Starting phenix.real_space_refine on Fri Mar 6 16:09:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nzw_0562/03_2026/6nzw_0562_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nzw_0562/03_2026/6nzw_0562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6nzw_0562/03_2026/6nzw_0562_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nzw_0562/03_2026/6nzw_0562_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6nzw_0562/03_2026/6nzw_0562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nzw_0562/03_2026/6nzw_0562.map" } resolution = 3.21 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= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 102 5.16 5 Cl 2 4.86 5 C 10606 2.51 5 N 2532 2.21 5 O 2764 1.98 5 H 15714 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 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: 31720 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "B" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "C" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "D" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "E" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "F" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'L9Y': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 2, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 2, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 2, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 2, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 2, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-1': 3, 'POV:plan-2': 2, 'POV:plan-3': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 5.34, per 1000 atoms: 0.17 Number of scatterers: 31720 At special positions: 0 Unit cell: (109.888, 103.36, 131.648, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 102 16.00 O 2764 8.00 N 2532 7.00 C 10606 6.00 H 15714 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 877.5 milliseconds 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 12 sheets defined 74.0% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 Processing helix chain 'A' and resid 22 through 25 Processing helix chain 'A' and resid 26 through 49 removed outlier: 3.533A pdb=" N TYR A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 116 removed outlier: 4.251A pdb=" N VAL A 109 " --> pdb=" O GLN A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 124 removed outlier: 3.729A pdb=" N LYS A 123 " --> pdb=" O HIS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 146 removed outlier: 3.518A pdb=" N LEU A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 131 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 4.495A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 removed outlier: 4.186A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 254 removed outlier: 3.673A pdb=" N LYS A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 286 removed outlier: 3.662A pdb=" N ARG A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 268 " --> pdb=" O TYR A 264 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A 284 " --> pdb=" O CYS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 289 No H-bonds generated for 'chain 'A' and resid 287 through 289' Processing helix chain 'A' and resid 314 through 346 removed outlier: 3.678A pdb=" N PHE A 331 " --> pdb=" O SER A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.828A pdb=" N ARG A 357 " --> pdb=" O PHE A 353 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 removed outlier: 3.821A pdb=" N GLN A 381 " --> pdb=" O HIS A 377 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 Processing helix chain 'A' and resid 395 through 408 removed outlier: 3.576A pdb=" N GLU A 399 " --> pdb=" O SER A 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 21 Processing helix chain 'B' and resid 22 through 25 Processing helix chain 'B' and resid 26 through 49 removed outlier: 3.533A pdb=" N TYR B 30 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 116 removed outlier: 4.251A pdb=" N VAL B 109 " --> pdb=" O GLN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 removed outlier: 3.729A pdb=" N LYS B 123 " --> pdb=" O HIS B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 146 removed outlier: 3.518A pdb=" N LEU B 130 " --> pdb=" O PRO B 126 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 131 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 140 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 165 removed outlier: 4.495A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 162 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 removed outlier: 4.188A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 254 removed outlier: 3.673A pdb=" N LYS B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 286 removed outlier: 3.662A pdb=" N ARG B 262 " --> pdb=" O ASP B 258 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR B 268 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE B 270 " --> pdb=" O ARG B 266 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR B 284 " --> pdb=" O CYS B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 289 No H-bonds generated for 'chain 'B' and resid 287 through 289' Processing helix chain 'B' and resid 314 through 346 removed outlier: 3.678A pdb=" N PHE B 331 " --> pdb=" O SER B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.827A pdb=" N ARG B 357 " --> pdb=" O PHE B 353 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU B 359 " --> pdb=" O SER B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 removed outlier: 3.821A pdb=" N GLN B 381 " --> pdb=" O HIS B 377 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 Processing helix chain 'B' and resid 395 through 408 removed outlier: 3.576A pdb=" N GLU B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 22 through 25 Processing helix chain 'C' and resid 26 through 49 removed outlier: 3.534A pdb=" N TYR C 30 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 116 removed outlier: 4.251A pdb=" N VAL C 109 " --> pdb=" O GLN C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 124 removed outlier: 3.729A pdb=" N LYS C 123 " --> pdb=" O HIS C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 146 removed outlier: 3.519A pdb=" N LEU C 130 " --> pdb=" O PRO C 126 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 131 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER C 140 " --> pdb=" O PHE C 136 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 removed outlier: 4.494A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS C 162 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 174 removed outlier: 4.187A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 254 removed outlier: 3.673A pdb=" N LYS C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR C 252 " --> pdb=" O LYS C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 286 removed outlier: 3.661A pdb=" N ARG C 262 " --> pdb=" O ASP C 258 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR C 268 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR C 284 " --> pdb=" O CYS C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 287 through 289 No H-bonds generated for 'chain 'C' and resid 287 through 289' Processing helix chain 'C' and resid 314 through 346 removed outlier: 3.678A pdb=" N PHE C 331 " --> pdb=" O SER C 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 removed outlier: 3.827A pdb=" N ARG C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 383 removed outlier: 3.820A pdb=" N GLN C 381 " --> pdb=" O HIS C 377 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 389 Processing helix chain 'C' and resid 395 through 408 removed outlier: 3.576A pdb=" N GLU C 399 " --> pdb=" O SER C 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 21 Processing helix chain 'D' and resid 22 through 25 Processing helix chain 'D' and