Starting phenix.real_space_refine on Fri Sep 27 16:18:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m19_23616/09_2024/7m19_23616.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m19_23616/09_2024/7m19_23616.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m19_23616/09_2024/7m19_23616.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m19_23616/09_2024/7m19_23616.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m19_23616/09_2024/7m19_23616.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7m19_23616/09_2024/7m19_23616.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 5 Type Number sf(0) Gaussians S 102 5.16 5 Cl 2 4.86 5 C 10639 2.51 5 N 2532 2.21 5 O 2764 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16039 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "B" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "C" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "D" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "E" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "F" Number of atoms: 2626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2626 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 73 Unusual residues: {'PEE': 3, 'YNJ': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'PEE': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PEE:plan-2': 3} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 10.35, per 1000 atoms: 0.65 Number of scatterers: 16039 At special positions: 0 Unit cell: (110.289, 101.193, 134.166, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 102 16.00 O 2764 8.00 N 2532 7.00 C 10639 6.00 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=2.04 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: 3.93 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 86 helices and 11 sheets defined 74.7% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.62 Creating SS restraints... Processing helix chain 'A' and resid 17 through 22 removed outlier: 3.668A pdb=" N LYS A 21 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Proline residue: A 22 - end of helix Processing helix chain 'A' and resid 23 through 49 removed outlier: 3.509A pdb=" N PHE A 27 " --> pdb=" O TRP A 23 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR A 28 " --> pdb=" O TRP A 24 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ASP A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 116 Processing helix chain 'A' and resid 120 through 146 Proline residue: A 126 - end of helix removed outlier: 4.406A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 165 removed outlier: 4.403A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 174 removed outlier: 4.013A pdb=" N ARG A 171 " --> pdb=" O PRO A 167 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N SER A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 255 Processing helix chain 'A' and resid 258 through 286 removed outlier: 3.642A pdb=" N ARG A 262 " --> pdb=" O ASP A 258 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 4.284A 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 Processing helix chain 'A' and resid 353 through 361 removed outlier: 4.611A pdb=" N GLU A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 391 through 394 removed outlier: 3.618A pdb=" N LEU A 394 " --> pdb=" O ALA A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 394' Processing helix chain 'A' and resid 395 through 408 Processing helix chain 'B' and resid 16 through 21 removed outlier: 3.820A pdb=" N ILE B 19 " --> pdb=" O ALA B 16 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LYS B 21 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 25 Processing helix chain 'B' and resid 26 through 49 removed outlier: 3.811A pdb=" N ILE B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 116 removed outlier: 3.540A pdb=" N TYR B 106 " --> pdb=" O ASP B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 146 removed outlier: 3.739A pdb=" N PHE B 125 " --> pdb=" O PHE B 121 " (cutoff:3.500A) Proline residue: B 126 - end of helix removed outlier: 4.805A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 146 through 166 removed outlier: 4.462A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 174 removed outlier: 4.097A pdb=" N ARG B 171 " --> pdb=" O PRO B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 255 Processing helix chain 'B' and resid 258 through 286 removed outlier: 3.959A pdb=" N THR B 268 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N VAL B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 4.775A 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 347 removed outlier: 4.021A pdb=" N SER B 347 " --> pdb=" O MET B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.906A pdb=" N ARG B 357 " --> pdb=" O PHE B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.495A pdb=" N SER B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 394 removed outlier: 3.687A pdb=" N PHE B 393 " --> pdb=" O PHE B 390 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 394 " --> pdb=" O ALA B 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 390 through 394' Processing helix chain 'B' and resid 395 through 408 Processing helix chain 'C' and resid 23 through 49 removed outlier: 3.620A pdb=" N PHE C 27 " --> pdb=" O TRP C 23 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR C 28 " --> pdb=" O TRP C 24 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 116 Processing helix chain 'C' and resid 119 through 146 removed outlier: 3.888A