Starting phenix.real_space_refine on Thu Mar 5 15:27:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u8s_20691/03_2026/6u8s_20691.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u8s_20691/03_2026/6u8s_20691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6u8s_20691/03_2026/6u8s_20691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u8s_20691/03_2026/6u8s_20691.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u8s_20691/03_2026/6u8s_20691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u8s_20691/03_2026/6u8s_20691.map" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.054 sd= 2.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 144 5.16 5 C 14512 2.51 5 N 3920 2.21 5 O 4480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23080 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "B" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "C" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "D" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "E" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "F" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "G" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "H" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 4.63, per 1000 atoms: 0.20 Number of scatterers: 23080 At special positions: 0 Unit cell: (122.85, 122.85, 118.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 144 16.00 P 24 15.00 O 4480 8.00 N 3920 7.00 C 14512 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.66 Conformation dependent library (CDL) restraints added in 1.1 seconds 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5392 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 32 sheets defined 41.5% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.523A pdb=" N ILE A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 75 through 85 removed outlier: 3.530A pdb=" N THR A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.612A pdb=" N LYS A 108 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 256 through 267 removed outlier: 4.110A pdb=" N LEU A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.700A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 342 through 355 removed outlier: 3.849A pdb=" N SER A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 3.855A pdb=" N ILE A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 420 removed outlier: 4.109A pdb=" N MET A 420 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 502 removed outlier: 3.589A pdb=" N GLY A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 removed outlier: 3.523A pdb=" N ILE B 6 " --> pdb=" O ALA B 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2 through 6' Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 75 through 85 removed outlier: 3.530A pdb=" N THR B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 removed outlier: 3.613A pdb=" N LYS B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 256 through 267 removed outlier: 4.112A pdb=" N LEU B 262 " --> pdb=" O TYR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.701A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.849A pdb=" N SER B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 378 removed outlier: 3.854A pdb=" N ILE B 373 " --> pdb=" O ASN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 420 removed outlier: 4.110A pdb=" N MET B 420 " --> pdb=" O LEU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 502 removed outlier: 3.588A pdb=" N GLY B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 removed outlier: 3.523A pdb=" N ILE C 6 " --> pdb=" O ALA C 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2 through 6' Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 75 through 85 removed outlier: 3.530A pdb=" N THR C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 109 removed outlier: 3.612A pdb=" N LYS C 108 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 256 through 267 removed outlier: 4.111A pdb=" N LEU C 262 " --> pdb=" O TYR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.700A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 342 through 355 removed outlier: 3.848A pdb=" N SER C 351 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 378 removed outlier: 3.855A pdb=" N ILE C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 420 removed outlier: 4.109A pdb=" N MET C 420 " --> pdb=" O LEU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 502 removed outlier: 3.589A pdb=" N GLY C 502 " --> pdb=" O GLN C 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 removed outlier: 3.523A pdb=" N ILE D 6 " --> pdb=" O ALA D 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2 through 6' Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 75 through 85 removed outlier: 3.530A pdb=" N THR D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 109 removed outlier: 3.612A pdb=" N LYS D 108 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 256 through 267 removed outlier: 4.111A pdb=" N LEU D 262 " --> pdb=" O TYR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.700A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 315 Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 342 through 355 removed outlier: 3.849A pdb=" N SER D 351 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 378 removed outlier: 3.855A pdb=" N ILE D 373 " --> pdb=" O ASN D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 420 removed outlier: 4.109A pdb=" N MET D 420 " --> pdb=" O LEU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 502 removed outlier: 3.589A pdb=" N GLY D 502 " --> pdb=" O GLN D 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 removed outlier: 3.523A pdb=" N ILE E 6 " --> pdb=" O ALA E 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2 through 6' Processing helix chain 'E' and resid 19 through 24 Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 75 through 85 removed outlier: 3.530A pdb=" N THR E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 109 removed outlier: 3.613A pdb=" N LYS E 108 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'E' and resid 256 through 267 removed outlier: 4.111A pdb=" N LEU E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 removed outlier: 3.701A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 315 Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 342 through 355 removed outlier: 3.848A pdb=" N SER E 351 " --> pdb=" O VAL E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 378 removed outlier: 3.855A pdb=" N ILE E 373 " --> pdb=" O ASN E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 420 removed outlier: 4.109A pdb=" N MET E 420 " --> pdb=" O LEU E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 502 removed outlier: 3.589A pdb=" N GLY E 502 " --> pdb=" O GLN E 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 6 removed outlier: 3.523A pdb=" N ILE F 6 " --> pdb=" O ALA F 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2 through 6' Processing helix chain 'F' and resid 19 through 24 Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 75 through 85 removed outlier: 3.530A pdb=" N THR F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 109 removed outlier: 3.613A pdb=" N LYS F 108 " --> pdb=" O VAL F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 256 through 267 removed outlier: 4.112A pdb=" N LEU F 262 " --> pdb=" O TYR F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 removed outlier: 3.700A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS F 293 " --> pdb=" O TYR F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 315 Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 342 through 355 removed outlier: 3.849A pdb=" N SER F 351 " --> pdb=" O VAL F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 378 removed outlier: 3.855A pdb=" N ILE F 373 " --> pdb=" O ASN F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 420 removed outlier: 4.109A pdb=" N MET F 420 " --> pdb=" O LEU F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 502 removed outlier: 3.588A pdb=" N GLY F 502 " --> pdb=" O GLN F 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 removed outlier: 3.522A pdb=" N ILE G 6 " --> pdb=" O ALA G 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 6' Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 75 through 85 removed outlier: 3.530A pdb=" N THR G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 109 removed outlier: 3.613A pdb=" N LYS G 108 " --> pdb=" O VAL G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 255 No H-bonds generated for 'chain 'G' and resid 253 through 255' Processing helix chain 'G' and resid 256 through 267 removed outlier: 4.112A pdb=" N LEU G 262 " --> pdb=" O TYR G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 removed outlier: 3.700A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS G 293 " --> pdb=" O TYR G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 315 Processing helix chain 'G' and resid 332 through 338 Processing helix chain 'G' and resid 342 through 355 removed outlier: 3.849A pdb=" N SER G 351 " --> pdb=" O VAL G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 378 removed outlier: 3.855A pdb=" N ILE G 373 " --> pdb=" O ASN G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 420 removed outlier: 4.109A pdb=" N MET G 420 " --> pdb=" O LEU G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 502 removed outlier: 3.588A pdb=" N GLY G 502 " --> pdb=" O GLN G 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 6 removed outlier: 3.523A pdb=" N ILE H 6 " --> pdb=" O ALA H 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 2 through 6' Processing helix chain 'H' and resid 19 through 24 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 75 through 85 removed outlier: 3.530A pdb=" N THR H 85 " --> pdb=" O ALA H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 109 removed outlier: 3.613A pdb=" N LYS H 108 " --> pdb=" O VAL H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 255 No H-bonds generated for 'chain 'H' and resid 253 through 255' Processing helix chain 'H' and resid 256 through 267 removed outlier: 4.111A pdb=" N LEU H 262 " --> pdb=" O TYR H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 removed outlier: 3.700A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS H 293 " --> pdb=" O TYR H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 315 Processing helix chain 'H' and resid 332 through 338 Processing helix chain 'H' and resid 342 through 355 removed outlier: 3.848A pdb=" N SER H 351 " --> pdb=" O VAL H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 378 removed outlier: 3.855A pdb=" N ILE H 373 " --> pdb=" O ASN H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 420 removed outlier: 4.109A pdb=" N MET H 420 " --> pdb=" O LEU H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 502 removed outlier: 3.589A pdb=" N GLY H 502 " --> pdb=" O GLN H 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.588A pdb=" N VAL A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL A 299 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ARG A 322 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY A 301 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE A 91 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.585A pdb=" N SER A 444 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER D 508 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.638A pdb=" N SER A 508 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 444 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.588A pdb=" N VAL B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL B 299 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ARG