resid 26 through 49 removed outlier: 3.534A pdb=" N TYR D 30 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 116 removed outlier: 4.250A pdb=" N VAL D 109 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 119 through 124 removed outlier: 3.729A pdb=" N LYS D 123 " --> pdb=" O HIS D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 146 removed outlier: 3.518A pdb=" N LEU D 130 " --> pdb=" O PRO D 126 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 131 " --> pdb=" O TYR D 127 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 165 removed outlier: 4.494A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS D 162 " --> pdb=" O SER D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 174 removed outlier: 4.187A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER D 174 " --> pdb=" O THR D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 254 removed outlier: 3.673A pdb=" N LYS D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR D 252 " --> pdb=" O LYS D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 286 removed outlier: 3.662A pdb=" N ARG D 262 " --> pdb=" O ASP D 258 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR D 268 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR D 284 " --> pdb=" O CYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 289 No H-bonds generated for 'chain 'D' and resid 287 through 289' Processing helix chain 'D' and resid 314 through 346 removed outlier: 3.677A pdb=" N PHE D 331 " --> pdb=" O SER D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 353 through 361 removed outlier: 3.828A pdb=" N ARG D 357 " --> pdb=" O PHE D 353 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 removed outlier: 3.820A pdb=" N GLN D 381 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 389 Processing helix chain 'D' and resid 395 through 408 removed outlier: 3.576A pdb=" N GLU D 399 " --> pdb=" O SER D 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 21 Processing helix chain 'E' and resid 22 through 25 Processing helix chain 'E' and resid 26 through 49 removed outlier: 3.533A pdb=" N TYR E 30 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE E 33 " --> pdb=" O ASP E 29 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU E 36 " --> pdb=" O SER E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 116 removed outlier: 4.251A pdb=" N VAL E 109 " --> pdb=" O GLN E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 119 through 124 removed outlier: 3.729A pdb=" N LYS E 123 " --> pdb=" O HIS E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 146 removed outlier: 3.519A pdb=" N LEU E 130 " --> pdb=" O PRO E 126 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 131 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER E 140 " --> pdb=" O PHE E 136 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 165 removed outlier: 4.494A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 174 removed outlier: 4.188A pdb=" N ARG E 171 " --> pdb=" O PRO E 167 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER E 174 " --> pdb=" O THR E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 254 removed outlier: 3.673A pdb=" N LYS E 246 " --> pdb=" O ALA E 242 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR E 252 " --> pdb=" O LYS E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 286 removed outlier: 3.662A pdb=" N ARG E 262 " --> pdb=" O ASP E 258 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR E 268 " --> pdb=" O TYR E 264 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE E 270 " --> pdb=" O ARG E 266 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL E 283 " --> pdb=" O ILE E 279 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR E 284 " --> pdb=" O CYS E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 287 through 289 No H-bonds generated for 'chain 'E' and resid 287 through 289' Processing helix chain 'E' and resid 314 through 346 removed outlier: 3.678A pdb=" N PHE E 331 " --> pdb=" O SER E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 361 removed outlier: 3.728A pdb=" N GLU E 359 " --> pdb=" O SER E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 383 removed outlier: 3.821A pdb=" N GLN E 381 " --> pdb=" O HIS E 377 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 384 through 389 Processing helix chain 'E' and resid 395 through 408 removed outlier: 3.576A pdb=" N GLU E 399 " --> pdb=" O SER E 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 16 through 21 Processing helix chain 'F' and resid 22 through 25 Processing helix chain 'F' and resid 26 through 49 removed outlier: 3.533A pdb=" N TYR F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE F 33 " --> pdb=" O ASP F 29 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU F 36 " --> pdb=" O SER F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 116 removed outlier: 4.251A pdb=" N VAL F 109 " --> pdb=" O GLN F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 119 through 124 removed outlier: 3.729A pdb=" N LYS F 123 " --> pdb=" O HIS F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 146 removed outlier: 3.518A pdb=" N LEU F 130 " --> pdb=" O PRO F 126 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU F 131 " --> pdb=" O TYR F 127 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER F 140 " --> pdb=" O PHE F 136 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 165 removed outlier: 4.495A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS F 162 " --> pdb=" O SER F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 174 removed outlier: 4.187A pdb=" N ARG F 171 " --> pdb=" O PRO F 167 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER F 174 " --> pdb=" O THR F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 254 removed outlier: 3.673A pdb=" N LYS F 246 " --> pdb=" O ALA F 242 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR F 252 " --> pdb=" O LYS F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 286 removed outlier: 3.661A pdb=" N ARG F 262 " --> pdb=" O ASP F 258 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR F 268 " --> pdb=" O TYR F 264 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE F 270 " --> pdb=" O ARG F 266 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL F 283 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR F 284 " --> pdb=" O CYS F 280 " (cutoff:3.500A) Processing helix chain 'F' and resid 287 through 289 No H-bonds generated for 'chain 'F' and resid 287 through 289' Processing helix chain 'F' and resid 314 through 346 removed outlier: 3.678A pdb=" N PHE F 331 " --> pdb=" O SER F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 353 through 361 removed outlier: 3.828A pdb=" N ARG F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU F 359 " --> pdb=" O SER F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 383 removed outlier: 3.820A pdb=" N GLN F 381 " --> pdb=" O HIS F 377 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR F 382 " --> pdb=" O LEU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 389 Processing helix chain 'F' and resid 395 through 408 removed outlier: 3.577A pdb=" N GLU F 399 " --> pdb=" O SER F 395 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 56 Processing sheet with id=AA2, first strand: chain 'A' and resid 60 through 61 Processing sheet with id=AA3, first strand: chain 'B' and resid 55 through 56 Processing sheet with id=AA4, first strand: chain 'B' and resid 60 through 61 Processing sheet with id=AA5, first strand: chain 'C' and resid 55 through 56 Processing sheet with id=AA6, first strand: chain 'C' and resid 60 through 61 Processing sheet with id=AA7, first strand: chain 'D' and resid 55 through 56 Processing sheet with id=AA8, first strand: chain 'D' and resid 60 through 61 Processing sheet with id=AA9, first strand: chain 'E' and resid 55 through 56 Processing sheet with id=AB1, first strand: chain 'E' and resid 60 through 61 Processing sheet with id=AB2, first strand: chain 'F' and resid 55 through 56 Processing sheet with id=AB3, first strand: chain 'F' and resid 60 through 61 911 hydrogen bonds defined for protein. 