pdb=" N LYS C 123 " --> pdb=" O HIS C 119 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE C 125 " --> pdb=" O PHE C 121 " (cutoff:3.500A) Proline residue: C 126 - end of helix removed outlier: 4.770A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 165 removed outlier: 4.382A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 174 removed outlier: 3.999A pdb=" N ARG C 171 " --> pdb=" O PRO C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 255 removed outlier: 3.514A pdb=" N GLU C 255 " --> pdb=" O ARG C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 286 removed outlier: 3.998A pdb=" N ILE C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N VAL C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 4.394A 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 347 removed outlier: 4.012A pdb=" N SER C 347 " --> pdb=" O MET C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 361 removed outlier: 3.898A pdb=" N ARG C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU C 359 " --> pdb=" O SER C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 383 Processing helix chain 'C' and resid 384 through 392 removed outlier: 4.168A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 408 Processing helix chain 'D' and resid 16 through 22 removed outlier: 4.113A pdb=" N ILE D 19 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Proline residue: D 22 - end of helix Processing helix chain 'D' and resid 23 through 49 removed outlier: 3.631A pdb=" N PHE D 27 " --> pdb=" O TRP D 23 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THR D 28 " --> pdb=" O TRP D 24 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASP D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 117 removed outlier: 3.739A pdb=" N ARG D 117 " --> pdb=" O CYS D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 146 removed outlier: 3.544A pdb=" N PHE D 125 " --> pdb=" O PHE D 121 " (cutoff:3.500A) Proline residue: D 126 - end of helix removed outlier: 5.093A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 166 removed outlier: 4.324A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 174 removed outlier: 4.008A pdb=" N ARG D 171 " --> pdb=" O PRO D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 255 removed outlier: 3.501A pdb=" N THR D 252 " --> pdb=" O LYS D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 286 removed outlier: 3.802A pdb=" N THR D 268 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N VAL D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) removed outlier: 4.096A 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 Processing helix chain 'D' and resid 353 through 361 removed outlier: 3.966A pdb=" N ARG D 357 " --> pdb=" O PHE D 353 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU D 359 " --> pdb=" O SER D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 383 removed outlier: 3.649A 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 390 through 394 Processing helix chain 'D' and resid 395 through 408 Processing helix chain 'E' and resid 16 through 22 removed outlier: 3.583A pdb=" N ILE E 19 " --> pdb=" O ALA E 16 " (cutoff:3.500A) Proline residue: E 22 - end of helix Processing helix chain 'E' and resid 23 through 49 removed outlier: 3.534A pdb=" N THR E 28 " --> pdb=" O TRP E 24 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 117 removed outlier: 3.510A pdb=" N TYR E 106 " --> pdb=" O ASP E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 146 removed outlier: 3.644A pdb=" N PHE E 125 " --> pdb=" O PHE E 121 " (cutoff:3.500A) Proline residue: E 126 - end of helix removed outlier: 4.561A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.958A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 146 through 166 removed outlier: 4.449A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 174 Processing helix chain 'E' and resid 234 through 255 removed outlier: 3.747A pdb=" N GLU E 255 " --> pdb=" O ARG E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 286 removed outlier: 3.726A pdb=" N THR E 268 " --> pdb=" O TYR E 264 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL E 283 " --> pdb=" O ILE E 279 " (cutoff:3.500A) removed outlier: 4.141A 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 Processing helix chain 'E' and resid 353 through 361 removed outlier: 4.167A pdb=" N ARG E 357 " --> pdb=" O PHE E 353 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU E 358 " --> pdb=" O GLU E 354 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N GLU E 359 " --> pdb=" O SER E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 381 Processing helix chain 'E' and resid 384 through 389 Processing helix chain 'E' and resid 395 through 408 Processing helix chain 'F' and resid 23 through 49 removed outlier: 3.601A pdb=" N PHE F 27 " --> pdb=" O TRP F 23 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR F 28 " --> pdb=" O TRP F 24 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 117 removed outlier: 3.581A pdb=" N ARG F 117 " --> pdb=" O CYS F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 146 removed outlier: 3.638A pdb=" N PHE F 125 " --> pdb=" O PHE F 121 " (cutoff:3.500A) Proline residue: F 126 - end of helix removed outlier: 4.628A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 146 through 165 removed outlier: 4.071A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 174 removed outlier: 4.120A pdb=" N ARG F 171 " --> pdb=" O PRO F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 