B 322 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY B 301 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE B 91 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.646A pdb=" N SER B 508 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 444 " --> pdb=" O GLU B 510 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.588A pdb=" N VAL C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL C 299 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ARG C 322 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY C 301 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE C 91 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.640A pdb=" N SER C 508 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER D 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.588A pdb=" N VAL D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL D 299 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ARG D 322 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY D 301 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE D 91 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AB9, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.589A pdb=" N VAL E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL E 299 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ARG E 322 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY E 301 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE E 91 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.587A pdb=" N SER E 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER H 508 " --> pdb=" O ALA E 446 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.624A pdb=" N SER E 508 " --> pdb=" O ALA F 446 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER F 444 " --> pdb=" O GLU E 510 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AC5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC6, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.589A pdb=" N VAL F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL F 299 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ARG F 322 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY F 301 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE F 91 " --> pdb=" O ALA F 249 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 508 through 510 removed outlier: 3.739A pdb=" N SER F 508 " --> pdb=" O ALA G 446 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER G 444 " --> pdb=" O GLU F 510 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AC9, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.589A pdb=" N VAL G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N MET G 385 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL G 299 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ARG G 322 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY G 301 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE G 91 " --> pdb=" O ALA G 249 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 508 through 510 removed outlier: 3.574A pdb=" N SER G 508 " --> pdb=" O ALA H 446 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER H 444 " --> pdb=" O GLU G 510 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AD4, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.588A pdb=" N VAL H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL H 299 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ARG H 322 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY H 301 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE H 91 " --> pdb=" O ALA H 249 " (cutoff:3.500A) 841 hydrogen bonds defined for protein. 2427 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.51 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.29: 3824 1.29 - 1.42: 5738 1.42 - 1.55: 13554 1.55 - 1.68: 124 1.68 - 1.80: 240 Bond restraints: 23480 Sorted by residual: bond pdb=" C3D NAD E 602 " pdb=" C4D NAD E 602 " ideal model delta sigma weight residual 1.531 1.301 0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C3D NAD G 602 " pdb=" C4D NAD G 602 " ideal model delta sigma weight residual 1.531 1.301 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3D NAD H 602 " pdb=" C4D NAD H 602 " ideal model delta sigma weight residual 1.531 1.301 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3D NAD C 602 " pdb=" C4D NAD C 602 " ideal model delta sigma weight residual 1.531 1.301 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3D NAD D 602 " pdb=" C4D NAD D 602 " ideal model delta sigma weight residual 1.531 1.301 0.230 2.00e-02 2.50e+03 1.32e+02 ... (remaining 23475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 30774 3.27 - 6.54: 847 6.54 - 9.82: 99 9.82 - 13.09: 48 13.09 - 16.36: 24 Bond angle restraints: 31792 Sorted by residual: angle pdb=" N1A NAD A 602 " pdb=" C6A NAD A 602 " pdb=" N6A NAD A 602 " ideal model delta sigma weight residual 119.35 102.99 16.36 3.00e+00 1.11e-01 2.97e+01 angle pdb=" N1A NAD E 602 " pdb=" C6A NAD E 602 " pdb=" N6A NAD E 602 " ideal model delta sigma weight residual 119.35 103.00 16.35 3.00e+00 1.11e-01 2.97e+01 angle pdb=" N1A NAD D 602 " pdb=" C6A NAD D 602 " pdb=" N6A NAD D 602 " ideal model delta sigma weight residual 119.35 103.00 16.35 3.00e+00 1.11e-01 2.97e+01 angle pdb=" N1A NAD C 602 " pdb=" C6A NAD C 602 " pdb=" N6A NAD C 602 " ideal model delta sigma weight residual 119.35 103.00 16.35 3.00e+00 1.11e-01 2.97e+01 angle pdb=" N1A NAD B 602 " pdb=" C6A NAD B 602 " pdb=" N6A NAD B 602 " ideal model delta sigma weight residual 119.35 103.00 16.35 3.00e+00 1.11e-01 2.97e+01 ... (remaining 31787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 12916 17.68 - 35.36: 812 35.36 - 53.04: 408 53.04 - 70.72: 88 70.72 - 88.41: 24 Dihedral angle restraints: 14248 sinusoidal: 5744 harmonic: 8504 Sorted by residual: dihedral pdb=" CA LEU B 