2625 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.60 Time building geometry restraints manager: 3.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15690 1.03 - 1.22: 42 1.22 - 1.42: 7124 1.42 - 1.61: 9150 1.61 - 1.81: 148 Bond restraints: 32154 Sorted by residual: bond pdb=" C31 POV C 901 " pdb=" O32 POV C 901 " ideal model delta sigma weight residual 1.206 1.355 -0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" C31 POV B 901 " pdb=" O32 POV B 901 " ideal model delta sigma weight residual 1.206 1.355 -0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" C31 POV D 901 " pdb=" O32 POV D 901 " ideal model delta sigma weight residual 1.206 1.354 -0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" C31 POV F 901 " pdb=" O32 POV F 901 " ideal model delta sigma weight residual 1.206 1.354 -0.148 2.00e-02 2.50e+03 5.50e+01 bond pdb=" C31 POV E 901 " pdb=" O32 POV E 901 " ideal model delta sigma weight residual 1.206 1.354 -0.148 2.00e-02 2.50e+03 5.49e+01 ... (remaining 32149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 57341 2.83 - 5.66: 411 5.66 - 8.48: 42 8.48 - 11.31: 10 11.31 - 14.14: 7 Bond angle restraints: 57811 Sorted by residual: angle pdb=" C32 POV C 901 " pdb=" C31 POV C 901 " pdb=" O31 POV C 901 " ideal model delta sigma weight residual 110.66 124.80 -14.14 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C32 POV B 901 " pdb=" C31 POV B 901 " pdb=" O31 POV B 901 " ideal model delta sigma weight residual 110.66 124.76 -14.10 3.00e+00 1.11e-01 2.21e+01 angle pdb=" C32 POV E 901 " pdb=" C31 POV E 901 " pdb=" O31 POV E 901 " ideal model delta sigma weight residual 110.66 124.76 -14.10 3.00e+00 1.11e-01 2.21e+01 angle pdb=" C32 POV A 901 " pdb=" C31 POV A 901 " pdb=" O31 POV A 901 " ideal model delta sigma weight residual 110.66 124.73 -14.07 3.00e+00 1.11e-01 2.20e+01 angle pdb=" C32 POV F 901 " pdb=" C31 POV F 901 " pdb=" O31 POV F 901 " ideal model delta sigma weight residual 110.66 124.72 -14.06 3.00e+00 1.11e-01 2.20e+01 ... (remaining 57806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.60: 13201 14.60 - 29.20: 1432 29.20 - 43.80: 461 43.80 - 58.40: 161 58.40 - 73.00: 31 Dihedral angle restraints: 15286 sinusoidal: 8014 harmonic: 7272 Sorted by residual: dihedral pdb=" CA GLN C 105 " pdb=" C GLN C 105 " pdb=" N TYR C 106 " pdb=" CA TYR C 106 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA GLN B 105 " pdb=" C GLN B 105 " pdb=" N TYR B 106 " pdb=" CA TYR B 106 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA GLN D 105 " pdb=" C GLN D 105 " pdb=" N TYR D 106 " pdb=" CA TYR D 106 " ideal model delta harmonic sigma weight residual 180.00 156.61 23.39 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 15283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1822 0.048 - 0.095: 477 0.095 - 0.143: 108 0.143 - 0.191: 0 0.191 - 0.238: 1 Chirality restraints: 2408 Sorted by residual: chirality pdb=" C24 L9Y A 904 " pdb=" C05 L9Y A 904 " pdb=" C25 L9Y A 904 " pdb=" C28 L9Y A 904 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE C 365 " pdb=" N ILE C 365 " pdb=" C ILE C 365 " pdb=" CB ILE C 365 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE D 365 " pdb=" N ILE D 365 " pdb=" C ILE D 365 " pdb=" CB ILE D 365 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 2405 not shown) Planarity restraints: 4479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN E 49 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.62e+00 pdb=" C GLN E 49 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN E 49 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP E 50 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 49 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.61e+00 pdb=" C GLN D 49 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN D 49 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP D 50 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 49 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.60e+00 pdb=" C GLN F 49 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN F 49 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP F 50 " 0.007 2.00e-02 2.50e+03 ... (remaining 4476 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 5554 2.29 - 2.87: 70578 2.87 - 3.44: 79648 3.44 - 4.02: 107617 4.02 - 4.60: 164457 Nonbonded interactions: 427854 Sorted by model distance: nonbonded pdb=" O CYS A 139 " pdb="HE21 GLN A 267 " model vdw 1.711 2.450 nonbonded pdb=" O CYS E 139 " pdb="HE21 GLN E 267 " model vdw 1.712 2.450 nonbonded pdb=" O CYS B 139 " pdb="HE21 GLN B 267 " model vdw 1.712 2.450 nonbonded pdb=" O CYS D 139 " pdb="HE21 GLN D 267 " model vdw 1.712 2.450 nonbonded pdb=" O CYS C 139 " pdb="HE21 GLN C 267 " model vdw 1.712 2.450 ... (remaining 427849 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 15 through 903) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 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: 0.160 Extract box with map and model: 0.300 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.680 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 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 : 0.008 0.149 16458 Z= 0.363 Angle : 0.896 14.138 22225 Z= 0.450 Chirality : 0.043 0.238 2408 Planarity : 0.003 0.027 2673 Dihedral : 13.903 72.998 6028 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.09 % Allowed : 9.97 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.71 (0.17), residues: 1842 helix: -2.99 (0.11), residues: 1134 sheet: -0.61 (0.54), residues: 96 loop : -1.19 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 346 TYR 0.017 0.002 TYR D 106 PHE 0.015 0.002 PHE D 156 TRP 0.015 0.002 TRP F 143 HIS 0.007 0.002 HIS F 377 Details of bonding type rmsd covalent geometry : bond 0.00824 (16440) covalent geometry : angle 0.89668 (22189) SS BOND : bond 0.00215 ( 18) SS BOND : angle 0.69957 ( 36) hydrogen bonds : bond 0.30088 ( 911) hydrogen bonds : angle 9.20448 ( 2625) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 337 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.7157 (t70) cc_final: 0.6933 (t70) REVERT: A 262 ARG cc_start: 0.7705 (mmt90) cc_final: 0.7219 (mtm-85) REVERT: A 269 ILE cc_start: 0.8312 (tt) cc_final: 0.8090 (tp) REVERT: A 288 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.8440 (t0) REVERT: B 244 PHE cc_start: 0.7403 (m-80) cc_final: 0.7114 (m-80) REVERT: B 262 ARG cc_start: 0.7526 (mmt90) cc_final: 0.7252 (mtm-85) REVERT: B 269 ILE cc_start: 0.8140 (tt) cc_final: 0.7855 (tp) REVERT: B 288 ASN cc_start: 0.8507 (OUTLIER) cc_final: 0.8120 (m-40) REVERT: B 381 GLN cc_start: 0.6533 (tp40) cc_final: 0.6311 (mm-40) REVERT: B 388 LYS cc_start: 0.6780 (tttt) cc_final: 0.6568 (tptp) REVERT: B 399 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7478 (tp30) REVERT: C 50 ASP cc_start: 0.7422 (t70) cc_final: 0.7218 (t70) REVERT: C 168 TRP cc_start: 0.7878 (t60) cc_final: 0.7572 (t60) REVERT: C 262 ARG cc_start: 0.7463 (mmt90) cc_final: 0.7116 (mtm-85) REVERT: C 269 ILE cc_start: 0.8187 (tt) cc_final: 0.7969 (tp) REVERT: C 284 TYR cc_start: 0.8470 (t80) cc_final: 0.8169 (t80) REVERT: C 288 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8047 (m-40) REVERT: C 377 HIS cc_start: 0.7694 (OUTLIER) cc_final: 0.6928 (m170) REVERT: C 381 GLN cc_start: 0.6858 (tp40) cc_final: 0.6596 (mm-40) REVERT: C 394 LEU cc_start: 0.8205 (tp) cc_final: 0.7816 (tp) REVERT: C 399 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7471 (tp30) REVERT: D 50 ASP cc_start: 0.7029 (t70) cc_final: 0.6814 (t70) REVERT: D 168 