Starting phenix.real_space_refine on Tue May 27 08:12:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u66_41946/05_2025/8u66_41946.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u66_41946/05_2025/8u66_41946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u66_41946/05_2025/8u66_41946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u66_41946/05_2025/8u66_41946.map" model { file = "/net/cci-nas-00/data/ceres_data/8u66_41946/05_2025/8u66_41946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u66_41946/05_2025/8u66_41946.cif" } resolution = 2.21 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= -0.001 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 128 5.16 5 C 17968 2.51 5 N 5064 2.21 5 O 6181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 29365 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3526 Classifications: {'peptide': 448} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 423} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 124 Classifications: {'water': 124} Link IDs: {None: 123} Chain: "B" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 125 Classifications: {'water': 125} Link IDs: {None: 124} Chain: "C" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "D" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Classifications: {'water': 121} Link IDs: {None: 120} Chain: "E" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 125 Classifications: {'water': 125} Link IDs: {None: 124} Chain: "F" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Classifications: {'water': 121} Link IDs: {None: 120} Chain: "G" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 121 Classifications: {'water': 121} Link IDs: {None: 120} Chain: "H" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Time building chain proxies: 15.93, per 1000 atoms: 0.54 Number of scatterers: 29365 At special positions: 0 Unit cell: (122.85, 122.85, 108.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 128 16.00 P 16 15.00 Mg 8 11.99 O 6181 8.00 N 5064 7.00 C 17968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 7.28 Conformation dependent library (CDL) restraints added in 3.5 seconds 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6464 Finding SS restraints... Secondary structure from input PDB file: 184 helices and 24 sheets defined 54.2% alpha, 12.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.71 Creating SS restraints... Processing helix chain 'A' and resid 13 through 18 Processing helix chain 'A' and resid 42 through 56 Processing helix chain 'A' and resid 62 through 68 Processing helix chain 'A' and resid 69 through 74 Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 98 through 107 Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.614A pdb=" N PHE A 113 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 140 through 149 Processing helix chain 'A' and resid 167 through 182 Processing helix chain 'A' and resid 199 through 219 Processing helix chain 'A' and resid 232 through 246 Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 259 through 274 Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.553A pdb=" N ARG A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL A 300 " --> pdb=" O HIS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 337 Processing helix chain 'A' and resid 369 through 371 No H-bonds generated for 'chain 'A' and resid 369 through 371' Processing helix chain 'A' and resid 372 through 381 Processing helix chain 'A' and resid 389 through 394 Processing helix chain 'A' and resid 398 through 419 Processing helix chain 'A' and resid 422 through 436 removed outlier: 5.851A pdb=" N ARG A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 448 Processing helix chain 'B' and resid 13 through 18 Processing helix chain 'B' and resid 42 through 56 Processing helix chain 'B' and resid 62 through 68 Processing helix chain 'B' and resid 69 through 74 Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'B' and resid 98 through 107 Processing helix chain 'B' and resid 109 through 113 removed outlier: 3.614A pdb=" N PHE B 113 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 132 Processing helix chain 'B' and resid 140 through 149 Processing helix chain 'B' and resid 167 through 182 Processing helix chain 'B' and resid 199 through 219 Processing helix chain 'B' and resid 232 through 246 Processing helix chain 'B' and resid 255 through 259 Processing helix chain 'B' and resid 259 through 274 Processing helix chain 'B' and resid 284 through 289 removed outlier: 3.552A pdb=" N ARG B 289 " --> pdb=" O ALA B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL B 300 " --> pdb=" O HIS B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 337 Processing helix chain 'B' and resid 369 through 371 No H-bonds generated for 'chain 'B' and resid 369 through 371' Processing helix chain 'B' and resid 372 through 381 Processing helix chain 'B' and resid 389 through 394 Processing helix chain 'B' and resid 398 through 419 Processing helix chain 'B' and resid 422 through 436 removed outlier: 5.851A pdb=" N ARG B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN B 429 " --> pdb=" O ALA B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 448 Processing helix chain 'C' and resid 13 through 18 Processing helix chain 'C' and resid 42 through 56 Processing helix chain 'C' and resid 62 through 68 Processing helix chain 'C' and resid 69 through 74 Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 98 through 107 Processing helix chain 'C' and resid 109 through 113 removed outlier: 3.614A pdb=" N PHE C 113 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 132 Processing helix chain 'C' and resid 140 through 149 Processing helix chain 'C' and resid 167 through 182 Processing helix chain 'C' and resid 199 through 219 Processing helix chain 'C' and resid 232 through 246 Processing helix chain 'C' and resid 255 through 259 Processing helix chain 'C' and resid 259 through 274 Processing helix chain 'C' and resid 284 through 289 removed outlier: 3.553A pdb=" N ARG C 289 " --> pdb=" O ALA C 285 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL C 300 " --> pdb=" O HIS C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 337 Processing helix chain 'C' and resid 369 through 371 No H-bonds generated for 'chain 'C' and resid 369 through 371' Processing helix chain 'C' and resid 372 through 381 Processing helix chain 'C' and resid 389 through 394 Processing helix chain 'C' and resid 398 through 419 Processing helix chain 'C' and resid 422 through 436 removed outlier: 5.850A pdb=" N ARG C 428 " --> pdb=" O LEU C 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 438 through 448 Processing helix chain 'D' and resid 13 through 18 Processing helix chain 'D' and resid 42 through 56 Processing helix chain 'D' and resid 62 through 68 Processing helix chain 'D' and resid 69 through 74 Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 98 through 107 Processing helix chain 'D' and resid 109 through 113 removed outlier: 3.614A pdb=" N PHE D 113 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 140 through 149 Processing helix chain 'D' and resid 167 through 182 Processing helix chain 'D' and resid 199 through 219 Processing helix chain 'D' and resid 232 through 246 Processing helix chain 'D' and resid 255 through 259 Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 284 through 289 removed outlier: 3.553A pdb=" N ARG D 289 " --> pdb=" O ALA D 285 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL D 300 " --> pdb=" O HIS D 296 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 337 Processing helix chain 'D' and resid 369 through 371 No H-bonds generated for 'chain 'D' and resid 369 through 371' Processing helix chain 'D' and resid 372 through 381 Processing helix chain 'D' and resid 389 through 394 Processing helix chain 'D' and resid 398 through 419 Processing helix chain 'D' and resid 422 through 436 removed outlier: 5.851A pdb=" N ARG D 428 " --> pdb=" O LEU D 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN D 429 " --> pdb=" O ALA D 425 " (cutoff:3.500A) Processing helix chain 'D' and resid 438 through 448 Processing helix chain 'E' and resid 13 through 18 Processing helix chain 'E' and resid 42 through 56 Processing helix chain 'E' and resid 62 through 68 Processing helix chain 'E' and resid 69 through 74 Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 98 through 107 Processing helix chain 'E' and resid 109 through 113 removed outlier: 3.613A pdb=" N PHE E 113 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 132 Processing helix chain 'E' and resid 140 through 149 Processing helix chain 'E' and resid 167 through 182 Processing helix chain 'E' and resid 199 through 219 Processing helix chain 'E' and resid 232 through 246 Processing helix chain 'E' and resid 255 through 259 Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 284 through 289 removed outlier: 3.553A pdb=" N ARG E 289 " --> pdb=" O ALA E 285 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL E 300 " --> pdb=" O HIS E 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 324 through 337 Processing helix chain 'E' and resid 369 through 371 No H-bonds generated for 'chain 'E' and resid 369 through 371' Processing helix chain 'E' and resid 372 through 381 Processing helix chain 'E' and resid 389 through 394 Processing helix chain 'E' and resid 398 through 419 Processing helix chain 'E' and resid 422 through 436 removed outlier: 5.850A pdb=" N ARG E 428 " --> pdb=" O LEU E 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN E 429 " --> pdb=" O ALA E 425 " (cutoff:3.500A) Processing helix chain 'E' and resid 438 through 448 Processing helix chain 'F' and resid 13 through 18 Processing helix chain 'F' and resid 42 