235 " pdb=" C LEU B 235 " pdb=" N ALA B 236 " pdb=" CA ALA B 236 " ideal model delta harmonic sigma weight residual -180.00 -157.62 -22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU F 235 " pdb=" C LEU F 235 " pdb=" N ALA F 236 " pdb=" CA ALA F 236 " ideal model delta harmonic sigma weight residual -180.00 -157.65 -22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU H 235 " pdb=" C LEU H 235 " pdb=" N ALA H 236 " pdb=" CA ALA H 236 " ideal model delta harmonic sigma weight residual 180.00 -157.67 -22.33 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 14245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2755 0.071 - 0.142: 785 0.142 - 0.212: 92 0.212 - 0.283: 8 0.283 - 0.354: 16 Chirality restraints: 3656 Sorted by residual: chirality pdb=" C3B NAD H 602 " pdb=" C2B NAD H 602 " pdb=" C4B NAD H 602 " pdb=" O3B NAD H 602 " both_signs ideal model delta sigma weight residual False -2.71 -2.36 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" C3B NAD B 602 " pdb=" C2B NAD B 602 " pdb=" C4B NAD B 602 " pdb=" O3B NAD B 602 " both_signs ideal model delta sigma weight residual False -2.71 -2.36 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C3B NAD D 602 " pdb=" C2B NAD D 602 " pdb=" C4B NAD D 602 " pdb=" O3B NAD D 602 " both_signs ideal model delta sigma weight residual False -2.71 -2.36 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 3653 not shown) Planarity restraints: 4000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 63 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PRO H 64 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO H 64 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 64 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 63 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.10e+00 pdb=" N PRO D 64 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 64 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 64 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 63 " 0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO A 64 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " 0.031 5.00e-02 4.00e+02 ... (remaining 3997 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6152 2.79 - 3.31: 21250 3.31 - 3.84: 40598 3.84 - 4.37: 47493 4.37 - 4.90: 79132 Nonbonded interactions: 194625 Sorted by model distance: nonbonded pdb=" O SER F 327 " pdb=" OG SER F 327 " model vdw 2.257 3.040 nonbonded pdb=" O SER H 327 " pdb=" OG SER H 327 " model vdw 2.257 3.040 nonbonded pdb=" O SER G 327 " pdb=" OG SER G 327 " model vdw 2.257 3.040 nonbonded pdb=" O SER E 327 " pdb=" OG SER E 327 " model vdw 2.257 3.040 nonbonded pdb=" O SER D 327 " pdb=" OG SER D 327 " model vdw 2.258 3.040 ... (remaining 194620 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' 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: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 20.850 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 : 0.012 0.230 23488 Z= 0.593 Angle : 1.355 16.360 31792 Z= 0.676 Chirality : 0.066 0.354 3656 Planarity : 0.007 0.056 4000 Dihedral : 15.528 88.405 8856 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 9.06 % Allowed : 8.05 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.07 (0.12), residues: 2960 helix: -3.47 (0.10), residues: 1064 sheet: -2.58 (0.18), residues: 456 loop : -1.97 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG C 407 TYR 0.019 0.003 TYR H 484 PHE 0.019 0.003 PHE B 401 HIS 0.007 0.001 HIS G 92 Details of bonding type rmsd covalent geometry : bond 0.01240 (23480) covalent geometry : angle 1.35527 (31792) hydrogen bonds : bond 0.20259 ( 841) hydrogen bonds : angle 8.62652 ( 2427) Misc. bond : bond 0.00121 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 1262 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8607 (m-30) cc_final: 0.8120 (m-30) REVERT: A 42 ILE cc_start: 0.8958 (pp) cc_final: 0.8739 (pt) REVERT: A 105 ARG cc_start: 0.9037 (mtm110) cc_final: 0.8664 (mtm110) REVERT: A 109 LYS cc_start: 0.9327 (mttp) cc_final: 0.9019 (mttt) REVERT: A 275 SER cc_start: 0.9145 (t) cc_final: 0.8857 (t) REVERT: A 276 SER cc_start: 0.8619 (p) cc_final: 0.8363 (p) REVERT: A 285 ASN cc_start: 0.9360 (m-40) cc_final: 0.9010 (m-40) REVERT: A 352 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8551 (tm-30) REVERT: A 395 GLU cc_start: 0.8753 (mp0) cc_final: 0.7955 (mp0) REVERT: A 399 GLU cc_start: 0.8555 (pm20) cc_final: 0.8294 (pm20) REVERT: A 404 ASP cc_start: 0.8922 (t0) cc_final: 0.8599 (t0) REVERT: B 25 ASN cc_start: 0.9039 (m110) cc_final: 0.8822 (p0) REVERT: B 28 ASP cc_start: 0.8633 (m-30) cc_final: 0.8182 (m-30) REVERT: B 50 ASP cc_start: 0.8853 (t70) cc_final: 0.8577 (t70) REVERT: B 105 ARG cc_start: 0.9104 (mtm110) cc_final: 0.8763 (mtm110) REVERT: B 106 LYS cc_start: 0.9576 (mtpt) cc_final: 0.9173 (mtpp) REVERT: B 109 LYS cc_start: 0.9364 (mttp) cc_final: 0.9106 (mttt) REVERT: B 274 ASP cc_start: 0.8815 (t0) cc_final: 0.8562 (t0) REVERT: B 276 SER cc_start: 0.8583 (p) cc_final: 0.8344 (p) REVERT: B 281 ILE cc_start: 0.9093 (tp) cc_final: 0.8879 (tp) REVERT: B 285 ASN cc_start: 0.9345 (m-40) cc_final: 0.9143 (m-40) REVERT: B 313 LEU cc_start: 0.9393 (mt) cc_final: 0.9130 (mp) REVERT: B 352 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8602 (tm-30) REVERT: B 395 GLU cc_start: 0.8812 (mp0) cc_final: 0.8116 (mp0) REVERT: B 399 GLU cc_start: 0.8567 (pm20) cc_final: 0.8336 (pm20) REVERT: B 400 TYR cc_start: 0.8116 (m-80) cc_final: 0.7864 (m-80) REVERT: B 404 ASP cc_start: 0.8929 (t0) cc_final: 0.8588 (t0) REVERT: C 28 ASP cc_start: 0.8626 (m-30) cc_final: 0.8172 (m-30) REVERT: C 50 ASP cc_start: 0.8882 (t70) cc_final: 0.8667 (t70) REVERT: C 93 HIS cc_start: 0.9315 (p-80) cc_final: 0.9064 (p90) REVERT: C 105 ARG cc_start: 0.9010 (mtm110) cc_final: 0.8809 (mtm110) REVERT: C 109 LYS