Starting phenix.real_space_refine on Wed Jun 25 06:55:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u66_41946/06_2025/8u66_41946.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u66_41946/06_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_41946/06_2025/8u66_41946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u66_41946/06_2025/8u66_41946.map" model { file = "/net/cci-nas-00/data/ceres_data/8u66_41946/06_2025/8u66_41946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u66_41946/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 15.06, per 1000 atoms: 0.51 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: 7.07 Conformation dependent library (CDL) restraints added in 3.3 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: 3.32 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: 10.56 Time building geometry restraints manager: 8.27 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: 0.23 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: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.190 Set scattering table: 0.240 Process input model: 60.900 Find NCS groups from input model: 0.590 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: 0.000 Load rotamer database and sin/cos tables:10.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.050 ------------------------------------------------------------------------------- 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 : 3.225 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: 2.1744 time to fit residues: 1070.4844 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 : 3.175 ------------------------------------------------------------------------------- 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 = 0.138755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.125330 restraints weight = 26110.515| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 0.81 r_work: 0.3335 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 0.026 29096 Z= 0.114 Angle : 0.505 5.057 39472 Z= 0.266 Chirality : 0.039 0.134 4152 Planarity : 0.004 0.024 5168 Dihedral : 9.278 179.881 4144 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 3.03 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 0.03983 ( 1384) hydrogen bonds : angle 5.47592 ( 3840) covalent geometry : bond 0.00243 (29096) covalent geometry : angle 0.50462 (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 : 3.202 Fit side-chains REVERT: A 208 MET cc_start: 0.9150 (mmm) cc_final: 0.8928 (mmm) REVERT: A 216 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7389 (tm-30) REVERT: A 234 GLU cc_start: 0.8106 (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: 0.8452 (mt) cc_final: 0.7979 (mt) REVERT: A 429 GLN cc_start: 0.7576 (tp-100) cc_final: 0.7352 (tp-100) REVERT: B 149 LYS cc_start: 0.8534 (mttt) cc_final: 0.8160 (mtmt) REVERT: B 208 MET cc_start: 0.9150 (mmm) cc_final: 0.8841 (mmm) REVERT: B 216 GLU cc_start: 0.7659 (tm-30) cc_final: 0.7383 (tm-30) REVERT: B 234 GLU cc_start: 0.8071 (mp0) cc_final: 0.7865 (mp0) REVERT: B 429 GLN cc_start: 0.7678 (tp-100) cc_final: 0.7337 (tp-100) REVERT: C 149 LYS cc_start: 0.8488 (mttp) cc_final: 0.8106 (mtmt) REVERT: C 208 MET cc_start: 0.9108 (mmm) cc_final: 0.8723 (mmp) REVERT: C 216 GLU cc_start: 0.7593 (tm-30) cc_final: 0.7315 (tm-30) REVERT: C 234 GLU cc_start: 0.8111 (mp0) cc_final: 0.7887 (mp0) REVERT: C 429 GLN cc_start: 0.7585 (tp-100) cc_final: 0.7350 (tp-100) REVERT: D 65 GLN cc_start: 0.7541 (pt0) cc_final: 0.7283 (pt0) REVERT: D 149 LYS cc_start: 0.8234 (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: 0.7749 (tm-30) cc_final: 0.7458 (tm-30) REVERT: D 276 MET cc_start: 0.9088 (mtm) cc_final: 0.8855 (mtm) REVERT: E 208 MET cc_start: 0.9131 (mmm) cc_final: 0.8815 (mmm) REVERT: E 216 GLU cc_start: 0.7615 (tm-30) cc_final: 0.7345 (tm-30) REVERT: E 234 GLU cc_start: 0.8101 (mp0) cc_final: 0.7892 (mp0) REVERT: E 429 GLN cc_start: 0.7657 (tp-100) cc_final: 0.7330 (tp-100) REVERT: F 208 MET cc_start: 0.9166 (mmm) cc_final: 0.8853 (mmm) REVERT: F 216 GLU cc_start: 0.7706 (tm-30) cc_final: 0.7406 (tm-30) REVERT: F 234 GLU cc_start: 0.8095 (mp0) cc_final: 0.7880 (mp0) REVERT: F 276 MET cc_start: 0.9118 (mtm) cc_final: 0.8859 (mtm) REVERT: F 429 GLN cc_start: 0.7608 (tp-100) cc_final: 0.7406 (tp-100) REVERT: G 65 GLN cc_start: 0.7503 (pt0) cc_final: 0.7279 (pt0) REVERT: G 149 LYS cc_start: 0.8248 (mmtt) cc_final: 0.7991 (mtmt) REVERT: G 208 MET cc_start: 0.9137 (mmm) cc_final: 0.8831 (mmm) REVERT: G 216 GLU cc_start: 0.7657 (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: 0.8870 (mtm) REVERT: G 429 GLN cc_start: 0.7612 (tp-100) cc_final: 0.7321 (tp-100) REVERT: H 149 LYS cc_start: 0.8529 (mttt) cc_final: 0.8132 (mtmt) REVERT: H 208 MET cc_start: 0.9136 (mmm) cc_final: 0.8837 (mmm) REVERT: H 216 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7450 (tm-30) REVERT: H 234 GLU cc_start: 0.8077 (mp0) cc_final: 0.7875 (mp0) REVERT: H 429 GLN cc_start: 0.7611 (tp-100) cc_final: 0.7318 (tp-100) outliers start: 48 outliers final: 8 residues processed: 439 average time/residue: 2.2086 time to fit residues: 1087.3973 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 : 3.707 ------------------------------------------------------------------------------- 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: 0.9980 chunk 293 optimal weight: 4.9990 chunk 152 optimal weight: 10.0000 chunk 142 optimal weight: 0.6980 chunk 143 optimal weight: 0.9980 chunk 331 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 