through 56 Processing helix chain 'F' and resid 62 through 68 Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 98 through 107 Processing helix chain 'F' and resid 109 through 113 removed outlier: 3.614A pdb=" N PHE F 113 " --> pdb=" O VAL F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 132 Processing helix chain 'F' and resid 140 through 149 Processing helix chain 'F' and resid 167 through 182 Processing helix chain 'F' and resid 199 through 219 Processing helix chain 'F' and resid 232 through 246 Processing helix chain 'F' and resid 255 through 259 Processing helix chain 'F' and resid 259 through 274 Processing helix chain 'F' and resid 284 through 289 removed outlier: 3.553A pdb=" N ARG F 289 " --> pdb=" O ALA F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL F 300 " --> pdb=" O HIS F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 324 through 337 Processing helix chain 'F' and resid 369 through 371 No H-bonds generated for 'chain 'F' and resid 369 through 371' Processing helix chain 'F' and resid 372 through 381 Processing helix chain 'F' and resid 389 through 394 Processing helix chain 'F' and resid 398 through 419 Processing helix chain 'F' and resid 422 through 436 removed outlier: 5.850A pdb=" N ARG F 428 " --> pdb=" O LEU F 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN F 429 " --> pdb=" O ALA F 425 " (cutoff:3.500A) Processing helix chain 'F' and resid 438 through 448 Processing helix chain 'G' and resid 13 through 18 Processing helix chain 'G' and resid 42 through 56 Processing helix chain 'G' and resid 62 through 68 Processing helix chain 'G' and resid 69 through 74 Processing helix chain 'G' and resid 90 through 94 Processing helix chain 'G' and resid 98 through 107 Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.614A pdb=" N PHE G 113 " --> pdb=" O VAL G 110 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 132 Processing helix chain 'G' and resid 140 through 149 Processing helix chain 'G' and resid 167 through 182 Processing helix chain 'G' and resid 199 through 219 Processing helix chain 'G' and resid 232 through 246 Processing helix chain 'G' and resid 255 through 259 Processing helix chain 'G' and resid 259 through 274 Processing helix chain 'G' and resid 284 through 289 removed outlier: 3.553A pdb=" N ARG G 289 " --> pdb=" O ALA G 285 " (cutoff:3.500A) Processing helix chain 'G' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL G 300 " --> pdb=" O HIS G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 324 through 337 Processing helix chain 'G' and resid 369 through 371 No H-bonds generated for 'chain 'G' and resid 369 through 371' Processing helix chain 'G' and resid 372 through 381 Processing helix chain 'G' and resid 389 through 394 Processing helix chain 'G' and resid 398 through 419 Processing helix chain 'G' and resid 422 through 436 removed outlier: 5.850A pdb=" N ARG G 428 " --> pdb=" O LEU G 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN G 429 " --> pdb=" O ALA G 425 " (cutoff:3.500A) Processing helix chain 'G' and resid 438 through 448 Processing helix chain 'H' and resid 13 through 18 Processing helix chain 'H' and resid 42 through 56 Processing helix chain 'H' and resid 62 through 68 Processing helix chain 'H' and resid 69 through 74 Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 98 through 107 Processing helix chain 'H' and resid 109 through 113 removed outlier: 3.614A pdb=" N PHE H 113 " --> pdb=" O VAL H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 132 Processing helix chain 'H' and resid 140 through 149 Processing helix chain 'H' and resid 167 through 182 Processing helix chain 'H' and resid 199 through 219 Processing helix chain 'H' and resid 232 through 246 Processing helix chain 'H' and resid 255 through 259 Processing helix chain 'H' and resid 259 through 274 Processing helix chain 'H' and resid 284 through 289 removed outlier: 3.553A pdb=" N ARG H 289 " --> pdb=" O ALA H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 308 removed outlier: 3.682A pdb=" N VAL H 300 " --> pdb=" O HIS H 296 " (cutoff:3.500A) Processing helix chain 'H' and resid 324 through 337 Processing helix chain 'H' and resid 369 through 371 No H-bonds generated for 'chain 'H' and resid 369 through 371' Processing helix chain 'H' and resid 372 through 381 Processing helix chain 'H' and resid 389 through 394 Processing helix chain 'H' and resid 398 through 419 Processing helix chain 'H' and resid 422 through 436 removed outlier: 5.850A pdb=" N ARG H 428 " --> pdb=" O LEU H 424 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N GLN H 429 " --> pdb=" O ALA H 425 " (cutoff:3.500A) Processing helix chain 'H' and resid 438 through 448 Processing sheet with id=AA1, first strand: chain 'A' and resid 76 through 81 removed outlier: 6.732A pdb=" N TYR A 86 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE A 80 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR A 84 " --> pdb=" O ILE A 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP A 123 " --> pdb=" O ALA A 32 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG A 34 " --> pdb=" O LEU A 121 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU A 121 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU A 36 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU A 119 " --> pdb=" O GLU A 36 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 157 removed outlier: 6.394A pdb=" N LEU A 155 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS A 313 " --> pdb=" O CYS A 279 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 251 " --> pdb=" O HIS A 278 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N HIS A 280 " --> pdb=" O ILE A 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL A 253 " --> pdb=" O HIS A 280 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS A 224 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N MET A 252 " --> pdb=" O HIS A 224 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU A 226 " --> pdb=" O MET A 252 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP A 254 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR A 186 " --> pdb=" O TRP A 225 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASN A 227 " --> pdb=" O THR A 186 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AA4, first strand: chain 'B' and resid 76 through 81 removed outlier: 6.732A pdb=" N TYR B 86 " --> pdb=" O TYR B 78 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE B 80 " --> pdb=" O THR B 84 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR B 84 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP B 123 " --> pdb=" O ALA B 32 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG B 34 " --> pdb=" O LEU B 121 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU B 121 " --> pdb=" O ARG B 34 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU B 36 " --> pdb=" O LEU B 119 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU B 119 " --> pdb=" O GLU B 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 155 through 157 removed outlier: 6.394A pdb=" N LEU B 155 " --> pdb=" O PHE B 386 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS B 313 " --> pdb=" O CYS B 279 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE B 251 " --> pdb=" O HIS B 278 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS B 280 " --> pdb=" O ILE B 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL B 253 " --> pdb=" O HIS B 280 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS B 224 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N MET B 252 " --> pdb=" O HIS B 224 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU B 226 " --> pdb=" O MET B 252 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP B 254 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR B 186 " --> pdb=" O TRP B 225 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASN B 227 " --> pdb=" O THR B 186 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 339 through 340 Processing sheet with id=AA7, first strand: chain 'C' and resid 76 through 81 removed outlier: 6.732A pdb=" N TYR C 86 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE C 80 " --> pdb=" O THR C 84 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR C 84 " --> pdb=" O ILE C 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP C 123 " --> pdb=" O ALA C 32 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG C 34 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU C 121 " --> pdb=" O ARG C 34 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU C 36 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU C 119 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 155 through 157 removed outlier: 6.395A pdb=" N LEU C 155 " --> pdb=" O PHE C 386 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS C 313 " --> pdb=" O CYS C 279 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE C 251 " --> pdb=" O HIS C 278 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS C 280 " --> pdb=" O ILE C 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL C 253 " --> pdb=" O HIS C 280 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS C 224 " --> pdb=" O TYR C 250 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET C 252 " --> pdb=" O HIS C 224 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU C 226 " --> pdb=" O MET C 252 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP C 254 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR C 186 " --> pdb=" O TRP C 225 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ASN C 227 " --> pdb=" O THR C 186 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 339 through 340 Processing sheet with id=AB1, first strand: chain 'D' and resid 76 through 81 removed outlier: 6.732A pdb=" N TYR D 86 