cc_start: 0.9343 (mttp) cc_final: 0.8537 (tptt) REVERT: C 259 ARG cc_start: 0.9026 (mtp85) cc_final: 0.8702 (ttm-80) REVERT: C 276 SER cc_start: 0.8550 (p) cc_final: 0.8259 (p) REVERT: C 284 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.9057 (pp) REVERT: C 285 ASN cc_start: 0.9364 (m-40) cc_final: 0.9022 (m-40) REVERT: C 352 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8517 (tm-30) REVERT: C 395 GLU cc_start: 0.8717 (mp0) cc_final: 0.7976 (mp0) REVERT: C 399 GLU cc_start: 0.8520 (pm20) cc_final: 0.8273 (pm20) REVERT: D 28 ASP cc_start: 0.8619 (m-30) cc_final: 0.8136 (m-30) REVERT: D 42 ILE cc_start: 0.9050 (pp) cc_final: 0.8841 (pt) REVERT: D 50 ASP cc_start: 0.8855 (t70) cc_final: 0.8601 (t70) REVERT: D 84 LEU cc_start: 0.8648 (mm) cc_final: 0.8332 (tp) REVERT: D 106 LYS cc_start: 0.9634 (mtpt) cc_final: 0.9247 (mtpp) REVERT: D 108 LYS cc_start: 0.9548 (OUTLIER) cc_final: 0.9337 (mttm) REVERT: D 109 LYS cc_start: 0.9352 (mttp) cc_final: 0.8715 (tptt) REVERT: D 275 SER cc_start: 0.9145 (t) cc_final: 0.8847 (t) REVERT: D 276 SER cc_start: 0.8599 (p) cc_final: 0.8302 (p) REVERT: D 285 ASN cc_start: 0.9375 (m-40) cc_final: 0.9038 (m-40) REVERT: D 352 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8519 (tm-30) REVERT: D 368 GLN cc_start: 0.9008 (mt0) cc_final: 0.8514 (mp10) REVERT: D 395 GLU cc_start: 0.8842 (mp0) cc_final: 0.8082 (mp0) REVERT: D 399 GLU cc_start: 0.8541 (pm20) cc_final: 0.8271 (pm20) REVERT: D 400 TYR cc_start: 0.8114 (m-80) cc_final: 0.7912 (m-80) REVERT: D 404 ASP cc_start: 0.8879 (t0) cc_final: 0.8576 (t0) REVERT: E 28 ASP cc_start: 0.8644 (m-30) cc_final: 0.8180 (m-30) REVERT: E 91 ILE cc_start: 0.8356 (mp) cc_final: 0.8154 (mp) REVERT: E 105 ARG cc_start: 0.9009 (mtm110) cc_final: 0.8796 (mtm110) REVERT: E 109 LYS cc_start: 0.9325 (mttp) cc_final: 0.8559 (tptt) REVERT: E 276 SER cc_start: 0.8599 (p) cc_final: 0.8354 (p) REVERT: E 285 ASN cc_start: 0.9343 (m-40) cc_final: 0.9005 (m-40) REVERT: E 352 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8496 (tm-30) REVERT: E 368 GLN cc_start: 0.9006 (mt0) cc_final: 0.8425 (mp10) REVERT: E 395 GLU cc_start: 0.8722 (mp0) cc_final: 0.7922 (mp0) REVERT: E 399 GLU cc_start: 0.8591 (pm20) cc_final: 0.8315 (pm20) REVERT: E 482 MET cc_start: 0.8964 (mtp) cc_final: 0.8706 (mtp) REVERT: F 28 ASP cc_start: 0.8611 (m-30) cc_final: 0.8112 (m-30) REVERT: F 50 ASP cc_start: 0.8882 (t70) cc_final: 0.8629 (t70) REVERT: F 84 LEU cc_start: 0.8760 (mm) cc_final: 0.8407 (tp) REVERT: F 98 GLU cc_start: 0.9347 (mp0) cc_final: 0.9105 (mp0) REVERT: F 108 LYS cc_start: 0.9564 (OUTLIER) cc_final: 0.9351 (mttm) REVERT: F 109 LYS cc_start: 0.9356 (mttp) cc_final: 0.9095 (mttm) REVERT: F 276 SER cc_start: 0.8565 (p) cc_final: 0.8326 (p) REVERT: F 281 ILE cc_start: 0.9082 (tp) cc_final: 0.8713 (tp) REVERT: F 285 ASN cc_start: 0.9295 (m-40) cc_final: 0.8982 (m110) REVERT: F 352 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8662 (tm-30) REVERT: F 368 GLN cc_start: 0.8986 (mt0) cc_final: 0.8453 (mp10) REVERT: F 395 GLU cc_start: 0.8842 (mp0) cc_final: 0.8137 (mp0) REVERT: F 399 GLU cc_start: 0.8650 (pm20) cc_final: 0.8331 (pm20) REVERT: F 400 TYR cc_start: 0.8125 (m-80) cc_final: 0.7886 (m-80) REVERT: F 404 ASP cc_start: 0.8959 (t0) cc_final: 0.8649 (t0) REVERT: F 482 MET cc_start: 0.8900 (mtp) cc_final: 0.8635 (mtp) REVERT: G 28 ASP cc_start: 0.8672 (m-30) cc_final: 0.8218 (m-30) REVERT: G 50 ASP cc_start: 0.8817 (t70) cc_final: 0.8577 (t0) REVERT: G 93 HIS cc_start: 0.9352 (p-80) cc_final: 0.9128 (p90) REVERT: G 98 GLU cc_start: 0.9286 (mp0) cc_final: 0.9051 (mp0) REVERT: G 108 LYS cc_start: 0.9630 (OUTLIER) cc_final: 0.9405 (mttm) REVERT: G 109 LYS cc_start: 0.9314 (mttp) cc_final: 0.8811 (tptt) REVERT: G 261 ASP cc_start: 0.9392 (p0) cc_final: 0.9154 (p0) REVERT: G 275 SER cc_start: 0.9061 (t) cc_final: 0.8741 (t) REVERT: G 276 SER cc_start: 0.8709 (p) cc_final: 0.8431 (p) REVERT: G 281 ILE cc_start: 0.9291 (tp) cc_final: 0.8928 (tp) REVERT: G 285 ASN cc_start: 0.9335 (m-40) cc_final: 0.8961 (m-40) REVERT: G 352 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8478 (tm-30) REVERT: G 395 GLU cc_start: 0.8755 (mp0) cc_final: 0.7978 (mp0) REVERT: G 399 GLU cc_start: 0.8459 (pm20) cc_final: 0.8212 (pm20) REVERT: G 406 ILE cc_start: 0.9345 (mp) cc_final: 0.9117 (mm) REVERT: G 482 MET cc_start: 0.9001 (mtp) cc_final: 0.8759 (mtp) REVERT: H 25 ASN cc_start: 0.9057 (m110) cc_final: 0.8830 (p0) REVERT: H 28 ASP cc_start: 0.8708 (m-30) cc_final: 0.8264 (m-30) REVERT: H 50 ASP cc_start: 0.8832 (t70) cc_final: 0.8563 (t70) REVERT: H 84 LEU cc_start: 0.8553 (mm) cc_final: 0.8239 (tp) REVERT: H 98 GLU cc_start: 0.9370 (mp0) cc_final: 0.9124 (mp0) REVERT: H 105 ARG cc_start: 0.9143 (mtm110) cc_final: 0.8796 (mtm110) REVERT: H 106 LYS cc_start: 0.9586 (mtpt) cc_final: 0.9214 (mtpp) REVERT: H 109 LYS cc_start: 0.9339 (mttp) cc_final: 0.9071 (mttt) REVERT: H 274 ASP cc_start: 0.8788 (t0) cc_final: 0.8548 (t0) REVERT: H 276 SER cc_start: 0.8614 (p) cc_final: 0.8276 (p) REVERT: H 281 ILE cc_start: 0.9197 (tp) cc_final: 0.8989 (tp) REVERT: H 285 ASN cc_start: 0.9406 (m-40) cc_final: 0.9184 (m110) REVERT: H 352 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8654 (tm-30) REVERT: H 395 GLU cc_start: 0.8790 (mp0) cc_final: 0.8073 (mp0) REVERT: H 399 GLU cc_start: 0.8502 (pm20) cc_final: 0.8278 (pm20) REVERT: H 400 TYR cc_start: 0.8104 (m-80) cc_final: 0.7875 (m-80) REVERT: H 482 MET cc_start: 0.8871 (mtp) cc_final: 0.8605 (mtp) outliers start: 216 outliers final: 108 residues processed: 1332 average time/residue: 0.1489 time to fit residues: 314.5568 Evaluate side-chains 1055 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 943 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 479 VAL Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 505 