chunk 251 optimal weight: 8.9990 chunk 275 optimal weight: 10.0000 chunk 141 optimal weight: 0.6980 chunk 175 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 B 345 GLN C 193 ASN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3507 r_free = 0.3507 target = 0.132331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.118709 restraints weight = 26059.123| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 0.81 r_work: 0.3250 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 29096 Z= 0.143 Angle : 0.546 6.091 39472 Z= 0.287 Chirality : 0.041 0.132 4152 Planarity : 0.004 0.026 5168 Dihedral : 9.052 170.682 4144 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.48 % Allowed : 12.25 % Favored : 86.26 % 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: 1.83 (0.14), residues: 3544 helix: 1.68 (0.13), residues: 1584 sheet: 0.83 (0.23), residues: 456 loop : 1.03 (0.17), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 354 HIS 0.004 0.001 HIS F 393 PHE 0.018 0.002 PHE F 297 TYR 0.025 0.002 TYR D 263 ARG 0.004 0.000 ARG B 442 Details of bonding type rmsd hydrogen bonds : bond 0.04407 ( 1384) hydrogen bonds : angle 5.34150 ( 3840) covalent geometry : bond 0.00307 (29096) covalent geometry : angle 0.54647 (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 454 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 412 time to evaluate : 3.348 Fit side-chains REVERT: A 65 GLN cc_start: 0.7591 (pt0) cc_final: 0.7301 (pt0) REVERT: A 216 GLU cc_start: 0.7766 (tm-30) cc_final: 0.7480 (tm-30) REVERT: A 234 GLU cc_start: 0.8119 (mp0) cc_final: 0.7897 (mp0) REVERT: A 338 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7154 (mm-30) REVERT: A 429 GLN cc_start: 0.7749 (tp-100) cc_final: 0.7510 (tp-100) REVERT: B 216 GLU cc_start: 0.7624 (tm-30) cc_final: 0.7332 (tm-30) REVERT: B 234 GLU cc_start: 0.8103 (mp0) cc_final: 0.7886 (mp0) REVERT: B 429 GLN cc_start: 0.7779 (tp-100) cc_final: 0.7569 (tp-100) REVERT: C 216 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7360 (tm-30) REVERT: C 234 GLU cc_start: 0.8120 (mp0) cc_final: 0.7877 (mp0) REVERT: C 429 GLN cc_start: 0.7738 (tp-100) cc_final: 0.7465 (tp-100) REVERT: D 65 GLN cc_start: 0.7564 (pt0) cc_final: 0.7352 (pt0) REVERT: D 216 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7526 (tm-30) REVERT: D 429 GLN cc_start: 0.7755 (tp40) cc_final: 0.7124 (tp-100) REVERT: E 65 GLN cc_start: 0.7594 (pt0) cc_final: 0.7306 (pt0) REVERT: E 216 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7466 (tm-30) REVERT: E 429 GLN cc_start: 0.7771 (tp-100) cc_final: 0.7560 (tp-100) REVERT: F 216 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7454 (tm-30) REVERT: F 429 GLN cc_start: 0.7764 (tp-100) cc_final: 0.7563 (tp-100) REVERT: G 216 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7447 (tm-30) REVERT: G 429 GLN cc_start: 0.7766 (tp-100) cc_final: 0.7517 (tp-100) REVERT: H 65 GLN cc_start: 0.7586 (pt0) cc_final: 0.7381 (pt0) REVERT: H 216 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7388 (tm-30) REVERT: H 234 GLU cc_start: 0.8089 (mp0) cc_final: 0.7861 (mp0) REVERT: H 429 GLN cc_start: 0.7740 (tp-100) cc_final: 0.7488 (tp-100) outliers start: 42 outliers final: 18 residues processed: 429 average time/residue: 2.5669 time to fit residues: 1225.4357 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 : 3.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 26 GLU 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 180 VAL Chi-restraints excluded: chain D residue 311 HIS Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 311 HIS Chi-restraints excluded: chain F residue 26 GLU Chi-restraints excluded: chain F residue 311 HIS Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 26 GLU 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: 5.9990 chunk 218 optimal weight: 6.9990 chunk 165 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 102 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 291 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 237 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 429 GLN B 345 GLN ** C 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 345 GLN ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 65 GLN ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 429 GLN ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.129023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.115169 restraints weight = 26334.492| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 0.82 r_work: 0.3195 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 2.14 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 29096 Z= 0.183 Angle : 0.602 7.149 39472 Z= 0.317 Chirality : 0.043 0.137 4152 Planarity : 0.004 0.026 5168 Dihedral : 9.316 170.153 4144 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.66 % Allowed : 12.68 % 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: 1.48 (0.14), residues: 3544 helix: 1.41 (0.13), residues: 1576 sheet: 0.72 (0.23), residues: 472 loop : 0.81 (0.17), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 354 HIS 0.004 0.001 HIS E 224 PHE 0.021 0.002 PHE F 297 TYR 0.030 0.002 TYR F 263 ARG 0.004 0.001 ARG A 442 Details of bonding type rmsd hydrogen bonds : bond 0.04810 ( 1384) hydrogen bonds : angle 5.52828 ( 3840) covalent geometry : bond 0.00397 (29096) covalent geometry : angle 0.60235 (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 461 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 414 time to evaluate : 2.985 Fit side-chains