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE D 80 " --> pdb=" O THR D 84 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR D 84 " --> pdb=" O ILE D 80 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP D 123 " --> pdb=" O ALA D 32 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG D 34 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU D 121 " --> pdb=" O ARG D 34 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N GLU D 36 " --> pdb=" O LEU D 119 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU D 119 " --> pdb=" O GLU D 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 155 through 157 removed outlier: 6.394A pdb=" N LEU D 155 " --> pdb=" O PHE D 386 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS D 313 " --> pdb=" O CYS D 279 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE D 251 " --> pdb=" O HIS D 278 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N HIS D 280 " --> pdb=" O ILE D 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL D 253 " --> pdb=" O HIS D 280 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS D 224 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET D 252 " --> pdb=" O HIS D 224 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU D 226 " --> pdb=" O MET D 252 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ASP D 254 " --> pdb=" O LEU D 226 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N THR D 186 " --> pdb=" O TRP D 225 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASN D 227 " --> pdb=" O THR D 186 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 339 through 340 Processing sheet with id=AB4, first strand: chain 'E' and resid 76 through 81 removed outlier: 6.732A pdb=" N TYR E 86 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE E 80 " --> pdb=" O THR E 84 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR E 84 " --> pdb=" O ILE E 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP E 123 " --> pdb=" O ALA E 32 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ARG E 34 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU E 121 " --> pdb=" O ARG E 34 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU E 36 " --> pdb=" O LEU E 119 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU E 119 " --> pdb=" O GLU E 36 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 155 through 157 removed outlier: 6.394A pdb=" N LEU E 155 " --> pdb=" O PHE E 386 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS E 313 " --> pdb=" O CYS E 279 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE E 251 " --> pdb=" O HIS E 278 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS E 280 " --> pdb=" O ILE E 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL E 253 " --> pdb=" O HIS E 280 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS E 224 " --> pdb=" O TYR E 250 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET E 252 " --> pdb=" O HIS E 224 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU E 226 " --> pdb=" O MET E 252 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP E 254 " --> pdb=" O LEU E 226 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR E 186 " --> pdb=" O TRP E 225 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ASN E 227 " --> pdb=" O THR E 186 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 339 through 340 Processing sheet with id=AB7, first strand: chain 'F' and resid 76 through 81 removed outlier: 6.732A pdb=" N TYR F 86 " --> pdb=" O TYR F 78 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE F 80 " --> pdb=" O THR F 84 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR F 84 " --> pdb=" O ILE F 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP F 123 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG F 34 " --> pdb=" O LEU F 121 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU F 121 " --> pdb=" O ARG F 34 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU F 36 " --> pdb=" O LEU F 119 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU F 119 " --> pdb=" O GLU F 36 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 155 through 157 removed outlier: 6.395A pdb=" N LEU F 155 " --> pdb=" O PHE F 386 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N HIS F 313 " --> pdb=" O CYS F 279 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE F 251 " --> pdb=" O HIS F 278 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS F 280 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL F 253 " --> pdb=" O HIS F 280 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N HIS F 224 " --> pdb=" O TYR F 250 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET F 252 " --> pdb=" O HIS F 224 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU F 226 " --> pdb=" O MET F 252 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ASP F 254 " --> pdb=" O LEU F 226 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR F 186 " --> pdb=" O TRP F 225 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASN F 227 " --> pdb=" O THR F 186 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 339 through 340 Processing sheet with id=AC1, first strand: chain 'G' and resid 76 through 81 removed outlier: 6.732A pdb=" N TYR G 86 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ILE G 80 " --> pdb=" O THR G 84 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP G 123 " --> pdb=" O ALA G 32 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG G 34 " --> pdb=" O LEU G 121 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU G 121 " --> pdb=" O ARG G 34 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU G 36 " --> pdb=" O LEU G 119 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU G 119 " --> pdb=" O GLU G 36 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 155 through 157 removed outlier: 6.394A pdb=" N LEU G 155 " --> pdb=" O PHE G 386 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS G 313 " --> pdb=" O CYS G 279 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE G 251 " --> pdb=" O HIS G 278 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS G 280 " --> pdb=" O ILE G 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL G 253 " --> pdb=" O HIS G 280 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS G 224 " --> pdb=" O TYR G 250 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET G 252 " --> pdb=" O HIS G 224 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N LEU G 226 " --> pdb=" O MET G 252 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N ASP G 254 " --> pdb=" O LEU G 226 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR G 186 " --> pdb=" O TRP G 225 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ASN G 227 " --> pdb=" O THR G 186 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 339 through 340 Processing sheet with id=AC4, first strand: chain 'H' and resid 76 through 81 removed outlier: 6.731A pdb=" N TYR H 86 " --> pdb=" O TYR H 78 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ILE H 80 " --> pdb=" O THR H 84 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THR H 84 " --> pdb=" O ILE H 80 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASP H 123 " --> pdb=" O ALA H 32 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG H 34 " --> pdb=" O LEU H 121 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N LEU H 121 " --> pdb=" O ARG H 34 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N GLU H 36 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LEU H 119 " --> pdb=" O GLU H 36 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 155 through 157 removed outlier: 6.394A pdb=" N LEU H 155 " --> pdb=" O PHE H 386 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS H 313 " --> pdb=" O CYS H 279 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE H 251 " --> pdb=" O HIS H 278 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N HIS H 280 " --> pdb=" O ILE H 251 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N VAL H 253 " --> pdb=" O HIS H 280 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N HIS H 224 " --> pdb=" O TYR H 250 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N MET H 252 " --> pdb=" O HIS H 224 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU H 226 " --> pdb=" O MET H 252 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N ASP H 254 " --> pdb=" O LEU H 226 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N THR H 186 " --> pdb=" O TRP H 225 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ASN H 227 " --> pdb=" O THR H 186 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 339 through 340 1384 hydrogen bonds defined for protein. 3840 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: 10.73 Time building geometry restraints manager: 8.