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 290 ILE Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 505 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 479 VAL Chi-restraints excluded: chain G residue 505 SER Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 505 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 25 ASN A 48 GLN A 93 HIS A 277 GLN A 309 GLN A 312 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN B 25 ASN B 48 GLN B 277 GLN B 309 GLN B 312 ASN B 343 GLN C 22 GLN C 25 ASN C 48 GLN C 243 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN D 22 GLN D 25 ASN D 48 GLN D 93 HIS D 277 GLN ** D 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 309 GLN D 312 ASN D 343 GLN E 22 GLN E 25 ASN E 48 GLN E 93 HIS ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 ASN E 334 GLN F 22 GLN F 48 GLN F 93 HIS ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN F 498 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN H 22 GLN H 25 ASN H 48 GLN H 93 HIS ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN H 334 GLN H 343 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.108111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.087486 restraints weight = 41441.894| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 4.06 r_work: 0.2853 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23488 Z= 0.166 Angle : 0.730 8.074 31792 Z= 0.367 Chirality : 0.047 0.162 3656 Planarity : 0.005 0.042 4000 Dihedral : 13.320 89.938 3925 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 7.21 % Allowed : 18.04 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.13), residues: 2960 helix: -2.26 (0.12), residues: 1120 sheet: -2.69 (0.18), residues: 464 loop : -1.64 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 407 TYR 0.019 0.002 TYR G 400 PHE 0.017 0.001 PHE E 401 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00395 (23480) covalent geometry : angle 0.73013 (31792) hydrogen bonds : bond 0.04228 ( 841) hydrogen bonds : angle 6.07084 ( 2427) Misc. bond : bond 0.00055 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1222 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 1050 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8810 (m-30) cc_final: 0.8468 (m-30) REVERT: A 50 ASP cc_start: 0.9035 (t0) cc_final: 0.8807 (t0) REVERT: A 105 ARG cc_start: 0.9161 (mtm110) cc_final: 0.8926 (mtm110) REVERT: A 109 LYS cc_start: 0.9406 (mttp) cc_final: 0.8776 (tptt) REVERT: A 276 SER cc_start: 0.8668 (p) cc_final: 0.8415 (p) REVERT: A 285 ASN cc_start: 0.9444 (m-40) cc_final: 0.9078 (m-40) REVERT: A 352 GLU cc_start: 0.9166 (tm-30) cc_final: 0.8865 (tm-30) REVERT: A 395 GLU cc_start: 0.8764 (mp0) cc_final: 0.8151 (mp0) REVERT: A 399 GLU cc_start: 0.8988 (pm20) cc_final: 0.8715 (mp0) REVERT: A 404 ASP cc_start: 0.9124 (t0) cc_final: 0.8817 (t0) REVERT: A 512 ARG cc_start: 0.7781 (ttm-80) cc_final: 0.7496 (ptm160) REVERT: B 25 ASN cc_start: 0.9100 (m-40) cc_final: 0.8838 (p0) REVERT: B 28 ASP cc_start: 0.8872 (m-30) cc_final: 0.8543 (m-30) REVERT: B 50 ASP cc_start: 0.9044 (t70) cc_final: 0.8744 (t0) REVERT: B 58 LYS cc_start: 0.9452 (mmtp) cc_final: 0.9193 (mmmm) REVERT: B 66 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8245 (p) REVERT: B 105 ARG cc_start: 0.9198 (mtm110) cc_final: 0.8879 (mtm110) REVERT: B 109 LYS cc_start: 0.9404 (mttp) cc_final: 0.9010 (mttp) REVERT: B 276 SER cc_start: 0.8742 (p) cc_final: 0.8466 (p) REVERT: B 281 ILE cc_start: 0.8928 (tp) cc_final: 0.8586 (tt) REVERT: B 285 ASN cc_start: 0.9425 (m-40) cc_final: 0.9191 (m-40) REVERT: B 322 ARG cc_start: 0.8334 (ppp80) cc_final: 0.8121 (ptm160) REVERT: B 352 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8965 (tm-30) REVERT: B 385 MET cc_start: 0.8867 (ttm) cc_final: 0.8563 (ttp) REVERT: B 395 GLU cc_start: 0.8865 (mp0) cc_final: 0.8369 (mp0) REVERT: B 399 GLU cc_start: 0.9058 (pm20) cc_final: 0.8823 (mp0) REVERT: B 400 TYR cc_start: 0.8418 (m-80) cc_final: 0.7526 (m-80) REVERT: B 404 ASP cc_start: 0.9147 (t0) cc_final: 0.8870 (t0) REVERT: B 407 ARG cc_start: 0.8786 (ttt-90) cc_final: 0.7755 (ttt-90) REVERT: B 449 ASP cc_start: 0.9277 (p0) cc_final: 0.9015 (p0) REVERT: B 461 ILE cc_start: 0.9143 (pp) cc_final: 0.8929 (pp) REVERT: B 512 ARG cc_start: 0.7799 (ttm-80) cc_final: 0.7528 (ptm160) REVERT: C 28 ASP cc_start: 0.8882 (m-30) cc_final: 0.8538 (m-30) REVERT: C 50 ASP cc_start: 0.9020 (t70) cc_final: 0.8726 (t0) REVERT: C 58 LYS cc_start: 0.9370 (mmtp) cc_final: 0.9122 (mmmm) REVERT: C 66 VAL cc_start: 0.8484 (OUTLIER) cc_final: 0.8252 (p) REVERT: C 105 ARG cc_start: 0.9159 (mtm110) cc_final: 0.8893 (mtm110) REVERT: C 109 LYS cc_start: 0.9415 (mttp) cc_final: 0.9019 (mttp) REVERT: C 276 SER cc_start: 0.8595 (p) cc_final: 0.8307 (p) REVERT: C 285 ASN cc_start: 0.9469 (m-40) cc_final: 0.9170 (m-40) REVERT: C 352 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8851 (tm-30) REVERT: C 385 MET cc_start: 0.8870 (ttm) cc_final: 0.8507 (ttp) REVERT: C 395 GLU cc_start: 0.8836 (mp0) cc_final: 0.8309 (mp0) REVERT: C 399 GLU cc_start: 0.8959 (pm20) cc_final: 0.8684 (mp0) REVERT: C 400 TYR cc_start: 0.8617 (m-80) cc_final: 0.7479 (m-10) REVERT: C 407 ARG cc_start: 0.8944 (ttt-90) cc_final: 0.7977 (ttt-90) REVERT: C 449 ASP cc_start: 0.9319 (p0) cc_final: 0.8904 (p0) REVERT: C 512 ARG cc_start: 0.7775 (ttm-80) cc_final: 0.7573 (ptm160) REVERT: D 1 MET cc_start: 0.6008 (ptp) cc_final: 0.5796 (ptp) REVERT: D 28 ASP cc_start: 0.8856 (m-30) cc_final: 0.8511 (m-30) REVERT: D 47 ASP cc_start: 0.9142 (p0) cc_final: 0.8886 (p0) REVERT: D 50 ASP cc_start: 0.9021 (t70) cc_final: 0.8740 (t0) REVERT: D 58 LYS cc_start: 0.9437 (mmtp) cc_final: 0.9180 (mmmm) REVERT: D 105 ARG cc_start: 0.9240 (mtm110) cc_final: 0.8814 (mtm110) REVERT: D 108 LYS cc_start: 0.9581 (OUTLIER) cc_final: 0.9322 (tppt) REVERT: D 258 TYR cc_start: 0.9208 (t80) cc_final: 0.8994 (t80) REVERT: D 275 SER cc_start: 0.9074 (t) cc_final: 0.8868 (t) REVERT: D 276 SER cc_start: 0.8615 (p) cc_final: 0.8408 (p) REVERT: D 285 ASN cc_start: 0.9442 (m-40) cc_final: 0.9077 (m-40) REVERT: D 312 ASN cc_start: 0.9058 (OUTLIER) cc_final: 0.8822 (t0) REVERT: D 352 GLU cc_start: 0.9160 (tm-30) cc_final: 0.8844 (tm-30) REVERT: D 355 ARG cc_start: 0.9596 (ptm-80) cc_final: 0.9282 (ptm-80) REVERT: D 385 MET cc_start: 0.8918 (ttm) cc_final: 0.8600 (ttp) REVERT: D 395 GLU cc_start: 0.8838 (mp0) cc_final: 0.8246 (mp0) REVERT: D 399 GLU cc_start: 0.9046 (pm20) cc_final: 0.8768 (pm20) REVERT: D 404 ASP cc_start: 0.9110 (t0) cc_final: 0.8814 (t0) REVERT: D 461 ILE cc_start: 0.9166 (pp) cc_final: 0.8958 (pp) REVERT: E 28 ASP cc_start: 0.8882 (m-30) cc_final: 0.8517 (m-30) REVERT: E 58 LYS cc_start: 0.9319 (mmtp) cc_final: 0.9008 (mmmm) REVERT: E 105 ARG cc_start: 0.9154 (mtm110) cc_final: 0.8905 (mtm110) REVERT: E 109 LYS cc_start: 0.9393 (mttp) cc_final: 0.8710 (tptt) REVERT: E 276 SER cc_start: 0.8613 (p) cc_final: 0.8325 (p) REVERT: E 281 ILE cc_start: 0.8802 (tp) cc_final: 0.8096 (tt) REVERT: E 285 ASN cc_start: 0.9413 (m-40) cc_final: 0.9045 (m-40) REVERT: E 322 ARG cc_start: 0.8196 (ppp80) cc_final: 0.7871 (ptm160) REVERT: E 352 GLU cc_start: 0.9156 (tm-30) cc_final: 0.8937 (tm-30) REVERT: E 385 MET cc_start: 0.8873 (ttm) cc_final: 0.8650 (ttp) REVERT: E 386 MET cc_start: 0.9316 (mtm) cc_final: 0.8976 (mtm) REVERT: E 395 GLU cc_start: 0.8725 (mp0) cc_final: 0.8072 (mp0) REVERT: E 399 GLU cc_start: 0.8940 (pm20) cc_final: 0.8663 (pm20) REVERT: E 400 TYR cc_start: 0.8612 (m-80) cc_final: 0.7619 (m-10) REVERT: E 407 ARG cc_start: 0.9023 (ttt-90) cc_final: 0.8254 (ttt-90) REVERT: E 438 LYS cc_start: 0.8174 (mmtt) cc_final: 0.7880 (mttp) REVERT: E 512 ARG cc_start: 0.7806 (ttm-80) cc_final: 0.7540 (ttm-80) REVERT: F 28 ASP cc_start: 0.8878 (m-30) cc_final: 0.8516 (m-30) REVERT: F 47 ASP cc_start: 0.9156 (p0) cc_final: 0.8930 (p0) REVERT: F 105 ARG cc_start: 0.9219 (mtm110) cc_final: 0.8949 (mtm110) REVERT: F 108 LYS cc_start: 0.9581 (OUTLIER) cc_final: 0.9309 (tppt) REVERT: F 109 LYS cc_start: 0.9395 (mttp) cc_final: 0.9167 (mtmm) REVERT: F 276 SER cc_start: 0.8670 (p) cc_final: 0.8393 (p) REVERT: F 279 ASN cc_start: 0.8915 (t0) cc_final: 0.8674 (t0) REVERT: F 281 ILE cc_start: 0.8934 (tp) cc_final: 0.8602 (tt) REVERT: F 285 ASN cc_start: 0.9398 (m-40) cc_final: 0.9149 (m110) REVERT: F 322 ARG cc_start: 0.8079 (ppp80) cc_final: 0.7476 (ptm160) REVERT: F 352 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8920 (tm-30) REVERT: F 385 MET cc_start: 0.8947 (ttm) cc_final: 0.8354 (ttp) REVERT: F 395 GLU cc_start: 0.8859 (mp0) cc_final: 0.8179 (mp0) REVERT: F 399 GLU cc_start: 0.9061 (pm20) cc_final: 0.8762 (pm20) REVERT: F 404 ASP cc_start: 0.9190 (t0) cc_final: 0.8939 (t0) REVERT: F 512 ARG cc_start: 0.7673 (ttm-80) cc_final: 0.7125 (ptm160) REVERT: G 28 ASP cc_start: 0.8957 (m-30) cc_final: 0.8668 (m-30) REVERT: G 50 ASP cc_start: 0.9020 (t70) cc_final: 0.8735 (t0) REVERT: G 51 LEU cc_start: 0.9359 (OUTLIER) cc_final: 0.9110 (pp) REVERT: G 105 ARG cc_start: 0.9165 (mtm110) cc_final: 0.8534 (mtm110) REVERT: G 108 LYS cc_start: 0.9627 (OUTLIER) cc_final: 0.9336 (mttm) REVERT: G 109 LYS cc_start: 0.9353 (mttp) cc_final: 0.9128 (mttt) REVERT: G 275 SER cc_start: 0.8953 (t) cc_final: 0.8724 (t) REVERT: G 285 ASN cc_start: 0.9368 (m-40) cc_final: 0.9016 (m-40) REVERT: G 352 GLU cc_start: 0.9152 (tm-30) cc_final: 0.8921 (tm-30) REVERT: G 395 GLU cc_start: 0.8760 (mp0) cc_final: 0.8164 (mp0) REVERT: G 399 GLU cc_start: 0.9006 (pm20) cc_final: 0.8691 (pm20) REVERT: G 400 TYR cc_start: 0.8485 (m-80) cc_final: 0.8030 (m-80) REVERT: G 407 ARG cc_start: 0.8943 (ttt-90) cc_final: 0.8384 (ptm-80) REVERT: G 512 ARG cc_start: 0.7574 (ttm-80) cc_final: 0.7372 (ptm160) REVERT: H 25 ASN cc_start: 0.9113 (m-40) cc_final: 0.8852 (p0) REVERT: H 28 ASP cc_start: 0.8982 (m-30) cc_final: 0.8627 (m-30) REVERT: H 50 ASP cc_start: 0.9018 (t70) cc_final: 0.8702 (t0) REVERT: H 58 LYS cc_start: 0.9449 (mmtp) cc_final: 0.9179 (mmmm) REVERT: H 105 ARG cc_start: 0.9261 (mtm110) cc_final: 0.8786 (mtm110) REVERT: H 109 LYS cc_start: 0.9405 (mttp) cc_final: 0.9199 (mttt) REVERT: H 276 SER cc_start: 0.8559 (p) cc_final: 0.8255 (p) REVERT: H 285 ASN cc_start: 0.9462 (m-40) cc_final: 0.9201 (m-40) REVERT: H 352 GLU cc_start: 0.9284 (tm-30) cc_final: 0.9028 (tm-30) REVERT: H 355 ARG cc_start: 0.9581 (ptm-80) cc_final: 0.9173 (ptm-80) REVERT: H 395 GLU cc_start: 0.8735 (mp0) cc_final: 0.8230 (mp0) REVERT: H 399 GLU cc_start: 0.8973 (pm20) cc_final: 0.8732 (pm20) outliers start: 172 outliers final: 80 residues processed: 1118 average time/residue: 0.1539 time to fit residues: 268.7895 Evaluate side-chains 1013 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 926 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 282 PHE Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 282 PHE Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 282 PHE Chi-restraints excluded: chain G residue 406 ILE Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 146 optimal weight: 2.9990 chunk 152 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 262 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 248 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 122 optimal weight: 6.