REVERT: A 216 GLU cc_start: 0.7670 (tm-30) cc_final: 0.7401 (tm-30) REVERT: A 429 GLN cc_start: 0.7868 (tp40) cc_final: 0.7603 (tp-100) REVERT: B 173 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.7995 (ttt-90) REVERT: B 216 GLU cc_start: 0.7610 (tm-30) cc_final: 0.7317 (tm-30) REVERT: B 234 GLU cc_start: 0.8147 (mp0) cc_final: 0.7899 (mp0) REVERT: B 429 GLN cc_start: 0.7868 (tp-100) cc_final: 0.7643 (tp-100) REVERT: C 65 GLN cc_start: 0.7578 (pt0) cc_final: 0.7342 (pt0) REVERT: C 173 ARG cc_start: 0.8692 (OUTLIER) cc_final: 0.7976 (ttt-90) REVERT: C 216 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7339 (tm-30) REVERT: C 422 ASP cc_start: 0.8156 (t0) cc_final: 0.7831 (t70) REVERT: C 429 GLN cc_start: 0.7857 (tp-100) cc_final: 0.7614 (tp-100) REVERT: D 65 GLN cc_start: 0.7642 (pt0) cc_final: 0.7429 (pt0) REVERT: D 216 GLU cc_start: 0.7693 (tm-30) cc_final: 0.7435 (tm-30) REVERT: D 252 MET cc_start: 0.9412 (OUTLIER) cc_final: 0.8847 (ptm) REVERT: D 429 GLN cc_start: 0.8002 (tp40) cc_final: 0.7584 (mm-40) REVERT: E 173 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7992 (ttt-90) REVERT: E 216 GLU cc_start: 0.7668 (tm-30) cc_final: 0.7399 (tm-30) REVERT: E 234 GLU cc_start: 0.8146 (mp0) cc_final: 0.7928 (mp0) REVERT: E 429 GLN cc_start: 0.7893 (tp-100) cc_final: 0.7679 (tp-100) REVERT: F 173 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7958 (ttt-90) REVERT: F 216 GLU cc_start: 0.7645 (tm-30) cc_final: 0.7353 (tm-30) REVERT: F 234 GLU cc_start: 0.8170 (mp0) cc_final: 0.7951 (mp0) REVERT: F 429 GLN cc_start: 0.7862 (tp-100) cc_final: 0.7650 (tp-100) REVERT: G 65 GLN cc_start: 0.7544 (pt0) cc_final: 0.7285 (pt0) REVERT: G 173 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.7973 (ttt-90) REVERT: G 216 GLU cc_start: 0.7637 (tm-30) cc_final: 0.7351 (tm-30) REVERT: G 234 GLU cc_start: 0.8156 (mp0) cc_final: 0.7941 (mp0) REVERT: G 429 GLN cc_start: 0.7882 (tp40) cc_final: 0.7616 (tp-100) REVERT: H 173 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7995 (ttt-90) REVERT: H 216 GLU cc_start: 0.7634 (tm-30) cc_final: 0.7349 (tm-30) REVERT: H 429 GLN cc_start: 0.7869 (tp-100) cc_final: 0.7628 (tp-100) outliers start: 47 outliers final: 32 residues processed: 451 average time/residue: 2.1815 time to fit residues: 1095.6093 Evaluate side-chains 447 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 408 time to evaluate : 3.323 ------------------------------------------------------------------------------- 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 173 ARG 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 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 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 173 ARG 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 173 ARG 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: 0.9980 chunk 215 optimal weight: 3.9990 chunk 232 optimal weight: 0.4980 chunk 258 optimal weight: 9.9990 chunk 117 optimal weight: 1.9990 chunk 216 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 178 optimal weight: 0.6980 chunk 243 optimal weight: 0.0870 chunk 278 optimal weight: 0.8980 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 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 65 GLN ** E 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 65 GLN ** F 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 65 GLN ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.133841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.120321 restraints weight = 26198.986| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 0.81 r_work: 0.3274 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3181 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 29096 Z= 0.116 Angle : 0.516 5.480 39472 Z= 0.272 Chirality : 0.039 0.128 4152 Planarity : 0.004 0.027 5168 Dihedral : 9.011 168.680 4144 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.66 % Allowed : 13.38 % Favored : 84.96 % 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: 1.62 (0.14), residues: 3544 helix: 1.55 (0.13), residues: 1584 sheet: 0.78 (0.25), residues: 416 loop : 0.84 (0.17), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 354 HIS 0.003 0.001 HIS D 224 PHE 0.013 0.002 PHE G 297 TYR 0.023 0.001 TYR D 263 ARG 0.004 0.000 ARG E 442 Details of bonding type rmsd hydrogen bonds : bond 0.03922 ( 1384) hydrogen bonds : angle 5.24440 ( 3840) covalent geometry : bond 0.00245 (29096) covalent geometry : angle 0.51614 (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 469 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 422 time to evaluate : 3.683 Fit side-chains REVERT: A 65 GLN cc_start: 0.7514 (pt0) cc_final: 0.7301 (pt0) REVERT: A 216 GLU cc_start: 0.7626 (tm-30) cc_final: 0.7328 (tm-30) REVERT: A 429 GLN cc_start: 0.7811 (tp40) cc_final: 0.7501 (tp-100) REVERT: B 65 GLN cc_start: 0.7559 (pt0) cc_final: 0.7336 (pt0) REVERT: B 117 ARG cc_start: 0.8338 (OUTLIER) cc_final: 0.7975 (ttp-170) REVERT: B 173 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7761 (ttt-90) REVERT: B 216 GLU cc_start: 0.7590 (tm-30) cc_final: 0.7265 (tm-30) REVERT: B 429 GLN cc_start: 0.7818 (tp-100) cc_final: 0.7546 (tp-100) REVERT: C 173 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7732 (ttt-90) REVERT: C 216 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7282 (tm-30) REVERT: C 252 MET cc_start: 0.9365 (OUTLIER) cc_final: 0.8839 (ptm) REVERT: C 422 ASP cc_start: 0.8131 (t0) cc_final: 0.7808 (t70) REVERT: C 429 GLN cc_start: 0.7810 (tp-100) cc_final: 0.7521 (tp-100) REVERT: D 173 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.7801 (ttt-90) REVERT: D 216 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7385 (tm-30) REVERT: D 252 MET cc_start: 0.9382 (OUTLIER) cc_final: 0.8817 (ptm) REVERT: D 429 GLN cc_start: 0.7888 (tp40) cc_final: 0.7170 (tp40) REVERT: E 65 GLN cc_start: 0.7518 (pt0) cc_final: 0.7306 (pt0) REVERT: E 173 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7775 (ttt-90) REVERT: E 216 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7293 (tm-30) REVERT: E 252 MET cc_start: 0.9378 (OUTLIER) cc_final: 0.8822 (ptm) REVERT: E 429 GLN cc_start: 0.7822 (tp-100) cc_final: 0.7578 (tp-100) REVERT: F 65 GLN cc_start: 0.7506 (pt0) cc_final: 0.7300 (pt0) REVERT: F 173 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7774 (ttt-90) REVERT: F 216 GLU cc_start: 0.7628 (tm-30) cc_final: 0.7302 (tm-30) REVERT: F 252 MET cc_start: 0.9359 (OUTLIER) cc_final: 0.8837 (ptm) REVERT: F 345 GLN cc_start: 0.8009 (mp10) cc_final: 0.7728 (mp-120) REVERT: F 429 GLN cc_start: 0.7797 (tp-100) cc_final: 0.7553 (tp-100) REVERT: G 65 GLN cc_start: 0.7567 (pt0) cc_final: 0.7306 (pt0) REVERT: G 173 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.7773 (ttt-90) REVERT: G 216 GLU cc_start: 0.7643 (tm-30) cc_final: 0.7322 (tm-30) REVERT: G 429 GLN cc_start: 0.7819 (tp40) cc_final: 0.7472 (tp-100) REVERT: H 149 LYS cc_start: 0.8644 (mttp) cc_final: 0.8436 (mppt) REVERT: H 173 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7801 (ttt-90) REVERT: H 216 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7326 (tm-30) REVERT: H 252 MET cc_start: 0.9386 (OUTLIER) cc_final: 0.8834 (ptm) REVERT: H 429 GLN cc_start: 0.7801 (tp-100) cc_final: 0.7561 (tp-100) outliers start: 47 outliers final: 18 residues processed: 450 average time/residue: 2.2590 time to fit residues: 1132.8970 Evaluate side-chains 452 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 421 time to evaluate : 3.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 173 ARG Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 311 HIS 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 173 ARG 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 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 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 173 ARG Chi-restraints excluded: chain G residue 286 VAL Chi-restraints excluded: chain G residue 311 HIS Chi-restraints excluded: chain H residue 173 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 352 random chunks: chunk 29 optimal weight: 1.9990 chunk 199 optimal weight: 5.9990 chunk 197 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 313 optimal weight: 10.0000 chunk 198 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 227 optimal weight: 0.6980 chunk 343 optimal weight: 5.9990 chunk 237 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3478 r_free = 0.3478 target = 0.129989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.116295 restraints weight = 26279.104| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 0.81 r_work: 0.3221 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 29096 Z= 0.165 Angle : 0.577 6.576 39472 Z= 0.304 Chirality : 0.041 0.132 4152 Planarity : 0.004 0.026 5168 Dihedral : 9.264 168.810 4144 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 2.19 % Allowed : 12.99 % Favored : 84.82 % 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: 1.50 (0.14), residues: 3544 helix: 1.45 (0.13), residues: 1576 sheet: 0.43 (0.22), residues: 488 loop : 0.91 (0.18), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 354 HIS 0.003 0.001 HIS D 311 PHE 0.020 0.002 PHE F 297 TYR 0.029 0.002 TYR D 263 ARG 0.005 0.000 ARG B 442 Details of bonding type rmsd hydrogen bonds : bond 0.04538 ( 1384) hydrogen bonds : angle 5.40824 ( 3840) covalent geometry : bond 0.00358 (29096) covalent geometry : angle 0.57729 (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 480 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 418 time to evaluate : 3.166 Fit side-chains REVERT: A 216 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7304 (tm-30) REVERT: A 252 MET cc_start: 0.9421 (OUTLIER) cc_final: 0.8719 (ptm) REVERT: A 338 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7245 (mm-30) REVERT: A 429 GLN cc_start: 0.7893 (tp40) cc_final: 0.7635 (tp-100) REVERT: B 117 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.7973 (ttp-170) REVERT: B 173 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7993 (ttt-90) REVERT: B 216 GLU cc_start: 0.7571 (tm-30) cc_final: 0.7275 (tm-30) REVERT: B 252 MET cc_start: 0.9417 (OUTLIER) cc_final: 0.8728 (ptm) REVERT: B 429 GLN cc_start: 0.7892 (tp-100) cc_final: 0.7634 (tp-100) REVERT: C 173 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7961 (ttt-90) REVERT: C 216 GLU cc_start: 0.7584 (tm-30) cc_final: 0.7290 (tm-30) REVERT: C 252 MET cc_start: 0.9416 (OUTLIER) cc_final: 0.8778 (ptm) REVERT: C 338 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7198 (mm-30) REVERT: C 422 ASP cc_start: 0.8163 (t0) cc_final: 0.7849 (t70) REVERT: C 429 GLN cc_start: 0.7887 (tp-100) cc_final: 0.7608 (tp-100) REVERT: D 65 GLN cc_start: 0.7561 (pt0) cc_final: 0.7355 (pt0) REVERT: D 173 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.7902 (ttt-90) REVERT: D 216 GLU cc_start: 0.7644 (tm-30) cc_final: 0.7357 (tm-30) REVERT: D 252 MET cc_start: 0.9420 (OUTLIER) cc_final: 0.8760 (ptm) REVERT: D 338 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7219 (mm-30) REVERT: D 429 GLN cc_start: 