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4693 1.32 - 1.44: 8100 1.44 - 1.56: 16079 1.56 - 1.68: 16 1.68 - 1.81: 208 Bond restraints: 29096 Sorted by residual: bond pdb=" NZ KCX E 187 " pdb=" CX KCX E 187 " ideal model delta sigma weight residual 1.411 1.329 0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" NZ KCX F 187 " pdb=" CX KCX F 187 " ideal model delta sigma weight residual 1.411 1.331 0.080 2.00e-02 2.50e+03 1.58e+01 bond pdb=" NZ KCX D 187 " pdb=" CX KCX D 187 " ideal model delta sigma weight residual 1.411 1.332 0.079 2.00e-02 2.50e+03 1.58e+01 bond pdb=" NZ KCX H 187 " pdb=" CX KCX H 187 " ideal model delta sigma weight residual 1.411 1.334 0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" NZ KCX C 187 " pdb=" CX KCX C 187 " ideal model delta sigma weight residual 1.411 1.334 0.077 2.00e-02 2.50e+03 1.47e+01 ... (remaining 29091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.64: 39172 2.64 - 5.28: 267 5.28 - 7.92: 13 7.92 - 10.56: 12 10.56 - 13.20: 8 Bond angle restraints: 39472 Sorted by residual: angle pdb=" C3 CAP H 502 " pdb=" C4 CAP H 502 " pdb=" C5 CAP H 502 " ideal model delta sigma weight residual 111.00 124.20 -13.20 3.00e+00 1.11e-01 1.94e+01 angle pdb=" C3 CAP E 502 " pdb=" C4 CAP E 502 " pdb=" C5 CAP E 502 " ideal model delta sigma weight residual 111.00 124.18 -13.18 3.00e+00 1.11e-01 1.93e+01 angle pdb=" C3 CAP G 502 " pdb=" C4 CAP G 502 " pdb=" C5 CAP G 502 " ideal model delta sigma weight residual 111.00 124.18 -13.18 3.00e+00 1.11e-01 1.93e+01 angle pdb=" C3 CAP D 502 " pdb=" C4 CAP D 502 " pdb=" C5 CAP D 502 " ideal model delta sigma weight residual 111.00 124.18 -13.18 3.00e+00 1.11e-01 1.93e+01 angle pdb=" C3 CAP B 502 " pdb=" C4 CAP B 502 " pdb=" C5 CAP B 502 " ideal model delta sigma weight residual 111.00 124.16 -13.16 3.00e+00 1.11e-01 1.92e+01 ... (remaining 39467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.78: 16529 34.78 - 69.56: 507 69.56 - 104.34: 84 104.34 - 139.12: 4 139.12 - 173.90: 4 Dihedral angle restraints: 17128 sinusoidal: 6952 harmonic: 10176 Sorted by residual: dihedral pdb=" C3 CAP H 502 " pdb=" C CAP H 502 " pdb=" C2 CAP H 502 " pdb=" O6 CAP H 502 " ideal model delta sinusoidal sigma weight residual 81.86 -92.04 173.90 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C3 CAP D 502 " pdb=" C CAP D 502 " pdb=" C2 CAP D 502 " pdb=" O6 CAP D 502 " ideal model delta sinusoidal sigma weight residual 81.86 -92.04 173.90 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C3 CAP E 502 " pdb=" C CAP E 502 " pdb=" C2 CAP E 502 " pdb=" O6 CAP E 502 " ideal model delta sinusoidal sigma weight residual 81.86 -92.03 173.89 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 17125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.350: 4144 0.350 - 0.700: 0 0.700 - 1.050: 0 1.050 - 1.400: 0 1.400 - 1.750: 8 Chirality restraints: 4152 Sorted by residual: chirality pdb=" C4 CAP B 502 " pdb=" C3 CAP B 502 " pdb=" C5 CAP B 502 " pdb=" O4 CAP B 502 " both_signs ideal model delta sigma weight residual False -2.47 -0.72 -1.75 2.00e-01 2.50e+01 7.66e+01 chirality pdb=" C4 CAP H 502 " pdb=" C3 CAP H 502 " pdb=" C5 CAP H 502 " pdb=" O4 CAP H 502 " both_signs ideal model delta sigma weight residual False -2.47 -0.72 -1.75 2.00e-01 2.50e+01 7.63e+01 chirality pdb=" C4 CAP G 502 " pdb=" C3 CAP G 502 " pdb=" C5 CAP G 502 " pdb=" O4 CAP G 502 " both_signs ideal model delta sigma weight residual False -2.47 -0.72 -1.75 2.00e-01 2.50e+01 7.63e+01 ... (remaining 4149 not shown) Planarity restraints: 5168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA KCX F 187 " -0.009 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C KCX F 187 " 0.033 2.00e-02 2.50e+03 pdb=" O KCX F 187 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP F 188 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA KCX A 187 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C KCX A 187 " 0.033 2.00e-02 2.50e+03 pdb=" O KCX A 187 " -0.012 2.00e-02 2.50e+03 pdb=" N ASP A 188 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA KCX B 187 " 0.009 2.00e-02 2.50e+03 1.88e-02 3.54e+00 pdb=" C KCX B 187 " -0.033 2.00e-02 2.50e+03 pdb=" O KCX B 187 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP B 188 " 0.011 2.00e-02 2.50e+03 ... (remaining 5165 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.48: 188 2.48 - 3.08: 21060 3.08 - 3.69: 51577 3.69 - 4.29: 83912 4.29 - 4.90: 129116 Nonbonded interactions: 285853 Sorted by model distance: nonbonded pdb=" OD1 ASP E 189 " pdb="MG MG E 501 " model vdw 1.869 2.170 nonbonded pdb=" OD1 ASP G 189 " pdb="MG MG G 501 " model vdw 1.870 2.170 nonbonded pdb=" OD1 ASP C 189 " pdb="MG MG C 501 " model vdw 1.871 2.170 nonbonded pdb=" OD1 ASP H 189 " pdb="MG MG H 501 " model vdw 1.871 2.170 nonbonded pdb=" OD1 ASP B 189 " pdb="MG MG B 501 " model vdw 1.872 2.170 ... (remaining 285848 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: 0.24 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.080 Check model and map are aligned: 0.230 Set scattering table: 0.280 Process input model: 62.340 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 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 : 0.004 0.082 29096 Z= 0.159 Angle : 0.561 13.198 39472 Z= 0.263 Chirality : 0.085 1.750 4152 Planarity : 0.003 0.022 5168 Dihedral : 16.747 173.903 10664 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.28 % Allowed : 11.41 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 2.01 (0.15), residues: 3544 helix: 1.76 (0.13), residues: 1664 sheet: 0.50 (0.25), residues: 424 loop : 1.32 (0.18), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 354 HIS 0.003 0.001 HIS E 311 PHE 0.012 0.001 PHE E 297 TYR 0.016 0.001 TYR C 263 ARG 0.001 0.000 ARG B 249 Details of bonding type rmsd hydrogen bonds : bond 0.14111 ( 1384) hydrogen bonds : angle 6.81192 ( 3840) covalent geometry : bond 0.00351 (29096) covalent geometry : angle 0.56069 (39472) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 449 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 441 time to evaluate : 3.018 Fit side-chains REVERT: A 149 LYS cc_start: 0.8079 (mmtt) cc_final: 0.7795 (mtmt) REVERT: A 208 MET cc_start: 0.8963 (mmm) cc_final: 0.8719 (mmm) REVERT: A 216 GLU cc_start: 0.7191 (tm-30) cc_final: 0.6925 (tm-30) REVERT: A 429 GLN cc_start: 0.6828 (tp-100) cc_final: 0.6564 (tp-100) REVERT: B 208 MET cc_start: 0.8936 (mmm) cc_final: 0.8718 (mmm) REVERT: B 216 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6914 (tm-30) REVERT: B 429 GLN cc_start: 0.6971 (tp-100) cc_final: 0.6697 (tp-100) REVERT: C 23 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7186 (mt-10) REVERT: C 216 GLU cc_start: 0.7174 (tm-30) cc_final: 0.6830 (tm-30) REVERT: C 429 GLN cc_start: 0.6872 (tp-100) cc_final: 0.6455 (tp-100) REVERT: D 23 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7183 (mt-10) REVERT: D 149 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7709 (mtmt) REVERT: D 216 GLU cc_start: 0.7207 (tm-30) cc_final: 0.6866 (tm-30) REVERT: D 217 GLU cc_start: 0.7270 (mt-10) cc_final: 0.7054 (mt-10) REVERT: D 252 MET cc_start: 0.9283 (ptm) cc_final: 0.9025 (ptm) REVERT: D 429 GLN cc_start: 0.6873 (tp-100) cc_final: 0.6535 (tp-100) REVERT: E 65 GLN cc_start: 0.6959 (pt0) cc_final: 0.6626 (pt0) REVERT: E 149 LYS cc_start: 0.8102 (mmtt) cc_final: 0.7789 (mtmt) REVERT: E 208 MET cc_start: 0.8917 (mmm) cc_final: 0.8678 (mmm) REVERT: E 216 GLU cc_start: 0.7208 (tm-30) cc_final: 0.6891 (tm-30) REVERT: E 429 GLN cc_start: 0.6942 (tp-100) cc_final: 0.6679 (tp-100) REVERT: F 149 LYS cc_start: 0.8107 (mmtt) cc_final: 0.7791 (mtmt) REVERT: F 208 MET cc_start: 0.8952 (mmm) cc_final: 0.8727 (mmm) REVERT: F 216 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6851 (tm-30) REVERT: F 429 GLN cc_start: 0.6821 (tp-100) cc_final: 0.6548 (tp-100) REVERT: G 65 GLN cc_start: 0.7020 (pt0) cc_final: 0.6710 (pt0) REVERT: G 149 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7822 (mtmt) REVERT: G 208 MET cc_start: 0.8935 (mmm) cc_final: 0.8726 (mmm) REVERT: G 216 GLU cc_start: 0.7265 (tm-30) cc_final: 0.6933 (tm-30) REVERT: G 429 GLN cc_start: 0.6902 (tp-100) cc_final: 0.6645 (tp-100) REVERT: H 208 MET cc_start: 0.8932 (mmm) cc_final: 0.8729 (mmm) REVERT: H 216 GLU cc_start: 0.7235 (tm-30) cc_final: 0.6932 (tm-30) REVERT: H 429 GLN cc_start: 0.6883 (tp-100) cc_final: 0.6615 (tp-100) outliers start: 8 outliers final: 8 residues processed: 441 average time/residue: 2.1010 time to fit residues: 1034.4904 Evaluate side-chains 411 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 403 time to evaluate : 3.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 311 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 297 optimal weight: 0.9980 chunk 266 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 91 optimal weight: 0.0000 chunk 179 optimal weight: 0.0980 chunk 142 optimal weight: 4.9990 chunk 275 optimal weight: 0.8980 chunk 106 optimal weight: 4.9990 chunk 167 optimal weight: 0.0770 chunk 205 optimal weight: 2.9990 chunk 319 optimal weight: 6.9990 overall best weight: 0.4142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 345 GLN B 345 GLN C 345 GLN D 109 ASN D 345 GLN E 345 GLN F 345 GLN G 345 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.138759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.125334 restraints weight = 26110.554| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 0.81 r_work: 0.3336 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 29096 Z= 0.114 Angle : 0.505 5.060 39472 Z= 0.266 Chirality : 0.039 0.134 4152 Planarity : 0.004 0.024 5168 Dihedral : 9.278 179.887 4144 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.69 % Allowed : 11.72 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.98 (0.15), residues: 3544 helix: 1.77 (0.13), residues: 1632 sheet: 0.76 (0.24), residues: 464 loop : 1.18 (0.18), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 63 HIS 0.004 0.001 HIS F 393 PHE 0.013 0.002 PHE G 297 TYR 0.020 0.001 TYR D 263 ARG 0.004 0.000 ARG B 442 Details of bonding type rmsd hydrogen bonds : bond 0.03981 ( 1384) hydrogen bonds : angle 5.47539 ( 3840) covalent geometry : bond 0.00243 (29096) covalent geometry : angle 0.50471 (39472) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 423 time to evaluate : 3.357 Fit side-chains REVERT: A 208 MET cc_start: 0.9150 (mmm) cc_final: 0.8928 (mmm) REVERT: A 216 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7386 (tm-30) REVERT: A 234 GLU cc_start: 0.8107 (mp0) cc_final: 0.7901 (mp0) REVERT: A 276 MET cc_start: 0.9121 (mtm) cc_final: 0.8885 (mtm) REVERT: A 277 ILE cc_start: 0.8451 (mt) cc_final: 0.7977 (mt) REVERT: A 429 GLN cc_start: 0.7568 (tp-100) cc_final: 0.7342 (tp-100) REVERT: B 149 LYS cc_start: 0.8531 (mttt) cc_final: 0.8159 (mtmt) REVERT: B 208 MET cc_start: 0.9149 (mmm) cc_final: 0.8841 (mmm) REVERT: B 216 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7385 (tm-30) REVERT: B 234 GLU cc_start: 0.8071 (mp0) cc_final: 0.7866 (mp0) REVERT: B 429 GLN cc_start: 0.7672 (tp-100) cc_final: 0.7328 (tp-100) REVERT: C 149 LYS cc_start: 0.8487 (mttp) cc_final: 0.8106 (mtmt) REVERT: C 208 MET cc_start: 0.9107 (mmm) cc_final: 0.8722 (mmp) REVERT: C 216 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7313 (tm-30) REVERT: C 234 GLU cc_start: 0.8112 (mp0) cc_final: 0.7888 (mp0) REVERT: C 429 GLN cc_start: 0.7579 (tp-100) cc_final: 0.7342 (tp-100) REVERT: D 65 GLN cc_start: 0.7543 (pt0) cc_final: 0.7285 (pt0) REVERT: D 149 LYS cc_start: 0.8235 (mmtt) cc_final: 0.7938 (mtmt) REVERT: D 208 MET cc_start: 0.9118 (mmm) cc_final: 0.8760 (mmp) REVERT: D 216 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7456 (tm-30) REVERT: D 276 MET cc_start: 0.9087 (mtm) cc_final: 0.8854 (mtm) REVERT: E 208 MET cc_start: 0.9131 (mmm) cc_final: 0.8815 (mmm) REVERT: E 216 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7344 (tm-30) REVERT: E 234 GLU cc_start: 0.8099 (mp0) cc_final: 0.7892 (mp0) REVERT: E 429 GLN cc_start: 0.7650 (tp-100) cc_final: 0.7319 (tp-100) REVERT: F 208 MET cc_start: 0.9166 (mmm) cc_final: 0.8853 (mmm) REVERT: F 216 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7404 (tm-30) REVERT: F 234 GLU cc_start: 0.8093 (mp0) cc_final: 0.7879 (mp0) REVERT: F 276 MET cc_start: 0.9118 (mtm) cc_final: 0.8858 (mtm) REVERT: F 429 GLN cc_start: 0.7601 (tp-100) cc_final: 0.7397 (tp-100) REVERT: G 65 GLN cc_start: 0.7505 (pt0) cc_final: 0.7281 (pt0) REVERT: G 149 LYS cc_start: 0.8247 (mmtt) cc_final: 0.7990 (mtmt) REVERT: G 208 MET cc_start: 0.9137 (mmm) cc_final: 0.8830 (mmm) REVERT: G 216 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7385 (tm-30) REVERT: G 234 GLU cc_start: 0.8074 (mp0) cc_final: 0.7860 (mp0) REVERT: G 276 MET cc_start: 0.9115 (mtm) cc_final: 0.8869 (mtm) REVERT: G 429 GLN cc_start: 0.7607 (tp-100) cc_final: 0.7312 (tp-100) REVERT: H 149 LYS cc_start: 0.8529 (mttt) cc_final: 0.8133 (mtmt) REVERT: H 208 MET cc_start: 0.9136 (mmm) cc_final: 0.8836 (mmm) REVERT: H 216 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7449 (tm-30) REVERT: H 234 GLU cc_start: 0.8077 (mp0) cc_final: 0.7875 (mp0) REVERT: H 429 GLN cc_start: 0.7603 (tp-100) cc_final: 0.7306 (tp-100) outliers start: 48 outliers final: 8 residues processed: 439 average time/residue: 2.0552 time to fit residues: 1011.1695 Evaluate side-chains 406 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 398 time to evaluate : 3.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 311 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 351 optimal weight: 0.5980 chunk 293 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 142 optimal weight: 0.5980 chunk 143 optimal weight: 0.6980 chunk 331 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 251 optimal weight: 8.9990 chunk 275 optimal weight: 9.9990 chunk 141 optimal weight: 0.7980 chunk 175 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 193 ASN ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN C 193 ASN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN D 345 GLN D 429 GLN E 193 ASN E 345 GLN F 193 ASN F 345 GLN G 193 ASN ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 ASN ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.135104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.121621 restraints weight = 26067.357| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 0.81 r_work: 0.3289 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 29096 Z= 0.121 Angle : 0.515 5.493 39472 Z= 0.270 Chirality : 0.040 0.130 4152 Planarity : 0.004 0.026 5168 Dihedral : 8.940 171.136 4144 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.38 % Allowed : 12.25 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.90 (0.15), residues: 3544 helix: 1.78 (0.13), residues: 1584 sheet: 0.85 (0.23), residues: 456 loop : 1.02 (0.18), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 354 HIS 0.003 0.001 HIS A 311 PHE 0.015 0.002 PHE B 297 TYR 0.023 0.001 TYR A 263 ARG 0.003 0.000 ARG D 153 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 1384) hydrogen bonds : angle 5.24671 ( 3840) covalent geometry : bond 0.00258 (29096) covalent geometry : angle 0.51461 (39472) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 414 time to evaluate : 3.053 Fit side-chains REVERT: A 216 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7467 (tm-30) REVERT: A 429 GLN cc_start: 0.7689 (tp-100) cc_final: 0.7365 (tp-100) REVERT: B 216 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7392 (tm-30) REVERT: B 234 GLU cc_start: 0.8106 (mp0) cc_final: 0.7889 (mp0) REVERT: B 429 GLN cc_start: 0.7768 (tp-100) cc_final: 0.7479 (tp-100) REVERT: C 65 GLN cc_start: 0.7561 (pt0) cc_final: 0.7337 (pt0) REVERT: C 216 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7308 (tm-30) REVERT: C 234 GLU cc_start: 0.8128 (mp0) cc_final: 0.7887 (mp0) REVERT: C 422 ASP cc_start: 0.8122 (t0) cc_final: 0.7760 (t70) REVERT: C 429 GLN cc_start: 0.7697 (tp-100) cc_final: 0.7370 (tp-100) REVERT: D 65 GLN cc_start: 0.7591 (pt0) cc_final: 0.7383 (pt0) REVERT: D 216 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7536 (tm-30) REVERT: D 276 MET cc_start: 0.9175 (mtm) cc_final: 0.8933 (mtm) REVERT: D 422 ASP cc_start: 0.8140 (t0) cc_final: 0.7813 (t70) REVERT: D 429 GLN cc_start: 0.7731 (tp40) cc_final: 0.7112 (tp-100) REVERT: E 216 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7445 (tm-30) REVERT: E 429 GLN cc_start: 0.7734 (tp-100) cc_final: 0.7362 (tp-100) REVERT: F 216 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7440 (tm-30) REVERT: F 234 GLU cc_start: 0.8099 (mp0) cc_final: 0.7879 (mp0) REVERT: F 276 MET cc_start: 0.9190 (mtm) cc_final: 0.8953 (mtm) REVERT: F 429 GLN cc_start: 0.7723 (tp-100) cc_final: 0.7480 (tp-100) REVERT: G 65 GLN cc_start: 0.7591 (pt0) cc_final: 0.7373 (pt0) REVERT: G 216 GLU cc_start: 0.7736 (tm-30) cc_final: 0.7468 (tm-30) REVERT: G 234 GLU cc_start: 0.8123 (mp0) cc_final: 0.7891 (mp0) REVERT: G 338 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7189 (mm-30) REVERT: G 429 GLN cc_start: 0.7715 (tp-100) cc_final: 0.7389 (tp-100) REVERT: H 216 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7460 (tm-30) REVERT: H 234 GLU cc_start: 0.8096 (mp0) cc_final: 0.7871 (mp0) REVERT: H 429 GLN cc_start: 0.7698 (tp-100) cc_final: 0.7367 (tp-100) outliers start: 39 outliers final: 18 residues processed: 430 average time/residue: 2.1473 time to fit residues: 1030.2570 Evaluate side-chains 422 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 404 time to evaluate : 3.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 64 SER Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 64 SER Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 64 SER Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 311 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 294 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 218 optimal weight: 6.9990 chunk 165 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 102 optimal weight: 0.2980 chunk 96 optimal weight: 5.9990 chunk 291 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 237 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 429 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 GLN ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 429 GLN ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 429 GLN ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 429 GLN ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 429 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.127436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.113639 restraints weight = 26428.501| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 0.81 r_work: 0.3182 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 29096 Z= 0.215 Angle : 0.634 7.533 39472 Z= 0.333 Chirality : 0.044 0.144 4152 Planarity : 0.005 0.028 5168 Dihedral : 9.382 170.261 4144 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.38 % Allowed : 12.96 % Favored : 85.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.47 (0.14), residues: 3544 helix: 1.38 (0.13), residues: 1576 sheet: 0.73 (0.22), residues: 472 loop : 0.81 (0.17), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 354 HIS 0.004 0.001 HIS E 296 PHE 0.023 0.003 PHE F 297 TYR 0.031 0.002 TYR D 263 ARG 0.004 0.001 ARG C 442 Details of bonding type rmsd hydrogen bonds : bond 0.05070 ( 1384) hydrogen bonds : angle 5.59315 ( 3840) covalent geometry : bond 0.00470 (29096) covalent geometry : angle 0.63351 (39472) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 448 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 409 time to evaluate : 3.282 Fit side-chains REVERT: A 65 GLN cc_start: 0.7616 (pt0) cc_final: 0.7313 (pt0) REVERT: A 216 GLU cc_start: 0.7688 (tm-30) cc_final: 0.7425 (tm-30) REVERT: A 429 GLN cc_start: 0.7865 (tp40) cc_final: 0.7625 (tp-100) REVERT: B 65 GLN cc_start: 0.7628 (pt0) cc_final: 0.7334 (pt0) REVERT: B 216 GLU cc_start: 0.7633 (tm-30) cc_final: 0.7342 (tm-30) REVERT: B 429 GLN cc_start: 0.7882 (tp40) cc_final: 0.7624 (tp-100) REVERT: C 65 GLN cc_start: 0.7664 (pt0) cc_final: 0.7439 (pt0) REVERT: C 173 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7994 (ttt-90) REVERT: C 216 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7351 (tm-30) REVERT: C 422 ASP cc_start: 0.8163 (t0) cc_final: 0.7842 (t70) REVERT: C 429 GLN cc_start: 0.7847 (tp40) cc_final: 0.7606 (tp-100) REVERT: D 65 GLN cc_start: 0.7618 (pt0) cc_final: 0.7416 (pt0) REVERT: D 216 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7419 (tm-30) REVERT: D 422 ASP cc_start: 0.8177 (t0) cc_final: 0.7878 (t70) REVERT: D 429 GLN cc_start: 0.8000 (tp40) cc_final: 0.7588 (mm-40) REVERT: E 65 GLN cc_start: 0.7622 (pt0) cc_final: 0.7323 (pt0) REVERT: E 216 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7419 (tm-30) REVERT: E 429 GLN cc_start: 0.7888 (tp40) cc_final: 0.7635 (tp-100) REVERT: F 65 GLN cc_start: 0.7615 (pt0) cc_final: 0.7324 (pt0) REVERT: F 173 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8000 (ttt-90) REVERT: F 216 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7403 (tm-30) REVERT: F 234 GLU cc_start: 0.8138 (mp0) cc_final: 0.7874 (mp0) REVERT: F 429 GLN cc_start: 0.7869 (tp40) cc_final: 0.7621 (tp-100) REVERT: G 65 GLN cc_start: 0.7681 (pt0) cc_final: 0.7471 (pt0) REVERT: G 216 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7374 (tm-30) REVERT: G 234 GLU cc_start: 0.8144 (mp0) cc_final: 0.7877 (mp0) REVERT: G 429 GLN cc_start: 0.7865 (tp40) cc_final: 0.7619 (tp-100) REVERT: H 65 GLN cc_start: 0.7560 (pt0) cc_final: 0.7305 (pt0) REVERT: H 216 GLU cc_start: 0.7656 (tm-30) cc_final: 0.7384 (tm-30) REVERT: H 234 GLU cc_start: 0.8139 (mp0) cc_final: 0.7880 (mp0) REVERT: H 429 GLN cc_start: 0.7878 (tp40) cc_final: 0.7630 (tp-100) outliers start: 39 outliers final: 31 residues processed: 440 average time/residue: 2.2449 time to fit residues: 1099.2003 Evaluate side-chains 436 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 403 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 311 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 315 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 232 optimal weight: 1.9990 chunk 258 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 178 optimal weight: 0.5980 chunk 243 optimal weight: 1.9990 chunk 278 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.130419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.116715 restraints weight = 26136.910| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 0.81 r_work: 0.3225 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 29096 Z= 0.152 Angle : 0.563 6.485 39472 Z= 0.297 Chirality : 0.041 0.129 4152 Planarity : 0.004 0.026 5168 Dihedral : 9.266 169.828 4144 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.52 % Allowed : 12.99 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.46 (0.14), residues: 3544 helix: 1.39 (0.13), residues: 1576 sheet: 0.52 (0.22), residues: 488 loop : 0.89 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 354 HIS 0.003 0.001 HIS D 224 PHE 0.017 0.002 PHE G 297 TYR 0.027 0.002 TYR A 263 ARG 0.004 0.000 ARG C 442 Details of bonding type rmsd hydrogen bonds : bond 0.04435 ( 1384) hydrogen bonds : angle 5.44036 ( 3840) covalent geometry : bond 0.00327 (29096) covalent geometry : angle 0.56295 (39472) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 418 time to evaluate : 3.099 Fit side-chains REVERT: A 173 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7859 (ttt-90) REVERT: A 216 GLU cc_start: 0.7654 (tm-30) cc_final: 0.7354 (tm-30) REVERT: A 429 GLN cc_start: 0.7839 (tp40) cc_final: 0.7622 (tp-100) REVERT: B 216 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7305 (tm-30) REVERT: B 429 GLN cc_start: 0.7875 (tp40) cc_final: 0.7648 (tp-100) REVERT: C 173 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7935 (ttt-90) REVERT: C 216 GLU cc_start: 0.7603 (tm-30) cc_final: 0.7314 (tm-30) REVERT: C 252 MET cc_start: 0.9389 (OUTLIER) cc_final: 0.8845 (ptm) REVERT: C 422 ASP cc_start: 0.8156 (t0) cc_final: 0.7848 (t70) REVERT: C 429 GLN cc_start: 0.7848 (tp40) cc_final: 0.7609 (tp-100) REVERT: D 65 GLN cc_start: 0.7645 (pt0) cc_final: 0.7384 (pt0) REVERT: D 173 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7995 (ttt-90) REVERT: D 216 GLU cc_start: 0.7673 (tm-30) cc_final: 0.7386 (tm-30) REVERT: D 252 MET cc_start: 0.9391 (OUTLIER) cc_final: 0.8832 (ptm) REVERT: D 422 ASP cc_start: 0.8161 (t0) cc_final: 0.7854 (t70) REVERT: E 173 ARG cc_start: 0.8685 (OUTLIER) cc_final: 0.7884 (ttt-90) REVERT: E 216 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7346 (tm-30) REVERT: E 252 MET cc_start: 0.9404 (OUTLIER) cc_final: 0.8781 (ptm) REVERT: E 429 GLN cc_start: 0.7876 (tp40) cc_final: 0.7652 (tp-100) REVERT: F 173 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7946 (ttt-90) REVERT: F 216 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7326 (tm-30) REVERT: F 429 GLN cc_start: 0.7848 (tp40) cc_final: 0.7627 (tp-100) REVERT: G 216 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7327 (tm-30) REVERT: G 429 GLN cc_start: 0.7853 (tp40) cc_final: 0.7634 (tp-100) REVERT: H 65 GLN cc_start: 0.7541 (pt0) cc_final: 0.7278 (pt0) REVERT: H 216 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7333 (tm-30) outliers start: 43 outliers final: 24 residues processed: 446 average time/residue: 2.1742 time to fit residues: 1080.9842 Evaluate side-chains 450 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 418 time to evaluate : 3.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 311 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 29 optimal weight: 5.9990 chunk 199 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 313 optimal weight: 8.9990 chunk 198 optimal weight: 3.9990 chunk 18 optimal weight: 0.5980 chunk 227 optimal weight: 0.8980 chunk 343 optimal weight: 5.9990 chunk 237 optimal weight: 3.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 GLN ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 65 GLN ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 65 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 GLN ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.130582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.116905 restraints weight = 26265.681| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 0.81 r_work: 0.3229 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 29096 Z= 0.149 Angle : 0.563 6.346 39472 Z= 0.296 Chirality : 0.041 0.130 4152 Planarity : 0.004 0.026 5168 Dihedral : 9.257 169.094 4144 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.82 % Allowed : 11.83 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.46 (0.14), residues: 3544 helix: 1.26 (0.12), residues: 1624 sheet: 0.60 (0.23), residues: 472 loop : 1.01 (0.18), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 354 HIS 0.003 0.001 HIS D 224 PHE 0.018 0.002 PHE F 297 TYR 0.027 0.002 TYR B 263 ARG 0.006 0.000 ARG B 442 Details of bonding type rmsd hydrogen bonds : bond 0.04389 ( 1384) hydrogen bonds : angle 5.41701 ( 3840) covalent geometry : bond 0.00322 (29096) covalent geometry : angle 0.56255 (39472) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 499 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 419 time to evaluate : 3.031 Fit side-chains REVERT: A 65 GLN cc_start: 0.7567 (pt0) cc_final: 0.7364 (pt0) REVERT: A 173 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7836 (ttt-90) REVERT: A 216 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7313 (tm-30) REVERT: A 252 MET cc_start: 0.9424 (OUTLIER) cc_final: 0.8707 (ptm) REVERT: A 338 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7219 (mm-30) REVERT: A 429 GLN cc_start: 0.7881 (tp40) cc_final: 0.7639 (tp-100) REVERT: B 65 GLN cc_start: 0.7572 (pt0) cc_final: 0.7341 (pt0) REVERT: B 117 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7973 (ttp-170) REVERT: B 216 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7264 (tm-30) REVERT: B 252 MET cc_start: 0.9420 (OUTLIER) cc_final: 0.8724 (ptm) REVERT: B 429 GLN cc_start: 0.7857 (tp40) cc_final: 0.7614 (tp-100) REVERT: C 65 GLN cc_start: 0.7561 (pt0) cc_final: 0.7330 (pt0) REVERT: C 173 ARG cc_start: 0.8642 (OUTLIER) cc_final: 0.7916 (ttt-90) REVERT: C 216 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7264 (tm-30) REVERT: C 252 MET cc_start: 0.9411 (OUTLIER) cc_final: 0.8797 (ptm) REVERT: C 422 ASP cc_start: 0.8147 (t0) cc_final: 0.7811 (t70) REVERT: C 429 GLN cc_start: 0.7854 (tp40) cc_final: 0.7597 (tp-100) REVERT: D 117 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.8139 (ttp-170) REVERT: D 173 ARG cc_start: 0.8657 (OUTLIER) cc_final: 0.7955 (ttt-90) REVERT: D 216 GLU cc_start: 0.7649 (tm-30) cc_final: 0.7356 (tm-30) REVERT: D 252 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.8774 (ptm) REVERT: D 422 ASP cc_start: 0.8170 (t0) cc_final: 0.7824 (t70) REVERT: D 429 GLN cc_start: 0.8031 (tp40) cc_final: 0.7549 (tp-100) REVERT: E 65 GLN cc_start: 0.7581 (pt0) cc_final: 0.7377 (pt0) REVERT: E 173 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7861 (ttt-90) REVERT: E 216 GLU cc_start: 0.7601 (tm-30) cc_final: 0.7316 (tm-30) REVERT: E 252 MET cc_start: 0.9414 (OUTLIER) cc_final: 0.8769 (ptm) REVERT: E 429 GLN cc_start: 0.7894 (tp40) cc_final: 0.7648 (tp-100) REVERT: F 65 GLN cc_start: 0.7552 (pt0) cc_final: 0.7325 (pt0) REVERT: F 173 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7914 (ttt-90) REVERT: F 216 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7289 (tm-30) REVERT: F 252 MET cc_start: 0.9415 (OUTLIER) cc_final: 0.8724 (ptm) REVERT: F 429 GLN cc_start: 0.7891 (tp40) cc_final: 0.7640 (tp-100) REVERT: G 65 GLN cc_start: 0.7579 (pt0) cc_final: 0.7360 (pt0) REVERT: G 216 GLU cc_start: 0.7612 (tm-30) cc_final: 0.7296 (tm-30) REVERT: G 252 MET cc_start: 0.9420 (OUTLIER) cc_final: 0.8723 (ptm) REVERT: G 429 GLN cc_start: 0.7887 (tp40) cc_final: 0.7638 (tp-100) REVERT: H 65 GLN cc_start: 0.7534 (pt0) cc_final: 0.7253 (pt0) REVERT: H 216 GLU cc_start: 0.7609 (tm-30) cc_final: 0.7292 (tm-30) REVERT: H 252 MET cc_start: 0.9417 (OUTLIER) cc_final: 0.8707 (ptm) REVERT: H 429 GLN cc_start: 0.7901 (tp-100) cc_final: 0.7414 (tp-100) outliers start: 80 outliers final: 32 residues processed: 476 average time/residue: 2.1109 time to fit residues: 1119.5958 Evaluate side-chains 468 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 421 time to evaluate : 3.