255 Processing helix chain 'F' and resid 258 through 286 removed outlier: 3.844A pdb=" N ARG F 262 " --> pdb=" O ASP F 258 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR F 268 " --> pdb=" O TYR F 264 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL F 283 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 4.283A 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 Processing helix chain 'F' and resid 353 through 361 removed outlier: 3.535A pdb=" N ARG F 357 " --> pdb=" O PHE F 353 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU F 359 " --> pdb=" O SER F 355 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 383 Processing helix chain 'F' and resid 383 through 389 removed outlier: 4.367A pdb=" N SER F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 408 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 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 53 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 53 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 removed outlier: 3.891A pdb=" N VAL D 293 " --> pdb=" O CYS D 310 " (cutoff:3.500A) 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 53 through 56 removed outlier: 3.555A pdb=" N VAL E 293 " --> pdb=" O CYS E 310 " (cutoff:3.500A) 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 53 through 56 removed outlier: 3.814A pdb=" N VAL F 293 " --> pdb=" O CYS F 310 " (cutoff:3.500A) 1005 hydrogen bonds defined for protein. 2949 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: 4.48 Time building geometry restraints manager: 4.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2379 1.31 - 1.44: 4937 1.44 - 1.57: 9006 1.57 - 1.69: 5 1.69 - 1.82: 146 Bond restraints: 16473 Sorted by residual: bond pdb=" C18 PEE B 902 " pdb=" C19 PEE B 902 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.39e+01 bond pdb=" C18 PEE C 903 " pdb=" C19 PEE C 903 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.38e+01 bond pdb=" C18 PEE F 902 " pdb=" C19 PEE F 902 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.38e+01 bond pdb=" C18 PEE C 904 " pdb=" C19 PEE C 904 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.37e+01 bond pdb=" C18 PEE E 902 " pdb=" C19 PEE E 902 " ideal model delta sigma weight residual 1.523 1.340 0.183 2.00e-02 2.50e+03 8.36e+01 ... (remaining 16468 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 21581 2.46 - 4.91: 491 4.91 - 7.37: 75 7.37 - 9.82: 37 9.82 - 12.28: 38 Bond angle restraints: 22222 Sorted by residual: angle pdb=" C THR E 48 " pdb=" N GLN E 49 " pdb=" CA GLN E 49 " ideal model delta sigma weight residual 121.90 114.34 7.56 1.26e+00 6.30e-01 3.60e+01 angle pdb=" N GLU E 154 " pdb=" CA GLU E 154 " pdb=" CB GLU E 154 " ideal model delta sigma weight residual 110.28 118.21 -7.93 1.55e+00 4.16e-01 2.62e+01 angle pdb=" C ASN F 370 " pdb=" N ASP F 371 " pdb=" CA ASP F 371 " ideal model delta sigma weight residual 121.54 129.43 -7.89 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C GLU F 245 " pdb=" N LYS F 246 " pdb=" CA LYS F 246 " ideal model delta sigma weight residual 120.68 113.66 7.02 1.70e+00 3.46e-01 1.70e+01 angle pdb=" C CYS B 280 " pdb=" N TYR B 281 " pdb=" CA TYR B 281 " ideal model delta sigma weight residual 122.36 115.31 7.05 1.72e+00 3.38e-01 1.68e+01 ... (remaining 22217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.81: 9067 24.81 - 49.61: 640 49.61 - 74.42: 45 74.42 - 99.23: 14 99.23 - 124.03: 8 Dihedral angle restraints: 9774 sinusoidal: 4122 harmonic: 5652 Sorted by residual: dihedral pdb=" CA GLN A 105 " pdb=" C GLN A 105 " pdb=" N TYR A 106 " pdb=" CA TYR A 106 " ideal model delta harmonic sigma weight residual 180.00 155.86 24.14 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA SER D 352 " pdb=" C SER D 352 " pdb=" N PHE D 353 " pdb=" CA PHE D 353 " ideal model delta harmonic sigma weight residual 180.00 -159.49 -20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" C12 PEE B 902 " pdb=" C10 PEE B 902 " pdb=" C11 PEE B 902 " pdb=" O4 PEE B 902 " ideal model delta sinusoidal sigma weight residual -19.47 104.56 -124.03 1 3.00e+01 1.11e-03 1.66e+01 ... (remaining 9771 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1922 0.062 - 0.124: 434 0.124 - 0.186: 48 0.186 - 0.248: 1 0.248 - 0.310: 3 Chirality restraints: 2408 Sorted by residual: chirality pdb=" CB VAL E 297 " pdb=" CA VAL E 297 " pdb=" CG1 VAL E 297 " pdb=" CG2 VAL E 297 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" C05 YNJ C 902 " pdb=" C06 YNJ C 902 " pdb=" C13 YNJ C 902 " pdb=" C27 YNJ C 902 " both_signs ideal model delta sigma weight residual False 3.00 2.70 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE E 365 " pdb=" CA ILE E 365 " pdb=" CG1 ILE E 365 " pdb=" CG2 ILE E 365 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.07e+00 ... (remaining 2405 not shown) Planarity restraints: 2673 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 275 " -0.018 2.00e-02 2.50e+03 2.52e-02 1.11e+01 pdb=" CG PHE D 275 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE D 275 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 PHE D 275 " -0.022 2.00e-02 2.50e+03 pdb=" CE1 PHE D 275 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 275 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 275 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 244 " -0.018 2.00e-02 2.50e+03 1.81e-02 5.76e+00 pdb=" CG PHE E 244 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE E 244 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE E 244 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE E 244 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE E 244 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 244 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 136 " -0.020 2.00e-02 2.50e+03 1.81e-02 5.73e+00 pdb=" CG PHE C 136 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 PHE C 136 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE C 136 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE C 136 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 136 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 136 " -0.003 2.00e-02 2.50e+03 ... (remaining 2670 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 2744 2.77 - 3.30: 15064 3.30 - 3.83: 26554 3.83 - 4.37: 28621 4.37 - 4.90: 50238 Nonbonded interactions: 123221 Sorted by model distance: nonbonded pdb=" OD2 ASP A 50 " pdb=" OH TYR A 114 " model vdw 2.231 3.040 nonbonded pdb=" O THR D 44 " pdb=" OG1 THR D 48 " model vdw 2.267 3.040 nonbonded pdb=" OD2 ASP E 50 " pdb=" OH TYR E 114 " model vdw 2.269 3.040 nonbonded pdb=" OD2 ASP C 50 " pdb=" OH TYR C 114 " model vdw 2.273 3.040 nonbonded pdb=" O SER D 395 " pdb=" OG SER D 398 " model vdw 2.273 3.040 ... (remaining 123216 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 408 or (resid 901 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O2 \ or name O4 )) or resid 903)) selection = (chain 'B' and (resid 15 through 408 or resid 901 or (resid 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name O2 or name O4 )))) selection = (chain 'C' and (resid 15 through 408 or resid 901 or (resid 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name O2 or name O4 )))) selection = (chain 'D' and (resid 15 through 408 or resid 901 or (resid 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name O2 or name O4 )))) selection = (chain 'E' and (resid 15 through 408 or resid 901 or (resid 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name O2 or name O4 )))) selection = (chain 'F' and (resid 15 through 408 or resid 901 or (resid 903 and (name C10 or \ name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C1 \ 7 or name O2 or name O4 )))) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.200 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: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.130 Process input model: 36.100 Find NCS groups from input model: 0.810 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 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 : 0.009 0.183 16473 Z= 0.632 Angle : 1.031 12.279 22222 Z= 0.508 Chirality : 0.052 0.310 2408 Planarity : 0.005 0.042 2673 Dihedral : 15.738 124.033 6060 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.06 % Allowed : 0.69 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.78 (0.19), residues: 1842 helix: 0.04 (0.14), residues: 1236 sheet: 0.66 (0.49), residues: 96 loop : -1.95 (0.25), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 143 HIS 0.019 0.002 HIS E 377 PHE 0.057 0.002 PHE D 275 TYR 0.022 0.002 TYR A 332 ARG 0.007 0.000 ARG D 357 *********************** 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 258 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 257 time to evaluate : 1.886 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8215 (tmt-80) cc_final: 0.7964 (tpt170) REVERT: B 325 TYR cc_start: 0.8747 (t80) cc_final: 0.8428 (t80) REVERT: C 336 CYS cc_start: 0.8318 (m) cc_final: 0.8114 (t) REVERT: D 37 MET cc_start: 0.8513 (ptp) cc_final: 0.8311 (ptt) REVERT: D 351 TYR cc_start: 0.6384 (t80) cc_final: 0.5922 (t80) REVERT: D 399 GLU cc_start: 0.8353 (mp0) cc_final: 0.7554 (mp0) REVERT: E 162 LYS cc_start: 0.8986 (ttmm) cc_final: 0.8758 (mmtm) REVERT: F 249 LYS cc_start: 0.9154 (tptt) cc_final: 0.8574 (pttt) outliers start: 1 outliers final: 0 residues processed: 257 average time/residue: 0.2926 time to fit residues: 114.5053 Evaluate side-chains 187 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 1.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.9990 chunk 140 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 chunk 145 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN A 155 HIS A 288 ASN B 253 HIS B 288 ASN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS F 400 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16473 Z= 0.252 Angle : 0.593 11.220 22222 Z= 0.322 Chirality : 0.042 0.139 2408 Planarity : 0.003 0.032 2673 Dihedral : 9.573 83.050 2298 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.83 % Allowed : 10.02 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.20), residues: 1842 helix: 0.88 (0.15), residues: 1284 sheet: 0.92 (0.49), residues: 96 loop : -1.86 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 143 HIS 0.007 0.001 HIS B 253 PHE 0.020 0.002 PHE C 136 TYR 0.017 0.001 TYR D 332 ARG 0.004 0.000 ARG C 403 *********************** 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 222 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 190 time to evaluate : 1.