0.8022 (tp40) cc_final: 0.7601 (tp-100) REVERT: E 173 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.7994 (ttt-90) REVERT: E 216 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7314 (tm-30) REVERT: E 252 MET cc_start: 0.9415 (OUTLIER) cc_final: 0.8764 (ptm) REVERT: E 429 GLN cc_start: 0.7897 (tp-100) cc_final: 0.7642 (tp-100) REVERT: F 173 ARG cc_start: 0.8669 (OUTLIER) cc_final: 0.7974 (ttt-90) REVERT: F 216 GLU cc_start: 0.7600 (tm-30) cc_final: 0.7309 (tm-30) REVERT: F 252 MET cc_start: 0.9413 (OUTLIER) cc_final: 0.8776 (ptm) REVERT: F 429 GLN cc_start: 0.7872 (tp-100) cc_final: 0.7613 (tp-100) REVERT: G 173 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7956 (ttt-90) REVERT: G 216 GLU cc_start: 0.7602 (tm-30) cc_final: 0.7314 (tm-30) REVERT: G 252 MET cc_start: 0.9417 (OUTLIER) cc_final: 0.8727 (ptm) REVERT: G 429 GLN cc_start: 0.7898 (tp40) cc_final: 0.7634 (tp-100) REVERT: H 173 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.7984 (ttt-90) REVERT: H 216 GLU cc_start: 0.7604 (tm-30) cc_final: 0.7319 (tm-30) REVERT: H 252 MET cc_start: 0.9424 (OUTLIER) cc_final: 0.8778 (ptm) REVERT: H 429 GLN cc_start: 0.7881 (tp-100) cc_final: 0.7630 (tp-100) outliers start: 62 outliers final: 28 residues processed: 462 average time/residue: 2.2135 time to fit residues: 1139.4672 Evaluate side-chains 463 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 419 time to evaluate : 3.479 ------------------------------------------------------------------------------- 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 252 MET Chi-restraints excluded: chain A residue 286 VAL Chi-restraints excluded: chain A residue 311 HIS Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 173 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 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 173 ARG 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 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 64 SER Chi-restraints excluded: chain G residue 173 ARG 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 64 SER Chi-restraints excluded: chain H residue 173 ARG 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: 5.9990 chunk 168 optimal weight: 0.2980 chunk 316 optimal weight: 1.9990 chunk 292 optimal weight: 1.9990 chunk 283 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 225 optimal weight: 6.9990 chunk 68 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 161 optimal weight: 0.7980 chunk 251 optimal weight: 7.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3500 r_free = 0.3500 target = 0.131737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.118134 restraints weight = 26166.553| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 0.81 r_work: 0.3245 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 2.13 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 29096 Z= 0.134 Angle : 0.549 6.155 39472 Z= 0.289 Chirality : 0.040 0.128 4152 Planarity : 0.004 0.027 5168 Dihedral : 9.172 168.594 4144 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.30 % Allowed : 13.42 % Favored : 84.29 % 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: 1.18 (0.14), residues: 3544 helix: 1.15 (0.13), residues: 1672 sheet: 0.80 (0.25), residues: 400 loop : 0.54 (0.17), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 354 HIS 0.004 0.001 HIS D 224 PHE 0.017 0.002 PHE F 297 TYR 0.026 0.002 TYR B 263 ARG 0.007 0.000 ARG D 442 Details of bonding type rmsd hydrogen bonds : bond 0.04182 ( 1384) hydrogen bonds : angle 5.30776 ( 3840) covalent geometry : bond 0.00289 (29096) covalent geometry : angle 0.54895 (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 480 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 415 time to evaluate : 3.215 Fit side-chains REVERT: A 216 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7258 (tm-30) REVERT: A 252 MET cc_start: 0.9412 (OUTLIER) cc_final: 0.8710 (ptm) REVERT: A 429 GLN cc_start: 0.7857 (tp40) cc_final: 0.7611 (tp-100) REVERT: B 117 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7981 (ttp-170) REVERT: B 173 ARG cc_start: 0.8643 (OUTLIER) cc_final: 0.7927 (ttt-90) REVERT: B 216 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7188 (tm-30) REVERT: B 252 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.8730 (ptm) REVERT: B 429 GLN cc_start: 0.7897 (tp-100) cc_final: 0.7637 (tp-100) REVERT: C 173 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.7911 (ttt-90) REVERT: C 216 GLU cc_start: 0.7523 (tm-30) cc_final: 0.7206 (tm-30) REVERT: C 252 MET cc_start: 0.9400 (OUTLIER) cc_final: 0.8782 (ptm) REVERT: C 422 ASP cc_start: 0.8163 (t0) cc_final: 0.7841 (t70) REVERT: C 429 GLN cc_start: 0.7920 (tp-100) cc_final: 0.7661 (tp-100) REVERT: D 65 GLN cc_start: 0.7553 (pt0) cc_final: 0.7292 (pt0) REVERT: D 173 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.7825 (ttt-90) REVERT: D 216 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7295 (tm-30) REVERT: D 252 MET cc_start: 0.9409 (OUTLIER) cc_final: 0.8760 (ptm) REVERT: D 429 GLN cc_start: 0.8013 (tp40) cc_final: 0.7475 (tp-100) REVERT: E 173 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.7938 (ttt-90) REVERT: E 216 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7213 (tm-30) REVERT: E 252 MET cc_start: 0.9403 (OUTLIER) cc_final: 0.8764 (ptm) REVERT: E 429 GLN cc_start: 0.7893 (tp-100) cc_final: 0.7637 (tp-100) REVERT: F 173 ARG cc_start: 0.8637 (OUTLIER) cc_final: 0.7909 (ttt-90) REVERT: F 216 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7257 (tm-30) REVERT: F 252 MET cc_start: 0.9399 (OUTLIER) cc_final: 0.8785 (ptm) REVERT: F 429 GLN cc_start: 0.7858 (tp-100) cc_final: 0.7591 (tp-100) REVERT: G 173 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.7925 (ttt-90) REVERT: G 216 GLU cc_start: 0.7539 (tm-30) cc_final: 0.7223 (tm-30) REVERT: G 252 MET cc_start: 0.9410 (OUTLIER) cc_final: 0.8734 (ptm) REVERT: G 429 GLN cc_start: 0.7873 (tp40) cc_final: 0.7626 (tp-100) REVERT: H 173 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7953 (ttt-90) REVERT: H 216 GLU cc_start: 0.7543 (tm-30) cc_final: 0.7231 (tm-30) REVERT: H 252 MET cc_start: 0.9406 (OUTLIER) cc_final: 0.8773 (ptm) REVERT: H 429 GLN cc_start: 0.7862 (tp-100) cc_final: 0.7607 (tp-100) outliers start: 65 outliers final: 34 residues processed: 462 average time/residue: 2.3427 time to fit residues: 1215.0073 Evaluate side-chains 466 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 416 time to evaluate : 4.015 ------------------------------------------------------------------------------- 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 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 64 SER Chi-restraints excluded: chain B residue 117 ARG Chi-restraints excluded: chain B residue 173 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 64 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 64 SER Chi-restraints excluded: chain D residue 173 ARG 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 64 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 173 ARG 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 64 SER Chi-restraints excluded: chain H residue 173 ARG 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: 3.9990 chunk 118 optimal weight: 9.9990 chunk 262 optimal weight: 7.9990 chunk 253 optimal weight: 3.9990 chunk 335 optimal weight: 4.9990 chunk 265 optimal weight: 3.9990 chunk 196 optimal weight: 2.9990 chunk 276 optimal weight: 3.9990 chunk 339 optimal weight: 7.9990 chunk 212 optimal weight: 0.6980 chunk 198 optimal weight: 1.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- 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** 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** ** H 345 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 429 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.127188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.113348 restraints weight = 26277.346| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 0.82 r_work: 0.3180 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 29096 Z= 0.242 Angle : 0.668 7.696 39472 Z= 0.352 Chirality : 0.045 0.152 4152 Planarity : 0.005 0.033 5168 Dihedral : 9.716 169.485 4144 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.87 % Allowed : 14.05 % Favored : 84.07 % 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: 1.24 (0.14), residues: 3544 helix: 1.18 (0.12), residues: 1576 sheet: 0.29 (0.22), residues: 488 loop : 0.84 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 354 HIS 0.005 0.002 HIS A 296 PHE 0.024 0.003 PHE F 297 TYR 0.035 0.003 TYR G 263 ARG 0.008 0.001 ARG G 442 Details of bonding type rmsd hydrogen bonds : bond 0.05230 ( 1384) hydrogen bonds : angle 5.64595 ( 3840) covalent geometry : bond 0.00533 (29096) covalent geometry : angle 0.66755 (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 483 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 430 time to evaluate : 3.412 Fit side-chains REVERT: A 216 GLU cc_start: 0.7505 (tm-30) cc_final: 0.7185 (tm-30) REVERT: A 252 MET cc_start: 0.9450 (OUTLIER) cc_final: 0.8722 (ptm) REVERT: A 277 ILE cc_start: 0.8690 (mt) cc_final: 0.8312 (mt) REVERT: B 173 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.7976 (ttt-90) REVERT: B 216 GLU cc_start: 0.7489 (tm-30) cc_final: 0.7270 (tm-30) REVERT: B 252 MET cc_start: 0.9444 (OUTLIER) cc_final: 0.8737 (ptm) REVERT: B 277 ILE cc_start: 0.8699 (mt) cc_final: 0.8316 (mt) REVERT: C 173 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.7953 (ttt-90) REVERT: C 216 GLU cc_start: 0.7492 (tm-30) cc_final: 0.7271 (tm-30) REVERT: C 252 MET cc_start: 0.9437 (OUTLIER) cc_final: 0.8795 (ptm) REVERT: D 173 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.7985 (ttt-90) REVERT: D 216 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7319 (tm-30) REVERT: D 252 MET cc_start: 0.9441 (OUTLIER) cc_final: 0.8766 (ptm) REVERT: D 277 ILE cc_start: 0.8702 (mt) cc_final: 0.8321 (mt) REVERT: D 429 GLN cc_start: 0.8129 (tp40) cc_final: 0.7741 (tp-100) REVERT: E 173 ARG cc_start: 0.8711 (OUTLIER) cc_final: 0.8133 (ttt-90) REVERT: E 216 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7203 (tm-30) REVERT: E 252 MET cc_start: 0.9436 (OUTLIER) cc_final: 0.8786 (ptm) REVERT: E 277 ILE cc_start: 0.8689 (mt) cc_final: 0.8287 (mt) REVERT: F 173 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8120 (ttt-90) REVERT: F 216 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7276 (tm-30) REVERT: F 252 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.8792 (ptm) REVERT: G 173 ARG cc_start: 0.8695 (OUTLIER) cc_final: 0.8128 (ttt-90) REVERT: G 216 GLU cc_start: 0.7502 (tm-30) cc_final: 0.7282 (tm-30) REVERT: G 252 MET cc_start: 0.9443 (OUTLIER) cc_final: 0.8742 (ptm) REVERT: H 173 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8151 (ttt-90) REVERT: H 216 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7306 (tm-30) REVERT: H 234 GLU cc_start: 0.8126 (mp0) cc_final: 0.7919 (mp0) REVERT: H 252 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.8786 (ptm) outliers start: 53 outliers final: 30 residues processed: 467 average time/residue: 2.5110 time to fit residues: 1299.6554 Evaluate side-chains 467 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 422 time to evaluate : 3.082 ------------------------------------------------------------------------------- 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 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 173 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 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 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 173 ARG 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 64 SER Chi-restraints excluded: chain H residue 173 ARG 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: 1.9990 chunk 282 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 150 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.4980 chunk 303 optimal weight: 3.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.3457 r_free = 0.3457 target = 0.128275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.114689 restraints weight = 26343.036| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 0.81 r_work: 0.3202 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 29096 Z= 0.190 Angle : 0.619 7.158 39472 Z= 0.327 Chirality : 0.043 0.137 4152 Planarity : 0.004 0.027 5168 Dihedral : 9.598 170.059 4144 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.08 % Allowed : 14.62 % 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: 1.23 (0.14), residues: 3544 helix: 1.17 (0.12), residues: 1576 sheet: 0.28 (0.22), residues: 488 loop : 0.86 (0.17), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 354 HIS 0.004 0.001 HIS C 224 PHE 0.021 0.002 PHE F 297 TYR 0.030 0.002 TYR B 263 ARG 0.008 0.001 ARG D 442 Details of bonding type rmsd hydrogen bonds : bond 0.04794 ( 1384) hydrogen bonds : angle 5.56448 ( 3840) covalent geometry : bond 0.00415 (29096) covalent geometry : angle 0.61926 (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 480 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 421 time to evaluate : 6.957 Fit side-chains REVERT: A 216 GLU cc_start: 0.7472 (tm-30) cc_final: 0.7250 (tm-30) REVERT: A 252 MET cc_start: 0.9439 (OUTLIER) cc_final: 0.8731 (ptm) REVERT: A 429 GLN cc_start: 0.7977 (tp-100) cc_final: 0.7632 (tp-100) REVERT: B 173 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7975 (ttt-90) REVERT: B 216 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7211 (tm-30) REVERT: B 252 MET cc_start: 0.9434 (OUTLIER) cc_final: 0.8743 (ptm) REVERT: B 429 GLN cc_start: 0.7997 (tp-100) cc_final: 0.7644 (tp-100) REVERT: C 173 ARG cc_start: 0.8663 (OUTLIER) cc_final: 0.7982 (ttt-90) REVERT: C 216 GLU cc_start: 0.7432 (tm-30) cc_final: 0.7210 (tm-30) REVERT: C 252 MET cc_start: 0.9424 (OUTLIER) cc_final: 0.8802 (ptm) REVERT: D 173 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8022 (ttt-90) REVERT: D 216 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7262 (tm-30) REVERT: D 252 MET cc_start: 0.9421 (OUTLIER) cc_final: 0.8769 (ptm) REVERT: D 429 GLN cc_start: 0.8107 (tp40) cc_final: 0.7685 (tp-100) REVERT: E 173 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8077 (ttt-90) REVERT: E 216 GLU cc_start: 0.7448 (tm-30) cc_final: 0.7109 (tm-30) REVERT: E 252 MET cc_start: 0.9423 (OUTLIER) cc_final: 0.8787 (ptm) REVERT: E 429 GLN cc_start: 0.8003 (tp-100) cc_final: 0.7656 (tp-100) REVERT: F 173 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.8064 (ttt-90) REVERT: F 216 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7216 (tm-30) REVERT: F 252 MET cc_start: 0.9418 (OUTLIER) cc_final: 0.8802 (ptm) REVERT: F 429 GLN cc_start: 0.7996 (tp-100) cc_final: 0.7643 (tp-100) REVERT: G 173 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7982 (ttt-90) REVERT: G 216 GLU cc_start: 0.7442 (tm-30) cc_final: 0.7226 (tm-30) REVERT: G 252 MET cc_start: 0.9435 (OUTLIER) cc_final: 0.8751 (ptm) REVERT: G 429 GLN cc_start: 0.7969 (tp-100) cc_final: 0.7625 (tp-100) REVERT: H 173 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8079 (ttt-90) REVERT: H 216 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7117 (tm-30) REVERT: H 252 MET cc_start: 0.9421 (OUTLIER) cc_final: 0.8786 (ptm) REVERT: H 429 GLN cc_start: 0.7997 (tp-100) cc_final: 0.7645 (tp-100) outliers start: 59 outliers final: 40 residues processed: 464 average time/residue: 2.3056 time to fit residues: 1192.4320 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 : 3.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER 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 64 SER Chi-restraints excluded: chain B residue 173 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 64 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 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 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 26 GLU Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 173 ARG 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 64 SER Chi-restraints excluded: chain H residue 173 ARG 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 345 optimal weight: 0.7980 chunk 4 optimal weight: 9.9990 chunk 294 optimal weight: 10.0000 chunk 139 optimal weight: 5.9990 chunk 181 optimal weight: 1.9990 chunk 246 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 151 optimal weight: 0.9980 chunk 240 optimal weight: 9.9990 chunk 268 optimal weight: 10.0000 chunk 304 optimal weight: 4.