TRP cc_start: 0.7961 (t60) cc_final: 0.7613 (t60) REVERT: D 244 PHE cc_start: 0.7257 (m-80) cc_final: 0.6642 (m-80) REVERT: D 262 ARG cc_start: 0.7620 (mmt90) cc_final: 0.7152 (mtm-85) REVERT: D 269 ILE cc_start: 0.8191 (tt) cc_final: 0.7961 (tp) REVERT: D 288 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8107 (m-40) REVERT: D 381 GLN cc_start: 0.6640 (tp40) cc_final: 0.6334 (mm110) REVERT: E 244 PHE cc_start: 0.7411 (m-80) cc_final: 0.6992 (m-80) REVERT: E 262 ARG cc_start: 0.7587 (mmt90) cc_final: 0.7285 (mtm-85) REVERT: E 269 ILE cc_start: 0.8187 (tt) cc_final: 0.7903 (tp) REVERT: E 288 ASN cc_start: 0.8502 (OUTLIER) cc_final: 0.8102 (m-40) REVERT: E 381 GLN cc_start: 0.6593 (tp40) cc_final: 0.6367 (mm-40) REVERT: E 399 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7485 (tp30) REVERT: F 50 ASP cc_start: 0.7409 (t70) cc_final: 0.7205 (t70) REVERT: F 168 TRP cc_start: 0.7911 (t60) cc_final: 0.7554 (t60) REVERT: F 262 ARG cc_start: 0.7331 (mmt90) cc_final: 0.6972 (mtm-85) REVERT: F 284 TYR cc_start: 0.8409 (t80) cc_final: 0.8134 (t80) REVERT: F 288 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8001 (m-40) REVERT: F 377 HIS cc_start: 0.7649 (OUTLIER) cc_final: 0.6960 (m170) REVERT: F 381 GLN cc_start: 0.6907 (tp40) cc_final: 0.6638 (mm110) REVERT: F 394 LEU cc_start: 0.8354 (tp) cc_final: 0.7973 (tp) REVERT: F 399 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7438 (tp30) REVERT: F 402 LEU cc_start: 0.8135 (tp) cc_final: 0.7907 (tp) outliers start: 54 outliers final: 20 residues processed: 391 average time/residue: 0.3120 time to fit residues: 176.1661 Evaluate side-chains 282 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 254 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 288 ASN Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 377 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS B 253 HIS C 253 HIS D 253 HIS E 253 HIS F 253 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.169309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.135995 restraints weight = 68302.119| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 2.58 r_work: 0.3766 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 16458 Z= 0.171 Angle : 0.596 5.196 22225 Z= 0.333 Chirality : 0.038 0.118 2408 Planarity : 0.004 0.025 2673 Dihedral : 8.324 50.054 2306 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.86 % Allowed : 12.43 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.18), residues: 1842 helix: -0.90 (0.13), residues: 1254 sheet: -0.51 (0.51), residues: 96 loop : -1.70 (0.30), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 389 TYR 0.014 0.001 TYR B 332 PHE 0.012 0.002 PHE A 372 TRP 0.010 0.001 TRP F 143 HIS 0.006 0.001 HIS F 253 Details of bonding type rmsd covalent geometry : bond 0.00382 (16440) covalent geometry : angle 0.59561 (22189) SS BOND : bond 0.00310 ( 18) SS BOND : angle 0.58920 ( 36) hydrogen bonds : bond 0.05909 ( 911) hydrogen bonds : angle 4.53105 ( 2625) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 264 time to evaluate : 0.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 LYS cc_start: 0.8643 (tptm) cc_final: 0.8293 (mtpt) REVERT: A 262 ARG cc_start: 0.8158 (mmt90) cc_final: 0.7147 (mtm-85) REVERT: A 288 ASN cc_start: 0.9151 (OUTLIER) cc_final: 0.8843 (t0) REVERT: A 346 ARG cc_start: 0.6926 (tpt-90) cc_final: 0.6642 (mmt180) REVERT: A 375 MET cc_start: 0.8084 (mtm) cc_final: 0.7825 (mtm) REVERT: B 248 LYS cc_start: 0.8657 (tptm) cc_final: 0.8279 (mtpt) REVERT: B 262 ARG cc_start: 0.8253 (mmt90) cc_final: 0.7405 (mtm-85) REVERT: B 280 CYS cc_start: 0.8788 (m) cc_final: 0.8531 (t) REVERT: B 377 HIS cc_start: 0.7291 (OUTLIER) cc_final: 0.6982 (m170) REVERT: B 399 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7492 (tp30) REVERT: C 262 ARG cc_start: 0.8152 (mmt90) cc_final: 0.7386 (mtp180) REVERT: C 377 HIS cc_start: 0.7254 (OUTLIER) cc_final: 0.6978 (m170) REVERT: C 399 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7564 (tp30) REVERT: D 248 LYS cc_start: 0.8698 (tptm) cc_final: 0.8305 (mtpt) REVERT: D 262 ARG cc_start: 0.8234 (mmt90) cc_final: 0.7208 (mtm-85) REVERT: D 288 ASN cc_start: 0.9159 (OUTLIER) cc_final: 0.8875 (t0) REVERT: D 346 ARG cc_start: 0.7103 (tpt-90) cc_final: 0.6857 (mmt180) REVERT: D 375 MET cc_start: 0.8038 (mtm) cc_final: 0.7828 (mtm) REVERT: D 399 GLU cc_start: 0.7911 (tp30) cc_final: 0.7674 (tp30) REVERT: E 262 ARG cc_start: 0.8231 (mmt90) cc_final: 0.7359 (mtm-85) REVERT: E 280 CYS cc_start: 0.8804 (m) cc_final: 0.8540 (t) REVERT: E 377 HIS cc_start: 0.7274 (OUTLIER) cc_final: 0.6994 (m170) REVERT: E 399 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7557 (tp30) REVERT: F 248 LYS cc_start: 0.8478 (tptt) cc_final: 0.8099 (mtpt) REVERT: F 262 ARG cc_start: 0.8032 (mmt90) cc_final: 0.7169 (mtm180) REVERT: F 377 HIS cc_start: 0.7264 (OUTLIER) cc_final: 0.6991 (m170) REVERT: F 394 LEU cc_start: 0.8081 (tp) cc_final: 0.7735 (tp) REVERT: F 399 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7513 (tp30) outliers start: 50 outliers final: 27 residues processed: 310 average time/residue: 0.2723 time to fit residues: 126.2725 Evaluate side-chains 269 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 236 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 377 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 153 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 65 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 288 ASN F 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.167043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.132734 restraints weight = 66682.116| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.55 r_work: 0.3635 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16458 Z= 0.143 Angle : 0.531 4.910 22225 Z= 0.293 Chirality : 0.036 0.128 2408 Planarity : 0.003 0.022 2673 Dihedral : 7.604 53.870 2292 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.89 % Allowed : 16.84 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.77 (0.19), residues: 1842 helix: 0.07 (0.15), residues: 1212 sheet: -0.17 (0.49), residues: 96 loop : -1.75 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 389 TYR 0.009 0.001 TYR B 332 PHE 0.014 0.001 PHE A 244 TRP 0.009 0.001 TRP C 143 HIS 0.005 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00321 (16440) covalent geometry : angle 0.53147 (22189) SS BOND : bond 0.00240 ( 18) SS BOND : angle 0.52548 ( 36) hydrogen bonds : bond 0.05067 ( 911) hydrogen bonds : angle 4.12768 ( 2625) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 255 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7522 (pt0) cc_final: 0.7296 (pt0) REVERT: A 248 LYS cc_start: 0.8703 (tptm) cc_final: 0.8266 (mtpt) REVERT: A 262 ARG cc_start: 0.8082 (mmt90) cc_final: 0.7021 (mtm-85) REVERT: A 359 GLU cc_start: 0.7295 (tp30) cc_final: 0.6947 (tm-30) REVERT: A 399 GLU cc_start: 0.7846 (tp30) cc_final: 0.7587 (tp30) REVERT: B 154 GLU cc_start: 0.7813 (pt0) cc_final: 0.7503 (pt0) REVERT: B 262 ARG cc_start: 0.8121 (mmt90) cc_final: 0.7233 (mtm-85) REVERT: B 280 CYS cc_start: 0.8907 (m) cc_final: 0.8598 (t) REVERT: B 377 HIS cc_start: 0.6981 (OUTLIER) cc_final: 0.6613 (m170) REVERT: B 399 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7463 (tp30) REVERT: C 262 ARG cc_start: 0.8113 (mmt90) cc_final: 0.7251 (mtp180) REVERT: C 288 ASN cc_start: 0.9080 (OUTLIER) cc_final: 0.8630 (m-40) REVERT: C 359 GLU cc_start: 0.7491 (tp30) cc_final: 0.7168 (tp30) REVERT: C 377 HIS cc_start: 0.6994 (OUTLIER) cc_final: 0.6718 (m170) REVERT: C 399 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7374 (tp30) REVERT: D 248 LYS cc_start: 0.8667 (tptm) cc_final: 0.8244 (mtpt) REVERT: D 262 ARG cc_start: 0.8130 (mmt90) cc_final: 0.7101 (mtm-85) REVERT: D 399 GLU cc_start: 0.7991 (tp30) cc_final: 0.7734 (tp30) REVERT: E 262 ARG cc_start: 0.8112 (mmt90) cc_final: 0.7231 (mtm-85) REVERT: E 280 CYS cc_start: 0.8872 (m) cc_final: 0.8567 (t) REVERT: E 377 HIS cc_start: 0.6919 (OUTLIER) cc_final: 0.6534 (m170) REVERT: E 399 GLU cc_start: 0.8036 (tm-30) cc_final: 0.7524 (tp30) REVERT: F 168 TRP cc_start: 0.7983 (t60) cc_final: 0.7580 (t60) REVERT: F 248 LYS cc_start: 0.8475 (tptt) cc_final: 0.8036 (mtpt) REVERT: F 262 ARG cc_start: 0.7940 (mmt90) cc_final: 0.7015 (mtm180) REVERT: F 288 ASN cc_start: 0.9073 (OUTLIER) cc_final: 0.8632 (m-40) REVERT: F 377 HIS cc_start: 0.6988 (OUTLIER) cc_final: 0.6689 (m170) REVERT: F 394 LEU cc_start: 0.7947 (tp) cc_final: 0.7699 (tp) REVERT: F 399 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7453 (tp30) outliers start: 33 outliers final: 19 residues processed: 285 average time/residue: 0.3049 time to fit residues: 126.2017 Evaluate side-chains 258 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 233 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 355 SER Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 377 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 63 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 53 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 126 optimal weight: 0.9990 chunk 100 optimal weight: 0.8980 chunk 71 optimal weight: 0.2980 chunk 83 optimal weight: 0.9980 chunk 175 optimal weight: 0.0970 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.163234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.128861 restraints weight = 65762.163| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.53 r_work: 0.3628 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16458 Z= 0.124 Angle : 0.501 4.479 22225 Z= 0.277 Chirality : 0.036 0.124 2408 Planarity : 0.002 0.022 2673 Dihedral : 7.263 59.252 2286 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.37 % Allowed : 18.10 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.19), residues: 1842 helix: 0.55 (0.15), residues: 1212 sheet: 0.07 (0.49), residues: 96 loop : -1.64 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 389 TYR 0.008 0.001 TYR E 332 PHE 0.016 0.001 PHE A 244 TRP 0.008 0.001 TRP E 143 HIS 0.004 0.001 HIS C 377 Details of bonding type rmsd covalent geometry : bond 0.00273 (16440) covalent geometry : angle 0.50104 (22189) SS BOND : bond 0.00224 ( 18) SS BOND : angle 0.47405 ( 36) hydrogen bonds : bond 0.04417 ( 911) hydrogen bonds : angle 3.91713 ( 2625) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 250 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7479 (pt0) cc_final: 0.7101 (pt0) REVERT: A 248 LYS cc_start: 0.8708 (tptm) cc_final: 0.8304 (mtpt) REVERT: A 262 ARG cc_start: 0.8183 (mmt90) cc_final: 0.7082 (mtm-85) REVERT: A 288 ASN cc_start: 0.9179 (OUTLIER) cc_final: 0.8937 (t0) REVERT: A 331 PHE cc_start: 0.7041 (t80) cc_final: 0.6655 (m-10) REVERT: A 359 GLU cc_start: 0.7314 (tp30) cc_final: 0.6944 (tm-30) REVERT: A 399 GLU cc_start: 0.7807 (tp30) cc_final: 0.7518 (tp30) REVERT: B 154 GLU cc_start: 0.7815 (pt0) cc_final: 0.7476 (pt0) REVERT: B 168 TRP cc_start: 0.8031 (t60) cc_final: 0.7614 (t60) REVERT: B 248 LYS cc_start: 0.8722 (tptm) cc_final: 0.8337 (mtpt) REVERT: B 262 ARG cc_start: 0.8118 (mmt90) cc_final: 0.7252 (mtm-85) REVERT: B 280 CYS cc_start: 0.8876 (m) cc_final: 0.8544 (t) REVERT: B 377 HIS cc_start: 0.6961 (OUTLIER) cc_final: 0.6754 (m170) REVERT: B 399 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7488 (tp30) REVERT: C 262 ARG cc_start: 0.8113 (mmt90) cc_final: 0.7219 (mtp180) REVERT: C 377 HIS cc_start: 0.6948 (OUTLIER) cc_final: 0.6664 (m170) REVERT: C 399 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7377 (tp30) REVERT: D 154 GLU cc_start: 0.7753 (pt0) cc_final: 0.7473 (pt0) REVERT: D 248 LYS cc_start: 0.8671 (tptm) cc_final: 0.8264 (mtpt) REVERT: D 262 ARG cc_start: 0.8231 (mmt90) cc_final: 0.7132 (mtm-85) REVERT: D 331 PHE cc_start: 0.7057 (t80) cc_final: 0.6634 (m-10) REVERT: D 399 GLU cc_start: 0.7948 (tp30) cc_final: 0.7665 (tp30) REVERT: E 262 ARG cc_start: 0.8122 (mmt90) cc_final: 0.7266 (mtm-85) REVERT: E 280 CYS cc_start: 0.8811 (m) cc_final: 0.8516 (t) REVERT: E 399 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7389 (tp30) REVERT: F 262 ARG cc_start: 0.7958 (mmt90) cc_final: 0.7113 (mtp180) REVERT: F 359 GLU cc_start: 0.7497 (tp30) cc_final: 0.6779 (pm20) REVERT: F 377 HIS cc_start: 0.6933 (OUTLIER) cc_final: 0.6687 (m170) REVERT: F 394 LEU cc_start: 0.7963 (tp) cc_final: 0.7706 (tp) REVERT: F 399 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7449 (tp30) outliers start: 24 outliers final: 19 residues processed: 273 average time/residue: 0.2811 time to fit residues: 116.1283 Evaluate side-chains 256 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 301 SER Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 377 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 101 optimal weight: 0.0670 chunk 176 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 40 optimal weight: 0.9990 chunk 131 optimal weight: 0.1980 chunk 15 optimal weight: 0.0970 chunk 135 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN B 105 GLN ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 GLN D 105 GLN E 105 GLN ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.167808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.133238 restraints weight = 66747.905| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 2.65 r_work: 0.3641 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 16458 Z= 0.108 Angle : 0.476 4.172 22225 Z= 0.263 Chirality : 0.035 0.125 2408 Planarity : 0.002 0.023 2673 Dihedral : 6.849 58.125 2280 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.78 % Allowed : 18.50 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.20), residues: 1842 helix: 0.92 (0.16), residues: 1212 sheet: 0.16 (0.48), residues: 96 loop : -1.49 (0.25), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 357 TYR 0.007 0.001 TYR D 332 PHE 0.017 0.001 PHE A 244 TRP 0.008 0.001 TRP E 143 HIS 0.004 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00234 (16440) covalent geometry : angle 0.47654 (22189) SS BOND : bond 0.00192 ( 18) SS BOND : angle 0.40926 ( 36) hydrogen bonds : bond 0.04031 ( 911) hydrogen bonds : angle 3.75200 ( 2625) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 265 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 LYS cc_start: 0.8683 (tptm) cc_final: 0.8274 (mtpt) REVERT: A 262 ARG cc_start: 0.8195 (mmt90) cc_final: 0.7090 (mtm-85) REVERT: A 288 ASN cc_start: 0.9235 (OUTLIER) cc_final: 0.8995 (t0) REVERT: A 289 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8378 (pt) REVERT: A 331 PHE cc_start: 0.7026 (t80) cc_final: 0.6646 (m-10) REVERT: A 376 LEU cc_start: 0.6006 (OUTLIER) cc_final: 0.5768 (tm) REVERT: A 377 HIS cc_start: 0.6706 (OUTLIER) cc_final: 0.6415 (m170) REVERT: A 399 GLU cc_start: 0.7846 (tp30) cc_final: 0.7550 (tp30) REVERT: B 18 ARG cc_start: 0.8127 (ptp-170) cc_final: 0.7730 (ptp90) REVERT: B 154 GLU cc_start: 0.7817 (pt0) cc_final: 0.7459 (pt0) REVERT: B 248 LYS cc_start: 0.8713 (tptm) cc_final: 0.8309 (mtpt) REVERT: B 262 ARG cc_start: 0.8125 (mmt90) cc_final: 0.7251 (mtm-85) REVERT: B 377 HIS cc_start: 0.7030 (OUTLIER) cc_final: 0.6730 (m170) REVERT: B 399 GLU cc_start: 0.7953 (tm-30) cc_final: 0.7485 (tp30) REVERT: C 262 ARG cc_start: 0.8182 (mmt90) cc_final: 0.7290 (mtp180) REVERT: C 376 LEU cc_start: 0.5984 (OUTLIER) cc_final: 0.5668 (tm) REVERT: C 377 HIS cc_start: 0.6888 (OUTLIER) cc_final: 0.6576 (m170) REVERT: C 399 GLU cc_start: 0.7810 (tm-30) cc_final: 0.7380 (tp30) REVERT: D 154 GLU cc_start: 0.7740 (pt0) cc_final: 0.7358 (pt0) REVERT: D 248 LYS cc_start: 0.8658 (tptm) cc_final: 0.8235 (mtpt) REVERT: D 262 ARG cc_start: 0.8249 (mmt90) cc_final: 0.7191 (mtm-85) REVERT: D 288 ASN