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 252 MET Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 252 MET Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 311 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 182 optimal weight: 4.9990 chunk 168 optimal weight: 0.0020 chunk 316 optimal weight: 2.9990 chunk 292 optimal weight: 1.9990 chunk 283 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 225 optimal weight: 7.9990 chunk 68 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 251 optimal weight: 7.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 65 GLN ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.130932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.117316 restraints weight = 26144.991| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 0.81 r_work: 0.3235 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 29096 Z= 0.144 Angle : 0.560 6.377 39472 Z= 0.295 Chirality : 0.041 0.129 4152 Planarity : 0.004 0.027 5168 Dihedral : 9.258 168.990 4144 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.94 % Allowed : 13.03 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.47 (0.14), residues: 3544 helix: 1.27 (0.13), residues: 1624 sheet: 0.56 (0.23), residues: 472 loop : 1.02 (0.18), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 354 HIS 0.004 0.001 HIS C 224 PHE 0.017 0.002 PHE F 297 TYR 0.027 0.002 TYR B 263 ARG 0.007 0.000 ARG E 442 Details of bonding type rmsd hydrogen bonds : bond 0.04308 ( 1384) hydrogen bonds : angle 5.38530 ( 3840) covalent geometry : bond 0.00310 (29096) covalent geometry : angle 0.56039 (39472) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 419 time to evaluate : 3.239 Fit side-chains REVERT: A 65 GLN cc_start: 0.7555 (pt0) cc_final: 0.7296 (pt0) REVERT: A 173 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7941 (ttt-90) REVERT: A 216 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7279 (tm-30) REVERT: A 252 MET cc_start: 0.9421 (OUTLIER) cc_final: 0.8705 (ptm) REVERT: A 429 GLN cc_start: 0.7858 (tp40) cc_final: 0.7617 (tp-100) REVERT: B 117 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7976 (ttp-170) REVERT: B 216 GLU cc_start: 0.7515 (tm-30) cc_final: 0.7199 (tm-30) REVERT: B 252 MET cc_start: 0.9416 (OUTLIER) cc_final: 0.8721 (ptm) REVERT: B 429 GLN cc_start: 0.7892 (tp40) cc_final: 0.7648 (tp-100) REVERT: C 173 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.7915 (ttt-90) REVERT: C 216 GLU cc_start: 0.7520 (tm-30) cc_final: 0.7204 (tm-30) REVERT: C 252 MET cc_start: 0.9407 (OUTLIER) cc_final: 0.8792 (ptm) REVERT: C 422 ASP cc_start: 0.8163 (t0) cc_final: 0.7834 (t70) REVERT: C 429 GLN cc_start: 0.7895 (tp40) cc_final: 0.7625 (tp-100) REVERT: D 65 GLN cc_start: 0.7567 (pt0) cc_final: 0.7361 (pt0) REVERT: D 117 ARG cc_start: 0.8370 (OUTLIER) cc_final: 0.8108 (ttp-170) REVERT: D 173 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.7961 (ttt-90) REVERT: D 216 GLU cc_start: 0.7623 (tm-30) cc_final: 0.7305 (tm-30) REVERT: D 252 MET cc_start: 0.9408 (OUTLIER) cc_final: 0.8774 (ptm) REVERT: D 422 ASP cc_start: 0.8164 (t0) cc_final: 0.7837 (t70) REVERT: D 429 GLN cc_start: 0.8035 (tp40) cc_final: 0.7549 (tp-100) REVERT: E 173 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.7960 (ttt-90) REVERT: E 216 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7264 (tm-30) REVERT: E 252 MET cc_start: 0.9408 (OUTLIER) cc_final: 0.8771 (ptm) REVERT: E 429 GLN cc_start: 0.7911 (tp40) cc_final: 0.7670 (tp-100) REVERT: F 173 ARG cc_start: 0.8641 (OUTLIER) cc_final: 0.7910 (ttt-90) REVERT: F 216 GLU cc_start: 0.7583 (tm-30) cc_final: 0.7264 (tm-30) REVERT: F 252 MET cc_start: 0.9413 (OUTLIER) cc_final: 0.8723 (ptm) REVERT: F 429 GLN cc_start: 0.7864 (tp40) cc_final: 0.7616 (tp-100) REVERT: G 216 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7274 (tm-30) REVERT: G 252 MET cc_start: 0.9420 (OUTLIER) cc_final: 0.8729 (ptm) REVERT: G 429 GLN cc_start: 0.7861 (tp40) cc_final: 0.7616 (tp-100) REVERT: H 65 GLN cc_start: 0.7561 (pt0) cc_final: 0.7341 (pt0) REVERT: H 216 GLU cc_start: 0.7588 (tm-30) cc_final: 0.7277 (tm-30) REVERT: H 252 MET cc_start: 0.9415 (OUTLIER) cc_final: 0.8705 (ptm) REVERT: H 429 GLN cc_start: 0.7898 (tp-100) cc_final: 0.7399 (tp-100) outliers start: 55 outliers final: 32 residues processed: 449 average time/residue: 2.1851 time to fit residues: 1093.7514 Evaluate side-chains 463 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 416 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 252 MET Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 252 MET Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 311 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 342 optimal weight: 8.9990 chunk 118 optimal weight: 7.9990 chunk 262 optimal weight: 5.9990 chunk 253 optimal weight: 2.9990 chunk 335 optimal weight: 4.9990 chunk 265 optimal weight: 0.0570 chunk 196 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 339 optimal weight: 10.0000 chunk 212 optimal weight: 0.7980 chunk 198 optimal weight: 9.9990 overall best weight: 2.1704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.127709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114171 restraints weight = 26372.048| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 0.80 r_work: 0.3194 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 29096 Z= 0.207 Angle : 0.630 7.281 39472 Z= 0.332 Chirality : 0.043 0.145 4152 Planarity : 0.004 0.028 5168 Dihedral : 9.598 169.568 4144 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.84 % Allowed : 13.98 % Favored : 84.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.31 (0.14), residues: 3544 helix: 1.23 (0.12), residues: 1576 sheet: 0.32 (0.22), residues: 488 loop : 0.90 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 354 HIS 0.005 0.001 HIS E 224 PHE 0.022 0.003 PHE B 297 TYR 0.033 0.002 TYR B 263 ARG 0.008 0.001 ARG H 442 Details of bonding type rmsd hydrogen bonds : bond 0.04956 ( 1384) hydrogen bonds : angle 5.58589 ( 3840) covalent geometry : bond 0.00454 (29096) covalent geometry : angle 0.63047 (39472) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 419 time to evaluate : 3.509 Fit side-chains REVERT: A 173 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7963 (ttt-90) REVERT: A 216 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7289 (tm-30) REVERT: A 252 MET cc_start: 0.9448 (OUTLIER) cc_final: 0.8710 (ptm) REVERT: B 216 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7265 (tm-30) REVERT: B 252 MET cc_start: 0.9439 (OUTLIER) cc_final: 0.8725 (ptm) REVERT: C 173 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8022 (ttt-90) REVERT: C 216 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7271 (tm-30) REVERT: C 252 MET cc_start: 0.9420 (OUTLIER) cc_final: 0.8792 (ptm) REVERT: D 65 GLN cc_start: 0.7588 (pt0) cc_final: 0.7349 (pt0) REVERT: D 117 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.8128 (ttp-170) REVERT: D 173 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7967 (ttt-90) REVERT: D 216 GLU cc_start: 0.7532 (tm-30) cc_final: 0.7219 (tm-30) REVERT: D 252 MET cc_start: 0.9419 (OUTLIER) cc_final: 0.8781 (ptm) REVERT: D 429 GLN cc_start: 0.8083 (tp40) cc_final: 0.7667 (tp-100) REVERT: E 173 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7988 (ttt-90) REVERT: E 216 GLU cc_start: 0.7500 (tm-30) cc_final: 0.7181 (tm-30) REVERT: E 252 MET cc_start: 0.9425 (OUTLIER) cc_final: 0.8783 (ptm) REVERT: F 173 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8015 (ttt-90) REVERT: F 216 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7283 (tm-30) REVERT: F 252 MET cc_start: 0.9435 (OUTLIER) cc_final: 0.8722 (ptm) REVERT: G 216 GLU cc_start: 0.7509 (tm-30) cc_final: 0.7191 (tm-30) REVERT: G 252 MET cc_start: 0.9440 (OUTLIER) cc_final: 0.8729 (ptm) REVERT: H 65 GLN cc_start: 0.7567 (pt0) cc_final: 0.7341 (pt0) REVERT: H 216 GLU cc_start: 0.7504 (tm-30) cc_final: 0.7296 (tm-30) REVERT: H 252 MET cc_start: 0.9438 (OUTLIER) cc_final: 0.8700 (ptm) REVERT: H 429 GLN cc_start: 0.7958 (tp-100) cc_final: 0.7509 (tp-100) outliers start: 52 outliers final: 34 residues processed: 454 average time/residue: 2.1475 time to fit residues: 1085.2330 Evaluate side-chains 456 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 408 time to evaluate : 3.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 105 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 252 MET Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 252 MET Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 311 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 270 optimal weight: 0.8980 chunk 282 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 0.8980 chunk 303 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.131112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.117529 restraints weight = 26215.865| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 0.81 r_work: 0.3237 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3144 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 29096 Z= 0.136 Angle : 0.561 6.249 39472 Z= 0.295 Chirality : 0.041 0.130 4152 Planarity : 0.004 0.028 5168 Dihedral : 9.306 169.219 4144 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.05 % Allowed : 14.02 % Favored : 83.