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8192 (tmt-80) cc_final: 0.7921 (tpt170) REVERT: A 288 ASN cc_start: 0.9382 (OUTLIER) cc_final: 0.9111 (t0) REVERT: B 17 TYR cc_start: 0.7670 (m-10) cc_final: 0.7459 (m-10) REVERT: B 325 TYR cc_start: 0.8870 (t80) cc_final: 0.8584 (t80) REVERT: C 161 LEU cc_start: 0.8790 (mm) cc_final: 0.8489 (mm) REVERT: E 162 LYS cc_start: 0.8772 (ttmm) cc_final: 0.8546 (mmtm) REVERT: E 168 TRP cc_start: 0.7295 (t60) cc_final: 0.6760 (t60) REVERT: E 399 GLU cc_start: 0.7984 (mp0) cc_final: 0.7781 (pt0) REVERT: F 154 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8457 (mm-30) REVERT: F 249 LYS cc_start: 0.9185 (tptt) cc_final: 0.8621 (pttt) REVERT: F 289 ILE cc_start: 0.9037 (pt) cc_final: 0.8744 (mt) outliers start: 32 outliers final: 17 residues processed: 207 average time/residue: 0.2667 time to fit residues: 84.2542 Evaluate side-chains 189 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 171 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 330 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.3980 chunk 52 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 169 optimal weight: 6.9990 chunk 182 optimal weight: 1.9990 chunk 150 optimal weight: 5.9990 chunk 167 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 135 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS B 155 HIS B 253 HIS ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 HIS E 287 HIS ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16473 Z= 0.238 Angle : 0.569 9.956 22222 Z= 0.307 Chirality : 0.041 0.124 2408 Planarity : 0.003 0.038 2673 Dihedral : 8.075 68.844 2298 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.23 % Allowed : 14.09 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1842 helix: 1.29 (0.15), residues: 1284 sheet: 1.25 (0.50), residues: 96 loop : -1.72 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 143 HIS 0.009 0.001 HIS B 253 PHE 0.019 0.001 PHE C 136 TYR 0.014 0.001 TYR A 332 ARG 0.003 0.000 ARG C 403 *********************** 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 226 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 187 time to evaluate : 1.814 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8219 (tmt-80) cc_final: 0.7927 (tpt170) REVERT: B 269 ILE cc_start: 0.8906 (tt) cc_final: 0.8694 (tp) REVERT: B 288 ASN cc_start: 0.9138 (OUTLIER) cc_final: 0.8785 (t0) REVERT: B 325 TYR cc_start: 0.8885 (t80) cc_final: 0.8664 (t80) REVERT: C 161 LEU cc_start: 0.8830 (mm) cc_final: 0.8533 (mm) REVERT: D 161 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7635 (pp) REVERT: D 280 CYS cc_start: 0.8741 (m) cc_final: 0.8416 (m) REVERT: E 18 ARG cc_start: 0.8016 (ptp-170) cc_final: 0.7409 (ptp90) REVERT: E 162 LYS cc_start: 0.8797 (ttmm) cc_final: 0.8566 (mmtm) REVERT: F 154 GLU cc_start: 0.8636 (mm-30) cc_final: 0.8336 (mm-30) REVERT: F 245 GLU cc_start: 0.8719 (mp0) cc_final: 0.8315 (mp0) REVERT: F 249 LYS cc_start: 0.9185 (tptt) cc_final: 0.8658 (pttt) REVERT: F 289 ILE cc_start: 0.9039 (pt) cc_final: 0.8812 (mt) REVERT: F 381 GLN cc_start: 0.8383 (tp-100) cc_final: 0.8018 (mm-40) outliers start: 39 outliers final: 26 residues processed: 210 average time/residue: 0.2622 time to fit residues: 83.9924 Evaluate side-chains 199 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 171 time to evaluate : 1.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain B residue 328 LEU Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 375 MET Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 330 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 87 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 169 optimal weight: 4.9990 chunk 179 optimal weight: 6.9990 chunk 88 optimal weight: 0.0270 chunk 160 optimal weight: 7.9990 chunk 48 optimal weight: 0.6980 overall best weight: 0.6640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS B 253 HIS E 105 GLN E 155 HIS ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 16473 Z= 0.153 Angle : 0.516 10.073 22222 Z= 0.279 Chirality : 0.040 0.203 2408 Planarity : 0.003 0.030 2673 Dihedral : 7.304 65.724 2298 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.23 % Allowed : 15.75 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.21), residues: 1842 helix: 1.65 (0.15), residues: 1260 sheet: 1.53 (0.51), residues: 96 loop : -1.34 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 143 HIS 0.010 0.001 HIS B 253 PHE 0.025 0.001 PHE C 250 TYR 0.018 0.001 TYR C 351 ARG 0.002 0.000 ARG A 357 *********************** 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 243 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 204 time to evaluate : 1.694 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8140 (tmt-80) cc_final: 0.7827 (tpt170) REVERT: A 399 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7230 (pt0) REVERT: B 269 ILE cc_start: 0.8879 (tt) cc_final: 0.8668 (tp) REVERT: B 288 ASN cc_start: 0.9074 (OUTLIER) cc_final: 0.8645 (t0) REVERT: B 325 TYR cc_start: 0.8823 (t80) cc_final: 0.8559 (t80) REVERT: C 161 LEU cc_start: 0.8801 (mm) cc_final: 0.8492 (mm) REVERT: D 351 TYR cc_start: 0.6410 (t80) cc_final: 0.6061 (t80) REVERT: E 162 LYS cc_start: 0.8830 (ttmm) cc_final: 0.8594 (mmtm) REVERT: F 154 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8338 (mm-30) REVERT: F 249 LYS cc_start: 0.9187 (tptt) cc_final: 0.8647 (pttt) outliers start: 39 outliers final: 23 residues processed: 231 average time/residue: 0.2609 time to fit residues: 92.2782 Evaluate side-chains 201 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 176 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 375 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 133 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 161 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS ** C 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN E 105 GLN E 155 HIS F 288 ASN ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16473 Z= 0.202 Angle : 0.543 8.997 22222 Z= 0.292 Chirality : 0.041 0.197 2408 Planarity : 0.003 0.030 2673 Dihedral : 7.124 64.008 2298 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.75 % Allowed : 17.41 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.21), residues: 1842 helix: 1.74 (0.15), residues: 1260 sheet: 1.61 (0.51), residues: 96 loop : -1.29 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 143 HIS 0.016 0.001 HIS B 253 PHE 0.014 0.001 PHE F 393 TYR 0.018 0.001 TYR C 351 ARG 0.002 0.000 ARG C 103 *********************** 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 231 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 183 time to evaluate : 1.878 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8217 (tmt-80) cc_final: 0.7874 (tpt170) REVERT: A 399 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7194 (pt0) REVERT: B 269 ILE cc_start: 0.8897 (tt) cc_final: 0.8691 (tp) REVERT: B 288 ASN cc_start: 0.9131 (OUTLIER) cc_final: 0.8675 (t0) REVERT: B 325 TYR cc_start: 0.8862 (t80) cc_final: 0.8594 (t80) REVERT: C 161 LEU cc_start: 0.8804 (mm) cc_final: 0.8539 (mm) REVERT: D 280 CYS cc_start: 0.8771 (m) cc_final: 0.8551 (m) REVERT: D 351 TYR cc_start: 0.6555 (t80) cc_final: 0.6185 (t80) REVERT: E 18 ARG cc_start: 0.8119 (ptp-170) cc_final: 0.7660 (ptp90) REVERT: E 162 LYS cc_start: 0.8844 (ttmm) cc_final: 0.8623 (mmtm) REVERT: F 249 LYS cc_start: 0.9188 (tptt) cc_final: 0.8731 (pptt) REVERT: F 328 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.8157 (tt) REVERT: F 381 GLN cc_start: 0.8387 (tp-100) cc_final: 0.8020 (mm-40) outliers start: 48 outliers final: 33 residues processed: 216 average time/residue: 0.2601 time to fit residues: 85.7464 Evaluate side-chains 203 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 167 time to evaluate : 2.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 375 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 8.9990 chunk 161 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS B 104 HIS B 155 HIS B 253 HIS E 155 HIS ** F 406 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16473 Z= 0.276 Angle : 0.585 9.075 22222 Z= 0.315 Chirality : 0.042 0.192 2408 Planarity : 0.003 0.026 2673 Dihedral : 7.287 62.257 2298 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.26 % Allowed : 17.70 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.21), residues: 1842 helix: 1.58 (0.15), residues: 1284 sheet: 1.58 (0.50), residues: 96 loop : -1.56 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 143 HIS 0.011 0.001 HIS B 253 PHE 0.015 0.001 PHE D 125 TYR 0.016 0.001 TYR C 351 ARG 0.002 0.000 ARG B 389 *********************** 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 235 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 178 time to evaluate : 2.039 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8279 (tmt-80) cc_final: 0.7951 (tpt170) REVERT: A 399 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7320 (pt0) REVERT: B 104 HIS cc_start: 0.8702 (OUTLIER) cc_final: 0.8078 (t-90) REVERT: B 269 ILE cc_start: 0.8903 (tt) cc_final: 0.8566 (mt) REVERT: B 288 ASN cc_start: 0.9206 (OUTLIER) cc_final: 0.8845 (t0) REVERT: B 325 TYR cc_start: 0.8922 (t80) cc_final: 0.8678 (t80) REVERT: C 161 LEU cc_start: 0.8840 (mm) cc_final: 0.8539 (mm) REVERT: C 275 PHE cc_start: 0.9093 (OUTLIER) cc_final: 0.8822 (t80) REVERT: D 280 CYS cc_start: 0.8713 (m) cc_final: 0.8502 (m) REVERT: F 249 LYS cc_start: 0.9182 (tptt) cc_final: 0.8708 (pptt) REVERT: F 328 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8141 (tt) REVERT: F 381 GLN cc_start: 0.8431 (tp-100) cc_final: 0.8058 (mm-40) outliers start: 57 outliers final: 44 residues processed: 220 average time/residue: 0.2604 time to fit residues: 87.4598 Evaluate side-chains 211 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 162 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain C residue 20 LEU Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 239 GLN Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 330 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 chunk 102 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 151 optimal weight: 5.9990 chunk 100 optimal weight: 0.5980 chunk 179 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 82 optimal weight: 0.0170 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS D 155 HIS E 155 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16473 Z= 0.150 Angle : 0.538 12.579 22222 Z= 0.286 Chirality : 0.040 0.166 2408 Planarity : 0.003 0.028 2673 Dihedral : 6.926 61.674 2298 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.26 % Allowed : 18.50 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.21), residues: 1842 helix: 1.82 (0.15), residues: 1260 sheet: 1.76 (0.51), residues: 96 loop : -1.25 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 143 HIS 0.013 0.001 HIS B 253 PHE 0.014 0.001 PHE A 125 TYR 0.013 0.001 TYR E 332 ARG 0.002 0.000 ARG C 103 *********************** 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 248 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 191 time to evaluate : 2.034 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8178 (tmt-80) cc_final: 0.7885 (tpt170) REVERT: A 399 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7269 (pt0) REVERT: B 143 TRP cc_start: 0.8472 (t60) cc_final: 0.8199 (t60) REVERT: B 269 ILE cc_start: 0.8885 (tt) cc_final: 0.8684 (tp) REVERT: B 288 ASN cc_start: 0.9099 (OUTLIER) cc_final: 0.8686 (t0) REVERT: B 325 TYR cc_start: 0.8826 (t80) cc_final: 0.8553 (t80) REVERT: C 161 LEU cc_start: 0.8817 (mm) cc_final: 0.8546 (mm) REVERT: C 275 PHE cc_start: 0.9022 (OUTLIER) cc_final: 0.8772 (t80) REVERT: C 330 ILE cc_start: 0.9526 (mm) cc_final: 0.9311 (tt) REVERT: D 280 CYS cc_start: 0.8666 (m) cc_final: 0.8425 (m) REVERT: D 351 TYR cc_start: 0.6417 (t80) cc_final: 0.6119 (t80) REVERT: E 18 ARG cc_start: 0.8023 (ptp-170) cc_final: 0.7605 (ptp90) REVERT: E 162 LYS cc_start: 0.8840 (ttmm) cc_final: 0.8616 (mmtm) REVERT: F 249 LYS cc_start: 0.9183 (tptt) cc_final: 0.8642 (pttt) REVERT: F 328 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8210 (tt) REVERT: F 381 GLN cc_start: 0.8480 (tp-100) cc_final: 0.8150 (mm-40) outliers start: 57 outliers final: 35 residues processed: 234 average time/residue: 0.2465 time to fit residues: 88.6920 Evaluate side-chains 208 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 169 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 330 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 107 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 88 optimal weight: 7.9990 chunk 16 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS B 253 HIS E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16473 Z= 0.173 Angle : 0.546 11.417 22222 Z= 0.290 Chirality : 0.041 0.212 2408 Planarity : 0.003 0.027 2673 Dihedral : 6.808 60.560 2298 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.09 % Allowed : 19.64 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.21), residues: 1842 helix: 1.83 (0.15), residues: 1260 sheet: 1.82 (0.51), residues: 96 loop : -1.27 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP C 342 HIS 0.012 0.001 HIS B 253 PHE 0.014 0.001 PHE B 125 TYR 0.013 0.001 TYR C 351 ARG 0.002 0.000 ARG C 103 *********************** 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 237 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 183 time to evaluate : 1.766 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8191 (tmt-80) cc_final: 0.7897 (tpt170) REVERT: A 399 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7273 (pt0) REVERT: B 143 TRP cc_start: 0.8463 (t60) cc_final: 0.8197 (t60) REVERT: B 269 ILE cc_start: 0.8889 (tt) cc_final: 0.8560 (mt) REVERT: B 288 ASN cc_start: 0.9150 (OUTLIER) cc_final: 0.8755 (t0) REVERT: B 325 TYR cc_start: 0.8825 (t80) cc_final: 0.8560 (t80) REVERT: C 161 LEU cc_start: 0.8856 (mm) cc_final: 0.8570 (mm) REVERT: C 275 PHE cc_start: 0.9009 (OUTLIER) cc_final: 0.8709 (t80) REVERT: C 330 ILE cc_start: 0.9547 (mm) cc_final: 0.9309 (tt) REVERT: D 280 CYS cc_start: 0.8647 (m) cc_final: 0.8418 (m) REVERT: D 351 TYR cc_start: 0.6388 (t80) cc_final: 0.6080 (t80) REVERT: E 18 ARG cc_start: 0.7979 (ptp-170) cc_final: 0.7480 (ptp90) REVERT: E 162 LYS cc_start: 0.8844 (ttmm) cc_final: 0.8632 (mmtm) REVERT: F 249 LYS cc_start: 0.9200 (tptt) cc_final: 0.8636 (pttt) REVERT: F 328 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8161 (tt) REVERT: F 381 GLN cc_start: 0.8490 (tp-100) cc_final: 0.8175 (mm-40) outliers start: 54 outliers final: 44 residues processed: 222 average time/residue: 0.2503 time to fit residues: 85.7281 Evaluate side-chains 217 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 169 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 330 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.7980 chunk 171 optimal weight: 0.0050 chunk 156 optimal weight: 3.9990 chunk 167 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 150 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 overall best weight: 0.8596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 104 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 HIS B 253 HIS E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16473 Z= 0.176 Angle : 0.552 10.686 22222 Z= 0.292 Chirality : 0.041 0.198 2408 Planarity : 0.003 0.027 2673 Dihedral : 6.742 59.570 2298 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.32 % Allowed : 19.70 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.21), residues: 1842 helix: 1.85 (0.15), residues: 1260 sheet: 1.87 (0.51), residues: 96 loop : -1.27 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 342 HIS 0.015 0.001 HIS B 253 PHE 0.014 0.001 PHE A 125 TYR 0.013 0.001 TYR C 351 ARG 0.002 0.000 ARG C 103 *********************** 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 235 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 177 time to evaluate : 1.960 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8200 (tmt-80) cc_final: 0.7894 (tpt170) REVERT: A 399 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7307 (pt0) REVERT: B 143 TRP cc_start: 0.8448 (t60) cc_final: 0.8186 (t60) REVERT: B 269 ILE cc_start: 0.8889 (tt) cc_final: 0.8561 (mt) REVERT: B 288 ASN cc_start: 0.9155 (OUTLIER) cc_final: 0.8761 (t0) REVERT: B 325 TYR cc_start: 0.8820 (t80) cc_final: 0.8560 (t80) REVERT: C 161 LEU cc_start: 0.8854 (mm) cc_final: 0.8571 (mm) REVERT: C 275 PHE cc_start: 0.9004 (OUTLIER) cc_final: 0.8700 (t80) REVERT: C 330 ILE cc_start: 0.9545 (mm) cc_final: 0.9310 (tt) REVERT: D 280 CYS cc_start: 0.8618 (m) cc_final: 0.8376 (m) REVERT: D 351 TYR cc_start: 0.6386 (t80) cc_final: 0.6076 (t80) REVERT: E 18 ARG cc_start: 0.8035 (ptp-170) cc_final: 0.7559 (ptp90) REVERT: F 249 LYS cc_start: 0.9198 (tptt) cc_final: 0.8640 (pttt) REVERT: F 328 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8160 (tt) outliers start: 58 outliers final: 49 residues processed: 218 average time/residue: 0.2485 time to fit residues: 83.8765 Evaluate side-chains 223 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 170 time to evaluate : 1.