cc_start: 0.9221 (OUTLIER) cc_final: 0.8995 (t0) REVERT: D 289 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8370 (pt) REVERT: D 331 PHE cc_start: 0.7042 (t80) cc_final: 0.6643 (m-10) REVERT: D 376 LEU cc_start: 0.6003 (OUTLIER) cc_final: 0.5757 (tm) REVERT: D 377 HIS cc_start: 0.6663 (OUTLIER) cc_final: 0.6385 (m170) REVERT: D 399 GLU cc_start: 0.7985 (tp30) cc_final: 0.7691 (tp30) REVERT: E 18 ARG cc_start: 0.8121 (ptp-170) cc_final: 0.7838 (ptp90) REVERT: E 262 ARG cc_start: 0.8133 (mmt90) cc_final: 0.7269 (mtm-85) REVERT: E 288 ASN cc_start: 0.8671 (t0) cc_final: 0.8468 (t0) REVERT: E 359 GLU cc_start: 0.7046 (tp30) cc_final: 0.6326 (pm20) REVERT: E 399 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7481 (tp30) REVERT: F 262 ARG cc_start: 0.8002 (mmt90) cc_final: 0.7155 (mtp180) REVERT: F 359 GLU cc_start: 0.7486 (tp30) cc_final: 0.6767 (pm20) REVERT: F 376 LEU cc_start: 0.6022 (OUTLIER) cc_final: 0.5702 (tm) REVERT: F 377 HIS cc_start: 0.6918 (OUTLIER) cc_final: 0.6612 (m170) REVERT: F 399 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7436 (tp30) outliers start: 31 outliers final: 15 residues processed: 295 average time/residue: 0.2817 time to fit residues: 123.1824 Evaluate side-chains 272 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 244 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 377 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 163 optimal weight: 0.3980 chunk 9 optimal weight: 0.9980 chunk 158 optimal weight: 0.2980 chunk 120 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 99 optimal weight: 0.0020 chunk 131 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 288 ASN E 288 ASN F 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.169431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.134458 restraints weight = 65813.706| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.69 r_work: 0.3637 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16458 Z= 0.110 Angle : 0.472 4.374 22225 Z= 0.260 Chirality : 0.035 0.124 2408 Planarity : 0.002 0.023 2673 Dihedral : 6.677 58.757 2280 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.12 % Allowed : 18.50 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.56 (0.20), residues: 1842 helix: 1.18 (0.16), residues: 1206 sheet: 0.37 (0.48), residues: 96 loop : -1.44 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 357 TYR 0.008 0.001 TYR D 332 PHE 0.017 0.001 PHE A 244 TRP 0.008 0.001 TRP E 143 HIS 0.004 0.001 HIS C 377 Details of bonding type rmsd covalent geometry : bond 0.00243 (16440) covalent geometry : angle 0.47247 (22189) SS BOND : bond 0.00182 ( 18) SS BOND : angle 0.39306 ( 36) hydrogen bonds : bond 0.03847 ( 911) hydrogen bonds : angle 3.64809 ( 2625) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 261 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 168 TRP cc_start: 0.7985 (t60) cc_final: 0.7463 (t60) REVERT: A 248 LYS cc_start: 0.8671 (tptm) cc_final: 0.8266 (mtpt) REVERT: A 262 ARG cc_start: 0.8198 (mmt90) cc_final: 0.7086 (mtm-85) REVERT: A 288 ASN cc_start: 0.9242 (OUTLIER) cc_final: 0.9014 (t0) REVERT: A 289 ILE cc_start: 0.8602 (OUTLIER) cc_final: 0.8375 (pt) REVERT: A 331 PHE cc_start: 0.7216 (t80) cc_final: 0.6831 (m-10) REVERT: A 376 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5790 (tm) REVERT: A 399 GLU cc_start: 0.7914 (tp30) cc_final: 0.7587 (tp30) REVERT: B 18 ARG cc_start: 0.8111 (ptp-170) cc_final: 0.7727 (ptp90) REVERT: B 154 GLU cc_start: 0.7772 (pt0) cc_final: 0.7476 (pt0) REVERT: B 248 LYS cc_start: 0.8715 (tptm) cc_final: 0.8310 (mtpt) REVERT: B 262 ARG cc_start: 0.8095 (mmt90) cc_final: 0.7250 (mtm-85) REVERT: B 377 HIS cc_start: 0.6982 (OUTLIER) cc_final: 0.6597 (m170) REVERT: B 399 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7498 (tp30) REVERT: C 262 ARG cc_start: 0.8165 (mmt90) cc_final: 0.7268 (mtp180) REVERT: C 331 PHE cc_start: 0.7176 (t80) cc_final: 0.6798 (m-10) REVERT: C 376 LEU cc_start: 0.6072 (OUTLIER) cc_final: 0.5735 (tm) REVERT: C 377 HIS cc_start: 0.6939 (OUTLIER) cc_final: 0.6542 (m170) REVERT: C 399 GLU cc_start: 0.7814 (tm-30) cc_final: 0.7560 (tp30) REVERT: D 154 GLU cc_start: 0.7760 (pt0) cc_final: 0.7367 (pt0) REVERT: D 248 LYS cc_start: 0.8671 (tptm) cc_final: 0.8259 (mtpt) REVERT: D 262 ARG cc_start: 0.8260 (mmt90) cc_final: 0.7195 (mtm-85) REVERT: D 288 ASN cc_start: 0.9225 (OUTLIER) cc_final: 0.9020 (t0) REVERT: D 289 ILE cc_start: 0.8604 (OUTLIER) cc_final: 0.8369 (pt) REVERT: D 331 PHE cc_start: 0.7121 (t80) cc_final: 0.6709 (m-10) REVERT: D 376 LEU cc_start: 0.5965 (OUTLIER) cc_final: 0.5729 (tm) REVERT: D 399 GLU cc_start: 0.8019 (tp30) cc_final: 0.7777 (tp30) REVERT: E 18 ARG cc_start: 0.8113 (ptp-170) cc_final: 0.7831 (ptp90) REVERT: E 262 ARG cc_start: 0.8072 (mmt90) cc_final: 0.7165 (mtm-85) REVERT: E 359 GLU cc_start: 0.7041 (tp30) cc_final: 0.6314 (pm20) REVERT: E 399 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7469 (tp30) REVERT: F 262 ARG cc_start: 0.8075 (mmt90) cc_final: 0.7178 (mtp180) REVERT: F 331 PHE cc_start: 0.7125 (t80) cc_final: 0.6746 (m-10) REVERT: F 359 GLU cc_start: 0.7476 (tp30) cc_final: 0.6769 (pm20) REVERT: F 376 LEU cc_start: 0.6011 (OUTLIER) cc_final: 0.5675 (tm) REVERT: F 377 HIS cc_start: 0.6968 (OUTLIER) cc_final: 0.6644 (m170) REVERT: F 399 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7475 (tp30) outliers start: 37 outliers final: 21 residues processed: 296 average time/residue: 0.2681 time to fit residues: 118.9242 Evaluate side-chains 278 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 246 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 377 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.9990 chunk 145 optimal weight: 0.6980 chunk 101 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 82 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 128 optimal weight: 0.4980 chunk 50 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.168054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.134343 restraints weight = 66448.175| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.58 r_work: 0.3619 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16458 Z= 0.136 Angle : 0.494 4.493 22225 Z= 0.273 Chirality : 0.036 0.123 2408 Planarity : 0.002 0.022 2673 Dihedral : 6.860 58.937 2280 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.35 % Allowed : 19.07 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.20), residues: 1842 helix: 1.23 (0.16), residues: 1218 sheet: 0.66 (0.50), residues: 96 loop : -1.34 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 103 TYR 0.012 0.001 TYR D 332 PHE 0.019 0.001 PHE A 244 TRP 0.009 0.001 TRP E 143 HIS 0.004 0.001 HIS F 377 Details of bonding type rmsd covalent geometry : bond 0.00310 (16440) covalent geometry : angle 0.49354 (22189) SS BOND : bond 0.00213 ( 18) SS BOND : angle 0.47243 ( 36) hydrogen bonds : bond 0.03881 ( 911) hydrogen bonds : angle 3.68487 ( 2625) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 260 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 LYS cc_start: 0.8668 (tptm) cc_final: 0.8262 (mtpt) REVERT: A 262 ARG cc_start: 0.8188 (mmt90) cc_final: 0.7113 (mtm-85) REVERT: A 289 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8440 (pt) REVERT: A 331 PHE cc_start: 0.7165 (t80) cc_final: 0.6806 (m-10) REVERT: A 376 LEU cc_start: 0.5771 (OUTLIER) cc_final: 0.5414 (tm) REVERT: A 399 GLU cc_start: 0.8019 (tp30) cc_final: 0.7657 (tp30) REVERT: B 18 ARG cc_start: 0.8118 (ptp-170) cc_final: 0.7714 (ptp90) REVERT: B 154 GLU cc_start: 0.7727 (pt0) cc_final: 0.7419 (pt0) REVERT: B 248 LYS cc_start: 0.8730 (tptm) cc_final: 0.8328 (mtpt) REVERT: B 262 ARG cc_start: 0.8163 (mmt90) cc_final: 0.7296 (mtm-85) REVERT: B 399 GLU cc_start: 0.7948 (tm-30) cc_final: 0.7513 (tp30) REVERT: C 262 ARG cc_start: 0.8280 (mmt90) cc_final: 0.7413 (mtp180) REVERT: C 376 LEU cc_start: 0.6137 (OUTLIER) cc_final: 0.5762 (tm) REVERT: C 377 HIS cc_start: 0.7033 (OUTLIER) cc_final: 0.6490 (m170) REVERT: C 399 GLU cc_start: 0.7908 (tm-30) cc_final: 0.7604 (tp30) REVERT: D 154 GLU cc_start: 0.7759 (pt0) cc_final: 0.7331 (pt0) REVERT: D 155 HIS cc_start: 0.7333 (t-170) cc_final: 0.6668 (m-70) REVERT: D 248 LYS cc_start: 0.8666 (tptm) cc_final: 0.8265 (mtpt) REVERT: D 262 ARG cc_start: 0.8241 (mmt90) cc_final: 0.7164 (mtm-85) REVERT: D 289 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8421 (pt) REVERT: D 331 PHE cc_start: 0.7196 (t80) cc_final: 0.6802 (m-10) REVERT: D 376 LEU cc_start: 0.5771 (OUTLIER) cc_final: 0.5402 (tm) REVERT: D 399 GLU cc_start: 0.8127 (tp30) cc_final: 0.7876 (tp30) REVERT: E 18 ARG cc_start: 0.8120 (ptp-170) cc_final: 0.7831 (ptp90) REVERT: E 248 LYS cc_start: 0.8700 (tptm) cc_final: 0.8287 (mtpt) REVERT: E 262 ARG cc_start: 0.8134 (mmt90) cc_final: 0.7204 (mtm-85) REVERT: E 399 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7671 (tp30) REVERT: F 262 ARG cc_start: 0.8188 (mmt90) cc_final: 0.7366 (mtp180) REVERT: F 376 LEU cc_start: 0.6014 (OUTLIER) cc_final: 0.5642 (tm) REVERT: F 377 HIS cc_start: 0.7029 (OUTLIER) cc_final: 0.6492 (m170) REVERT: F 399 GLU cc_start: 0.7753 (tm-30) cc_final: 0.7446 (tp30) outliers start: 41 outliers final: 20 residues processed: 300 average time/residue: 0.2857 time to fit residues: 129.0288 Evaluate side-chains 278 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 250 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 377 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 50 optimal weight: 0.7980 chunk 168 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 92 optimal weight: 0.9990 chunk 154 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 ASN D 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.166186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.132141 restraints weight = 66597.498| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.63 r_work: 0.3593 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7481 moved from start: 0.4117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16458 Z= 0.161 Angle : 0.516 4.500 22225 Z= 0.285 Chirality : 0.037 0.121 2408 Planarity : 0.002 0.022 2673 Dihedral : 6.892 58.651 2274 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.41 % Allowed : 19.24 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.20), residues: 1842 helix: 1.23 (0.16), residues: 1218 sheet: 0.76 (0.50), residues: 96 loop : -1.32 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 103 TYR 0.010 0.001 TYR D 332 PHE 0.017 0.001 PHE A 244 TRP 0.009 0.001 TRP B 143 HIS 0.004 0.001 HIS F 377 Details of bonding type rmsd covalent geometry : bond 0.00373 (16440) covalent geometry : angle 0.51589 (22189) SS BOND : bond 0.00246 ( 18) SS BOND : angle 0.53238 ( 36) hydrogen bonds : bond 0.03971 ( 911) hydrogen bonds : angle 3.76542 ( 2625) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 259 time to evaluate : 0.850 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 HIS cc_start: 0.7406 (t-170) cc_final: 0.6654 (m-70) REVERT: A 248 LYS cc_start: 0.8676 (tptm) cc_final: 0.8265 (mtpt) REVERT: A 262 ARG cc_start: 0.8250 (mmt90) cc_final: 0.7193 (mtm-85) REVERT: A 288 ASN cc_start: 0.9191 (t160) cc_final: 0.8799 (m-40) REVERT: A 331 PHE cc_start: 0.7254 (t80) cc_final: 0.6850 (m-10) REVERT: A 376 LEU cc_start: 0.5922 (OUTLIER) cc_final: 0.5578 (tm) REVERT: A 399 GLU cc_start: 0.8023 (tp30) cc_final: 0.7740 (tp30) REVERT: B 18 ARG cc_start: 0.8066 (ptp-170) cc_final: 0.7705 (ptp90) REVERT: B 154 GLU cc_start: 0.7739 (pt0) cc_final: 0.7508 (pt0) REVERT: B 155 HIS cc_start: 0.7410 (t-170) cc_final: 0.6752 (m-70) REVERT: B 248 LYS cc_start: 0.8709 (tptm) cc_final: 0.8312 (mtpt) REVERT: B 262 ARG cc_start: 0.8193 (mmt90) cc_final: 0.7337 (mtm-85) REVERT: B 399 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7569 (tp30) REVERT: C 262 ARG cc_start: 0.8315 (mmt90) cc_final: 0.7485 (mtp180) REVERT: C 331 PHE cc_start: 0.7578 (t80) cc_final: 0.7017 (m-10) REVERT: C 376 LEU cc_start: 0.6235 (OUTLIER) cc_final: 0.5859 (tm) REVERT: C 377 HIS cc_start: 0.7061 (OUTLIER) cc_final: 0.6405 (m170) REVERT: C 399 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7578 (tp30) REVERT: D 154 GLU cc_start: 0.7770 (pt0) cc_final: 0.7339 (pt0) REVERT: D 155 HIS cc_start: 0.7394 (t-170) cc_final: 0.6694 (m-70) REVERT: D 248 LYS cc_start: 0.8664 (tptm) cc_final: 0.8261 (mtpt) REVERT: D 262 ARG cc_start: 0.8230 (mmt90) cc_final: 0.7203 (mtm-85) REVERT: D 288 ASN cc_start: 0.9170 (t160) cc_final: 0.8764 (m-40) REVERT: D 331 PHE cc_start: 0.7262 (t80) cc_final: 0.6883 (m-10) REVERT: D 376 LEU cc_start: 0.5898 (OUTLIER) cc_final: 0.5544 (tm) REVERT: D 399 GLU cc_start: 0.8174 (tp30) cc_final: 0.7948 (tp30) REVERT: E 18 ARG cc_start: 0.8101 (ptp-170) cc_final: 0.7821 (ptp90) REVERT: E 248 LYS cc_start: 0.8703 (tptm) cc_final: 0.8295 (mtpt) REVERT: E 262 ARG cc_start: 0.8183 (mmt90) cc_final: 0.7282 (mtm-85) REVERT: E 399 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7764 (tp30) REVERT: F 262 ARG cc_start: 0.8228 (mmt90) cc_final: 0.7431 (mtp180) REVERT: F 331 PHE cc_start: 0.7599 (t80) cc_final: 0.7004 (m-10) REVERT: F 376 LEU cc_start: 0.6083 (OUTLIER) cc_final: 0.5697 (tm) REVERT: F 377 HIS cc_start: 0.7069 (OUTLIER) cc_final: 0.6375 (m170) REVERT: F 399 GLU cc_start: 0.7774 (tm-30) cc_final: 0.7454 (tp30) outliers start: 42 outliers final: 24 residues processed: 299 average time/residue: 0.2701 time to fit residues: 123.0668 Evaluate side-chains 281 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 251 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 326 ILE Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 377 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 159 optimal weight: 0.0970 chunk 129 optimal weight: 5.9990 chunk 131 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 67 optimal weight: 4.9990 chunk 176 optimal weight: 0.6980 chunk 69 optimal weight: 0.3980 chunk 166 optimal weight: 0.9980 chunk 183 optimal weight: 0.5980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.168025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.134239 restraints weight = 65851.379| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.53 r_work: 0.3635 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3503 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.4254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16458 Z= 0.101 Angle : 0.477 4.401 22225 Z= 0.260 Chirality : 0.035 0.124 2408 Planarity : 0.002 0.023 2673 Dihedral : 6.526 58.368 2274 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.60 % Allowed : 19.93 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.21), residues: 1842 helix: 1.48 (0.16), residues: 1218 sheet: 0.95 (0.50), residues: 96 loop : -1.28 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 309 TYR 0.009 0.001 TYR E 284 PHE 0.009 0.001 PHE D 372 TRP 0.009 0.001 TRP A 168 HIS 0.004 0.001 HIS A 377 Details of bonding type rmsd covalent geometry : bond 0.00221 (16440) covalent geometry : angle 0.47715 (22189) SS BOND : bond 0.00169 ( 18) SS BOND : angle 0.34171 ( 36) hydrogen bonds : bond 0.03621 ( 911) hydrogen bonds : angle 3.59858 ( 2625) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 274 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7556 (pm20) REVERT: A 155 HIS cc_start: 0.7369 (t-170) cc_final: 0.6623 (m-70) REVERT: A 262 ARG cc_start: 0.8161 (mmt90) cc_final: 0.7109 (mtm-85) REVERT: A 331 PHE cc_start: 0.7157 (t80) cc_final: 0.6812 (m-10) REVERT: A 376 LEU cc_start: 0.5984 (OUTLIER) cc_final: 0.5664 (tm) REVERT: A 399 GLU cc_start: 0.8058 (tp30) cc_final: 0.7814 (tp30) REVERT: B 18 ARG cc_start: 0.8037 (ptp-170) cc_final: 