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 1.10 (0.14), residues: 3544 helix: 1.01 (0.12), residues: 1672 sheet: 0.52 (0.23), residues: 472 loop : 0.68 (0.18), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 354 HIS 0.004 0.001 HIS F 224 PHE 0.017 0.002 PHE B 297 TYR 0.026 0.002 TYR F 263 ARG 0.009 0.000 ARG C 442 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 1384) hydrogen bonds : angle 5.37877 ( 3840) covalent geometry : bond 0.00292 (29096) covalent geometry : angle 0.56109 (39472) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 407 time to evaluate : 3.084 Fit side-chains REVERT: A 173 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7900 (ttt-90) REVERT: A 216 GLU cc_start: 0.7417 (tm-30) cc_final: 0.7081 (tm-30) REVERT: A 252 MET cc_start: 0.9423 (OUTLIER) cc_final: 0.8704 (ptm) REVERT: A 429 GLN cc_start: 0.7887 (tp-100) cc_final: 0.7542 (tp-100) REVERT: B 117 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7981 (ttp-170) REVERT: B 216 GLU cc_start: 0.7406 (tm-30) cc_final: 0.7144 (tm-30) REVERT: B 252 MET cc_start: 0.9415 (OUTLIER) cc_final: 0.8725 (ptm) REVERT: B 429 GLN cc_start: 0.7925 (tp-100) cc_final: 0.7579 (tp-100) REVERT: C 173 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7869 (ttt-90) REVERT: C 216 GLU cc_start: 0.7401 (tm-30) cc_final: 0.7136 (tm-30) REVERT: C 252 MET cc_start: 0.9396 (OUTLIER) cc_final: 0.8789 (ptm) REVERT: C 429 GLN cc_start: 0.7955 (tp-100) cc_final: 0.7597 (tp-100) REVERT: D 117 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8094 (ttp-170) REVERT: D 173 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7916 (ttt-90) REVERT: D 216 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7135 (tm-30) REVERT: D 252 MET cc_start: 0.9400 (OUTLIER) cc_final: 0.8768 (ptm) REVERT: D 429 GLN cc_start: 0.8061 (tp40) cc_final: 0.7596 (tp-100) REVERT: E 173 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7918 (ttt-90) REVERT: E 216 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7154 (tm-30) REVERT: E 252 MET cc_start: 0.9391 (OUTLIER) cc_final: 0.8769 (ptm) REVERT: E 429 GLN cc_start: 0.7901 (tp-100) cc_final: 0.7560 (tp-100) REVERT: F 173 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.7975 (ttt-90) REVERT: F 216 GLU cc_start: 0.7418 (tm-30) cc_final: 0.7080 (tm-30) REVERT: F 252 MET cc_start: 0.9412 (OUTLIER) cc_final: 0.8726 (ptm) REVERT: F 429 GLN cc_start: 0.7887 (tp-100) cc_final: 0.7539 (tp-100) REVERT: G 216 GLU cc_start: 0.7431 (tm-30) cc_final: 0.7101 (tm-30) REVERT: G 252 MET cc_start: 0.9420 (OUTLIER) cc_final: 0.8735 (ptm) REVERT: G 429 GLN cc_start: 0.7886 (tp-100) cc_final: 0.7537 (tp-100) REVERT: H 65 GLN cc_start: 0.7539 (pt0) cc_final: 0.7285 (pt0) REVERT: H 216 GLU cc_start: 0.7427 (tm-30) cc_final: 0.7104 (tm-30) REVERT: H 252 MET cc_start: 0.9418 (OUTLIER) cc_final: 0.8705 (ptm) REVERT: H 429 GLN cc_start: 0.7923 (tp-100) cc_final: 0.7330 (tp-100) outliers start: 58 outliers final: 40 residues processed: 445 average time/residue: 2.1066 time to fit residues: 1045.9927 Evaluate side-chains 465 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 410 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 252 MET Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 252 MET Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 311 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 345 optimal weight: 0.5980 chunk 4 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 139 optimal weight: 2.9990 chunk 181 optimal weight: 1.9990 chunk 246 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 240 optimal weight: 5.9990 chunk 268 optimal weight: 0.9990 chunk 304 optimal weight: 6.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.128649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.114872 restraints weight = 26226.381| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 0.82 r_work: 0.3200 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 29096 Z= 0.191 Angle : 0.622 6.977 39472 Z= 0.327 Chirality : 0.043 0.142 4152 Planarity : 0.004 0.037 5168 Dihedral : 9.534 169.380 4144 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.12 % Allowed : 14.58 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.99 (0.14), residues: 3544 helix: 0.89 (0.12), residues: 1672 sheet: 0.46 (0.23), residues: 472 loop : 0.68 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 354 HIS 0.004 0.001 HIS D 311 PHE 0.021 0.002 PHE B 297 TYR 0.031 0.002 TYR B 263 ARG 0.011 0.001 ARG H 442 Details of bonding type rmsd hydrogen bonds : bond 0.04801 ( 1384) hydrogen bonds : angle 5.53944 ( 3840) covalent geometry : bond 0.00418 (29096) covalent geometry : angle 0.62155 (39472) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7088 Ramachandran restraints generated. 3544 Oldfield, 0 Emsley, 3544 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 474 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 414 time to evaluate : 3.345 Fit side-chains REVERT: A 173 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7929 (ttt-90) REVERT: A 216 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7253 (tm-30) REVERT: A 252 MET cc_start: 0.9445 (OUTLIER) cc_final: 0.8724 (ptm) REVERT: B 252 MET cc_start: 0.9437 (OUTLIER) cc_final: 0.8729 (ptm) REVERT: B 429 GLN cc_start: 0.8028 (tp-100) cc_final: 0.7683 (tp-100) REVERT: C 173 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8014 (ttt-90) REVERT: C 252 MET cc_start: 0.9424 (OUTLIER) cc_final: 0.8793 (ptm) REVERT: D 117 ARG cc_start: 0.8386 (OUTLIER) cc_final: 0.8118 (ttp-170) REVERT: D 173 ARG cc_start: 0.8661 (OUTLIER) cc_final: 0.7941 (ttt-90) REVERT: D 216 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7288 (tm-30) REVERT: D 252 MET cc_start: 0.9426 (OUTLIER) cc_final: 0.8783 (ptm) REVERT: D 429 GLN cc_start: 0.8099 (tp40) cc_final: 0.7684 (tp-100) REVERT: E 173 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7961 (ttt-90) REVERT: E 216 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7263 (tm-30) REVERT: E 252 MET cc_start: 0.9425 (OUTLIER) cc_final: 0.8791 (ptm) REVERT: E 429 GLN cc_start: 0.8048 (tp-100) cc_final: 0.7709 (tp-100) REVERT: F 173 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8024 (ttt-90) REVERT: F 216 GLU cc_start: 0.7474 (tm-30) cc_final: 0.7258 (tm-30) REVERT: F 252 MET cc_start: 0.9434 (OUTLIER) cc_final: 0.8728 (ptm) REVERT: G 216 GLU cc_start: 0.7480 (tm-30) cc_final: 0.7264 (tm-30) REVERT: G 252 MET cc_start: 0.9440 (OUTLIER) cc_final: 0.8736 (ptm) REVERT: H 65 GLN cc_start: 0.7625 (pt0) cc_final: 0.7365 (pt0) REVERT: H 216 GLU cc_start: 0.7482 (tm-30) cc_final: 0.7275 (tm-30) REVERT: H 252 MET cc_start: 0.9437 (OUTLIER) cc_final: 0.8720 (ptm) REVERT: H 429 GLN cc_start: 0.7957 (tp-100) cc_final: 0.7515 (tp-100) outliers start: 60 outliers final: 46 residues processed: 458 average time/residue: 2.1123 time to fit residues: 1079.6942 Evaluate side-chains 473 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 413 time to evaluate : 3.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 173 ARG Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 252 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain B residue 180 VAL Chi-restraints excluded: chain B residue 252 MET Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 173 ARG Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 252 MET Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 105 SER Chi-restraints excluded: chain D residue 117 ARG Chi-restraints excluded: chain D residue 173 ARG Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 252 MET Chi-restraints excluded: chain D residue 286 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain D residue 378 SER Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 180 VAL Chi-restraints excluded: chain E residue 252 MET Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain E residue 378 SER Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 180 VAL Chi-restraints excluded: chain F residue 252 MET Chi-restraints excluded: chain F residue 286 VAL Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain F residue 378 SER Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 180 VAL Chi-restraints excluded: chain G residue 252 MET Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain G residue 378 SER Chi-restraints excluded: chain H residue 26 GLU Chi-restraints excluded: chain H residue 105 SER Chi-restraints excluded: chain H residue 180 VAL Chi-restraints excluded: chain H residue 252 MET Chi-restraints excluded: chain H residue 286 VAL Chi-restraints excluded: chain H residue 311 HIS Chi-restraints excluded: chain H residue 378 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 229 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 322 optimal weight: 0.3980 chunk 91 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 290 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 4 optimal weight: 10.0000 chunk 286 optimal weight: 8.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.128745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.115255 restraints weight = 26346.739| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 0.80 r_work: 0.3210 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3116 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 29096 Z= 0.178 Angle : 0.612 6.955 39472 Z= 0.322 Chirality : 0.042 0.137 4152 Planarity : 0.004 0.044 5168 Dihedral : 9.518 169.569 4144 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.26 % Allowed : 14.44 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.17 % 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: 0.98 (0.14), residues: 3544 helix: 0.88 (0.12), residues: 1672 sheet: 0.45 (0.23), residues: 472 loop : 0.69 (0.17), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 354 HIS 0.004 0.001 HIS D 224 PHE 0.020 0.002 PHE B 297 TYR 0.030 0.002 TYR A 263 ARG 0.010 0.001 ARG D 442 Details of bonding type rmsd hydrogen bonds : bond 0.04677 ( 1384) hydrogen bonds : angle 5.51624 ( 3840) covalent geometry : bond 0.00390 (29096) covalent geometry : angle 0.61167 (39472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23318.88 seconds wall clock time: 401 minutes 44.03 seconds (24104.03 seconds total)