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 144 PHE Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 0.8980 chunk 176 optimal weight: 0.6980 chunk 107 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 185 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 HIS B 253 HIS E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16473 Z= 0.175 Angle : 0.554 10.192 22222 Z= 0.293 Chirality : 0.041 0.247 2408 Planarity : 0.003 0.027 2673 Dihedral : 6.644 58.777 2298 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.21 % Allowed : 19.93 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.21), residues: 1842 helix: 1.85 (0.15), residues: 1260 sheet: 1.91 (0.51), residues: 96 loop : -1.27 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 342 HIS 0.011 0.001 HIS B 253 PHE 0.014 0.001 PHE A 125 TYR 0.014 0.001 TYR C 351 ARG 0.002 0.000 ARG C 103 ********************** 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 227 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 171 time to evaluate : 1.795 Fit side-chains revert: symmetry clash REVERT: A 171 ARG cc_start: 0.8237 (tmt-80) cc_final: 0.7940 (tpt170) REVERT: A 399 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7307 (pt0) REVERT: B 143 TRP cc_start: 0.8438 (t60) cc_final: 0.8171 (t60) REVERT: B 269 ILE cc_start: 0.8888 (tt) cc_final: 0.8561 (mt) REVERT: B 288 ASN cc_start: 0.9153 (OUTLIER) cc_final: 0.8764 (t0) REVERT: B 325 TYR cc_start: 0.8814 (t80) cc_final: 0.8528 (t80) REVERT: B 375 MET cc_start: 0.8431 (mtp) cc_final: 0.8222 (mtp) REVERT: C 161 LEU cc_start: 0.8861 (mm) cc_final: 0.8582 (mm) REVERT: C 275 PHE cc_start: 0.8997 (OUTLIER) cc_final: 0.8690 (t80) REVERT: C 330 ILE cc_start: 0.9547 (mm) cc_final: 0.9329 (tt) REVERT: D 280 CYS cc_start: 0.8589 (m) cc_final: 0.8335 (m) REVERT: D 325 TYR cc_start: 0.8885 (t80) cc_final: 0.8680 (t80) REVERT: D 351 TYR cc_start: 0.6368 (t80) cc_final: 0.6052 (t80) REVERT: E 18 ARG cc_start: 0.8022 (ptp-170) cc_final: 0.7550 (ptp90) REVERT: F 249 LYS cc_start: 0.9215 (tptt) cc_final: 0.8667 (pttt) REVERT: F 328 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8162 (tt) outliers start: 56 outliers final: 50 residues processed: 211 average time/residue: 0.2464 time to fit residues: 80.5979 Evaluate side-chains 223 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 169 time to evaluate : 1.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 281 TYR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 375 MET Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 155 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 253 HIS Chi-restraints excluded: chain B residue 265 MET Chi-restraints excluded: chain B residue 279 ILE Chi-restraints excluded: chain B residue 281 TYR Chi-restraints excluded: chain B residue 288 ASN Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 379 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 47 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 143 TRP Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 277 LEU Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 331 PHE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 355 SER Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 40 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 280 CYS Chi-restraints excluded: chain E residue 281 TYR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 328 LEU Chi-restraints excluded: chain F residue 31 ILE Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 143 TRP Chi-restraints excluded: chain F residue 155 HIS Chi-restraints excluded: chain F residue 279 ILE Chi-restraints excluded: chain F residue 293 VAL Chi-restraints excluded: chain F residue 328 LEU Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 336 CYS Chi-restraints excluded: chain F residue 379 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 0.6980 chunk 157 optimal weight: 0.6980 chunk 45 optimal weight: 8.9990 chunk 136 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 147 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 151 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 HIS B 253 HIS D 400 ASN E 105 GLN E 155 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 239 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.129166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.104750 restraints weight = 35941.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.104829 restraints weight = 14089.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.105539 restraints weight = 11279.457| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16473 Z= 0.164 Angle : 0.546 9.963 22222 Z= 0.290 Chirality : 0.041 0.257 2408 Planarity : 0.003 0.028 2673 Dihedral : 6.528 58.433 2298 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.09 % Allowed : 19.93 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.21), residues: 1842 helix: 1.86 (0.15), residues: 1260 sheet: 1.93 (0.52), residues: 96 loop : -1.26 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 342 HIS 0.012 0.001 HIS B 253 PHE 0.014 0.001 PHE A 125 TYR 0.013 0.001 TYR C 351 ARG 0.002 0.000 ARG C 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2933.49 seconds wall clock time: 54 minutes 54.80 seconds (3294.80 seconds total)