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3458 r_free = 0.3458 target = 0.128302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.114525 restraints weight = 26226.024| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 0.81 r_work: 0.3198 rms_B_bonded: 1.22 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 29096 Z= 0.195 Angle : 0.630 7.077 39472 Z= 0.332 Chirality : 0.043 0.139 4152 Planarity : 0.005 0.045 5168 Dihedral : 9.628 169.859 4144 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.19 % Allowed : 14.62 % Favored : 83.19 % 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: 1.17 (0.14), residues: 3544 helix: 0.98 (0.12), residues: 1624 sheet: 0.41 (0.23), residues: 472 loop : 0.93 (0.18), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 354 HIS 0.004 0.001 HIS C 224 PHE 0.021 0.003 PHE F 297 TYR 0.031 0.002 TYR A 263 ARG 0.010 0.001 ARG C 442 Details of bonding type rmsd hydrogen bonds : bond 0.04854 ( 1384) hydrogen bonds : angle 5.59367 ( 3840) covalent geometry : bond 0.00427 (29096) covalent geometry : angle 0.62984 (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 480 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 418 time to evaluate : 3.341 Fit side-chains REVERT: A 216 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7249 (tm-30) REVERT: A 252 MET cc_start: 0.9444 (OUTLIER) cc_final: 0.8737 (ptm) REVERT: B 173 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7986 (ttt-90) REVERT: B 216 GLU cc_start: 0.7430 (tm-30) cc_final: 0.7210 (tm-30) REVERT: B 252 MET cc_start: 0.9440 (OUTLIER) cc_final: 0.8746 (ptm) REVERT: C 173 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.7974 (ttt-90) REVERT: C 216 GLU cc_start: 0.7426 (tm-30) cc_final: 0.7202 (tm-30) REVERT: C 252 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.8804 (ptm) REVERT: D 173 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7938 (ttt-90) REVERT: D 216 GLU cc_start: 0.7508 (tm-30) cc_final: 0.7295 (tm-30) REVERT: D 252 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.8772 (ptm) REVERT: D 429 GLN cc_start: 0.8116 (tp40) cc_final: 0.7696 (tp-100) REVERT: E 173 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8087 (ttt-90) REVERT: E 216 GLU cc_start: 0.7443 (tm-30) cc_final: 0.7225 (tm-30) REVERT: E 252 MET cc_start: 0.9428 (OUTLIER) cc_final: 0.8788 (ptm) REVERT: F 173 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.8078 (ttt-90) REVERT: F 216 GLU cc_start: 0.7469 (tm-30) cc_final: 0.7247 (tm-30) REVERT: F 252 MET cc_start: 0.9423 (OUTLIER) cc_final: 0.8798 (ptm) REVERT: G 173 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7991 (ttt-90) REVERT: G 216 GLU cc_start: 0.7439 (tm-30) cc_final: 0.7217 (tm-30) REVERT: G 252 MET cc_start: 0.9444 (OUTLIER) cc_final: 0.8751 (ptm) REVERT: H 173 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8083 (ttt-90) REVERT: H 216 GLU cc_start: 0.7447 (tm-30) cc_final: 0.7230 (tm-30) REVERT: H 252 MET cc_start: 0.9430 (OUTLIER) cc_final: 0.8790 (ptm) outliers start: 62 outliers final: 45 residues processed: 466 average time/residue: 2.2327 time to fit residues: 1159.8805 Evaluate side-chains 477 residues out of total 2832 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 417 time to evaluate : 3.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER 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 64 SER Chi-restraints excluded: chain B residue 173 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 B residue 378 SER Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 64 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 C residue 378 SER Chi-restraints excluded: chain D residue 26 GLU 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 64 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 64 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 F residue 378 SER Chi-restraints excluded: chain G residue 26 GLU Chi-restraints excluded: chain G residue 64 SER Chi-restraints excluded: chain G residue 173 ARG 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 64 SER Chi-restraints excluded: chain H residue 173 ARG 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: 6.9990 chunk 222 optimal weight: 8.9990 chunk 322 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 94 optimal weight: 0.9980 chunk 290 optimal weight: 8.9990 chunk 109 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 286 optimal weight: 0.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 = 0.3447 r_free = 0.3447 target = 0.127445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113665 restraints weight = 26278.365| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 0.81 r_work: 0.3178 rms_B_bonded: 1.21 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 29096 Z= 0.223 Angle : 0.663 7.481 39472 Z= 0.349 Chirality : 0.044 0.146 4152 Planarity : 0.005 0.040 5168 Dihedral : 9.731 169.921 4144 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.26 % Allowed : 14.62 % Favored : 83.12 % 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: 0.90 (0.12), residues: 1624 sheet: 0.37 (0.23), residues: 472 loop : 0.92 (0.18), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 354 HIS 0.004 0.002 HIS G 296 PHE 0.023 0.003 PHE F 297 TYR 0.034 0.002 TYR B 263 ARG 0.010 0.001 ARG A 442 Details of bonding type rmsd hydrogen bonds : bond 0.05071 ( 1384) hydrogen bonds : angle 5.66983 ( 3840) covalent geometry : bond 0.00490 (29096) covalent geometry : angle 0.66330 (39472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24648.80 seconds wall clock time: 429 minutes 46.02 seconds (25786.02 seconds total)