometry : bond 0.00198 (23002) covalent geometry : angle 0.49317 (31264) SS BOND : bond 0.00629 ( 4) SS BOND : angle 1.36605 ( 8) hydrogen bonds : bond 0.03483 ( 1056) hydrogen bonds : angle 4.22311 ( 3003) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10783.60 seconds wall clock time: 183 minutes 31.77 seconds (11011.77 seconds total)