0.7676 (ptp90) REVERT: B 154 GLU cc_start: 0.7775 (pt0) cc_final: 0.7553 (pt0) REVERT: B 248 LYS cc_start: 0.8720 (tptm) cc_final: 0.8331 (mtpt) REVERT: B 262 ARG cc_start: 0.8101 (mmt90) cc_final: 0.7185 (mtm-85) REVERT: C 262 ARG cc_start: 0.8262 (mmt90) cc_final: 0.7378 (mtp180) REVERT: C 331 PHE cc_start: 0.7498 (t80) cc_final: 0.6988 (m-10) REVERT: C 376 LEU cc_start: 0.6038 (OUTLIER) cc_final: 0.5728 (tm) REVERT: C 377 HIS cc_start: 0.6972 (OUTLIER) cc_final: 0.6363 (m170) REVERT: C 399 GLU cc_start: 0.7863 (tm-30) cc_final: 0.7595 (tp30) REVERT: D 154 GLU cc_start: 0.7806 (pt0) cc_final: 0.7363 (pt0) REVERT: D 155 HIS cc_start: 0.7361 (t-170) cc_final: 0.6669 (m-70) REVERT: D 248 LYS cc_start: 0.8666 (tptm) cc_final: 0.8260 (mtpt) REVERT: D 262 ARG cc_start: 0.8197 (mmt90) cc_final: 0.7165 (mtm-85) REVERT: D 331 PHE cc_start: 0.7214 (t80) cc_final: 0.6819 (m-10) REVERT: D 376 LEU cc_start: 0.5932 (OUTLIER) cc_final: 0.5614 (tm) REVERT: D 399 GLU cc_start: 0.8188 (tp30) cc_final: 0.7914 (tp30) REVERT: E 18 ARG cc_start: 0.8041 (ptp-170) cc_final: 0.7792 (ptp90) REVERT: E 248 LYS cc_start: 0.8708 (tptm) cc_final: 0.8306 (mtpt) REVERT: E 262 ARG cc_start: 0.8137 (mmt90) cc_final: 0.7210 (mtm-85) REVERT: E 399 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7751 (tp30) REVERT: F 262 ARG cc_start: 0.8167 (mmt90) cc_final: 0.7263 (mtp180) REVERT: F 331 PHE cc_start: 0.7531 (t80) cc_final: 0.7009 (m-10) REVERT: F 376 LEU cc_start: 0.6151 (OUTLIER) cc_final: 0.5868 (tm) REVERT: F 377 HIS cc_start: 0.7042 (OUTLIER) cc_final: 0.6497 (m170) REVERT: F 394 LEU cc_start: 0.7745 (tp) cc_final: 0.7316 (tp) outliers start: 28 outliers final: 19 residues processed: 299 average time/residue: 0.2732 time to fit residues: 123.7924 Evaluate side-chains 284 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 258 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 377 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 69 optimal weight: 0.9980 chunk 82 optimal weight: 0.2980 chunk 172 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 21 optimal weight: 0.3980 chunk 36 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 176 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 173 optimal weight: 0.0770 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.168219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.134463 restraints weight = 65564.528| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.57 r_work: 0.3632 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 16458 Z= 0.105 Angle : 0.482 4.538 22225 Z= 0.262 Chirality : 0.035 0.125 2408 Planarity : 0.002 0.022 2673 Dihedral : 6.208 59.108 2270 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.89 % Allowed : 19.64 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.21), residues: 1842 helix: 1.55 (0.16), residues: 1212 sheet: 1.00 (0.49), residues: 96 loop : -1.25 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 103 TYR 0.009 0.001 TYR A 284 PHE 0.009 0.001 PHE C 374 TRP 0.008 0.001 TRP A 168 HIS 0.004 0.001 HIS C 377 Details of bonding type rmsd covalent geometry : bond 0.00233 (16440) covalent geometry : angle 0.48174 (22189) SS BOND : bond 0.00179 ( 18) SS BOND : angle 0.36796 ( 36) hydrogen bonds : bond 0.03548 ( 911) hydrogen bonds : angle 3.57319 ( 2625) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 274 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 GLN cc_start: 0.7962 (OUTLIER) cc_final: 0.7589 (pm20) REVERT: A 154 GLU cc_start: 0.7576 (pt0) cc_final: 0.7341 (pt0) REVERT: A 155 HIS cc_start: 0.7369 (t-170) cc_final: 0.6637 (m-70) REVERT: A 248 LYS cc_start: 0.8677 (tptm) cc_final: 0.8270 (mtpt) REVERT: A 262 ARG cc_start: 0.8100 (mmt90) cc_final: 0.7025 (mtm-85) REVERT: A 288 ASN cc_start: 0.9249 (t160) cc_final: 0.8773 (m-40) REVERT: A 331 PHE cc_start: 0.7219 (t80) cc_final: 0.6842 (m-10) REVERT: A 399 GLU cc_start: 0.8097 (tp30) cc_final: 0.7860 (tp30) REVERT: B 18 ARG cc_start: 0.8040 (ptp-170) cc_final: 0.7689 (ptp90) REVERT: B 154 GLU cc_start: 0.7784 (pt0) cc_final: 0.7464 (pt0) REVERT: B 248 LYS cc_start: 0.8717 (tptm) cc_final: 0.8323 (mtpt) REVERT: B 262 ARG cc_start: 0.8098 (mmt90) cc_final: 0.7177 (mtm-85) REVERT: C 262 ARG cc_start: 0.8236 (mmt90) cc_final: 0.7262 (mtp180) REVERT: C 284 TYR cc_start: 0.9120 (t80) cc_final: 0.8910 (t80) REVERT: C 331 PHE cc_start: 0.7545 (t80) cc_final: 0.7014 (m-10) REVERT: C 376 LEU cc_start: 0.6076 (OUTLIER) cc_final: 0.5722 (tm) REVERT: C 377 HIS cc_start: 0.6964 (OUTLIER) cc_final: 0.6320 (m170) REVERT: C 399 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7591 (tp30) REVERT: D 154 GLU cc_start: 0.7790 (pt0) cc_final: 0.7348 (pt0) REVERT: D 155 HIS cc_start: 0.7358 (t-170) cc_final: 0.6690 (m-70) REVERT: D 248 LYS cc_start: 0.8664 (tptm) cc_final: 0.8251 (mtpt) REVERT: D 262 ARG cc_start: 0.8187 (mmt90) cc_final: 0.7156 (mtm-85) REVERT: D 288 ASN cc_start: 0.9224 (t160) cc_final: 0.8743 (m-40) REVERT: D 289 ILE cc_start: 0.8599 (OUTLIER) cc_final: 0.8348 (pt) REVERT: D 331 PHE cc_start: 0.7236 (t80) cc_final: 0.6832 (m-10) REVERT: D 399 GLU cc_start: 0.8219 (tp30) cc_final: 0.7945 (tp30) REVERT: E 18 ARG cc_start: 0.8072 (ptp-170) cc_final: 0.7819 (ptp90) REVERT: E 248 LYS cc_start: 0.8710 (tptm) cc_final: 0.8299 (mtpt) REVERT: E 262 ARG cc_start: 0.8041 (mmt90) cc_final: 0.7092 (mtm-85) REVERT: E 399 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7735 (tp30) REVERT: F 262 ARG cc_start: 0.8188 (mmt90) cc_final: 0.7255 (mtp180) REVERT: F 331 PHE cc_start: 0.7503 (t80) cc_final: 0.7025 (m-10) REVERT: F 376 LEU cc_start: 0.6024 (OUTLIER) cc_final: 0.5676 (tm) REVERT: F 377 HIS cc_start: 0.6974 (OUTLIER) cc_final: 0.6382 (m170) REVERT: F 394 LEU cc_start: 0.7699 (tp) cc_final: 0.7279 (tp) outliers start: 33 outliers final: 22 residues processed: 302 average time/residue: 0.2697 time to fit residues: 123.6604 Evaluate side-chains 294 residues out of total 1746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 266 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 GLN Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 281 TYR Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 377 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 44 optimal weight: 5.9990 chunk 173 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 129 optimal weight: 0.0570 chunk 65 optimal weight: 0.9980 chunk 172 optimal weight: 0.0970 chunk 185 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 152 optimal weight: 1.9990 chunk 169 optimal weight: 3.9990 overall best weight: 0.3874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.169446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.135626 restraints weight = 65705.211| |-----------------------------------------------------------------------------| r_work (start): 0.3785 rms_B_bonded: 2.61 r_work: 0.3641 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 16458 Z= 0.100 Angle : 0.480 4.423 22225 Z= 0.260 Chirality : 0.035 0.128 2408 Planarity : 0.002 0.023 2673 Dihedral : 6.057 59.297 2270 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.95 % Allowed : 19.93 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.21), residues: 1842 helix: 1.68 (0.16), residues: 1212 sheet: 1.10 (0.50), residues: 96 loop : -1.23 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 357 TYR 0.009 0.001 TYR B 284 PHE 0.009 0.001 PHE D 372 TRP 0.008 0.001 TRP A 168 HIS 0.006 0.001 HIS B 377 Details of bonding type rmsd covalent geometry : bond 0.00219 (16440) covalent geometry : angle 0.47972 (22189) SS BOND : bond 0.00171 ( 18) SS BOND : angle 0.35234 ( 36) hydrogen bonds : bond 0.03477 ( 911) hydrogen bonds : angle 3.54341 ( 2625) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8800.62 seconds wall clock time: 149 minutes 47.40 seconds (8987.40 seconds total)