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN B 93 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN E 22 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN F 498 GLN G 22 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 ASN ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN H 22 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.104378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.083749 restraints weight = 41895.362| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 3.93 r_work: 0.2785 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 23488 Z= 0.206 Angle : 0.700 7.594 31792 Z= 0.358 Chirality : 0.048 0.161 3656 Planarity : 0.004 0.045 4000 Dihedral : 11.959 88.894 3801 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 5.45 % Allowed : 20.81 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.14), residues: 2960 helix: -1.66 (0.14), residues: 1120 sheet: -2.28 (0.20), residues: 464 loop : -1.31 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 407 TYR 0.020 0.002 TYR H 400 PHE 0.013 0.001 PHE H 401 HIS 0.003 0.001 HIS H 507 Details of bonding type rmsd covalent geometry : bond 0.00484 (23480) covalent geometry : angle 0.70015 (31792) hydrogen bonds : bond 0.03939 ( 841) hydrogen bonds : angle 5.56869 ( 2427) Misc. bond : bond 0.00134 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1107 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 977 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8778 (m-30) cc_final: 0.8464 (m-30) REVERT: A 50 ASP cc_start: 0.9099 (t0) cc_final: 0.8861 (t0) REVERT: A 51 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.8999 (pp) REVERT: A 66 VAL cc_start: 0.8294 (OUTLIER) cc_final: 0.8072 (p) REVERT: A 105 ARG cc_start: 0.9180 (mtm110) cc_final: 0.8698 (mtm110) REVERT: A 109 LYS cc_start: 0.9417 (mttp) cc_final: 0.9169 (mptt) REVERT: A 258 TYR cc_start: 0.9096 (t80) cc_final: 0.8853 (t80) REVERT: A 276 SER cc_start: 0.8918 (p) cc_final: 0.8649 (p) REVERT: A 285 ASN cc_start: 0.9461 (m-40) cc_final: 0.9139 (m-40) REVERT: A 352 GLU cc_start: 0.9268 (tm-30) cc_final: 0.9007 (tm-30) REVERT: A 395 GLU cc_start: 0.8872 (mp0) cc_final: 0.8133 (mp0) REVERT: A 399 GLU cc_start: 0.8979 (pm20) cc_final: 0.8719 (mp0) REVERT: A 400 TYR cc_start: 0.8578 (m-80) cc_final: 0.8089 (m-10) REVERT: A 404 ASP cc_start: 0.9182 (t0) cc_final: 0.8876 (t70) REVERT: A 407 ARG cc_start: 0.9027 (ttt-90) cc_final: 0.8397 (ttt-90) REVERT: A 438 LYS cc_start: 0.8972 (mttt) cc_final: 0.8483 (mmtt) REVERT: A 449 ASP cc_start: 0.9415 (p0) cc_final: 0.9152 (p0) REVERT: A 455 LYS cc_start: 0.9162 (mppt) cc_final: 0.8704 (mppt) REVERT: B 28 ASP cc_start: 0.8852 (m-30) cc_final: 0.8551 (m-30) REVERT: B 50 ASP cc_start: 0.9051 (t70) cc_final: 0.8839 (t0) REVERT: B 51 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9053 (pp) REVERT: B 66 VAL cc_start: 0.8433 (OUTLIER) cc_final: 0.8119 (p) REVERT: B 88 ILE cc_start: 0.9157 (tp) cc_final: 0.8885 (tp) REVERT: B 105 ARG cc_start: 0.9218 (mtm110) cc_final: 0.8753 (mtm110) REVERT: B 109 LYS cc_start: 0.9446 (mttp) cc_final: 0.9206 (mptt) REVERT: B 258 TYR cc_start: 0.9106 (t80) cc_final: 0.8881 (t80) REVERT: B 276 SER cc_start: 0.8920 (p) cc_final: 0.8629 (p) REVERT: B 281 ILE cc_start: 0.8957 (tp) cc_final: 0.8646 (tp) REVERT: B 285 ASN cc_start: 0.9454 (m-40) cc_final: 0.9229 (m-40) REVERT: B 352 GLU cc_start: 0.9241 (tm-30) cc_final: 0.8992 (tm-30) REVERT: B 395 GLU cc_start: 0.8908 (mp0) cc_final: 0.8354 (mp0) REVERT: B 399 GLU cc_start: 0.9059 (pm20) cc_final: 0.8830 (mp0) REVERT: B 404 ASP cc_start: 0.9170 (t0) cc_final: 0.8902 (t0) REVERT: B 438 LYS cc_start: 0.9018 (mttt) cc_final: 0.8796 (tttt) REVERT: C 28 ASP cc_start: 0.8816 (m-30) cc_final: 0.8505 (m-30) REVERT: C 50 ASP cc_start: 0.9146 (t70) cc_final: 0.8879 (t0) REVERT: C 51 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8916 (pp) REVERT: C 66 VAL cc_start: 0.8296 (OUTLIER) cc_final: 0.8058 (p) REVERT: C 105 ARG cc_start: 0.9167 (mtm110) cc_final: 0.8705 (mtm110) REVERT: C 109 LYS cc_start: 0.9429 (mttp) cc_final: 0.9154 (mptt) REVERT: C 258 TYR cc_start: 0.9061 (t80) cc_final: 0.8784 (t80) REVERT: C 276 SER cc_start: 0.8675 (p) cc_final: 0.8382 (p) REVERT: C 279 ASN cc_start: 0.9116 (t0) cc_final: 0.8018 (t0) REVERT: C 281 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8783 (tt) REVERT: C 285 ASN cc_start: 0.9498 (m-40) cc_final: 0.9296 (m-40) REVERT: C 352 GLU cc_start: 0.9260 (tm-30) cc_final: 0.8982 (tm-30) REVERT: C 355 ARG cc_start: 0.9585 (ptm-80) cc_final: 0.9374 (ptm-80) REVERT: C 395 GLU cc_start: 0.8927 (mp0) cc_final: 0.8352 (mp0) REVERT: C 438 LYS cc_start: 0.9019 (mttt) cc_final: 0.8539 (mmtt) REVERT: D 25 ASN cc_start: 0.9179 (m-40) cc_final: 0.8917 (p0) REVERT: D 28 ASP cc_start: 0.8840 (m-30) cc_final: 0.8533 (m-30) REVERT: D 51 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9005 (pp) REVERT: D 105 ARG cc_start: 0.9196 (mtm110) cc_final: 0.8848 (mtm110) REVERT: D 109 LYS cc_start: 0.9381 (mttt) cc_final: 0.9100 (mttt) REVERT: D 258 TYR cc_start: 0.9215 (t80) cc_final: 0.8981 (t80) REVERT: D 276 SER cc_start: 0.8762 (p) cc_final: 0.8480 (p) REVERT: D 285 ASN cc_start: 0.9460 (m-40) cc_final: 0.9201 (m-40) REVERT: D 332 ILE cc_start: 0.8964 (pp) cc_final: 0.8671 (pp) REVERT: D 352 GLU cc_start: 0.9232 (tm-30) cc_final: 0.8953 (tm-30) REVERT: D 395 GLU cc_start: 0.8863 (mp0) cc_final: 0.8215 (mp0) REVERT: D 399 GLU cc_start: 0.8995 (pm20) cc_final: 0.8739 (pm20) REVERT: D 404 ASP cc_start: 0.9175 (t0) cc_final: 0.8896 (t0) REVERT: D 438 LYS cc_start: 0.8473 (mmtt) cc_final: 0.8107 (mmtm) REVERT: E 28 ASP cc_start: 0.8861 (m-30) cc_final: 0.8522 (m-30) REVERT: E 51 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9101 (pp) REVERT: E 105 ARG cc_start: 0.9167 (mtm110) cc_final: 0.8905 (mtm110) REVERT: E 109 LYS cc_start: 0.9414 (mttp) cc_final: 0.8947 (tmtt) REVERT: E 258 TYR cc_start: 0.9087 (t80) cc_final: 0.8837 (t80) REVERT: E 276 SER cc_start: 0.8834 (p) cc_final: 0.8543 (p) REVERT: E 285 ASN cc_start: 0.9443 (m-40) cc_final: 0.9218 (m-40) REVERT: E 322 ARG cc_start: 0.8412 (ppp80) cc_final: 0.7861 (ptm160) REVERT: E 352 GLU cc_start: 0.9273 (tm-30) cc_final: 0.8993 (tm-30) REVERT: E 386 MET cc_start: 0.9276 (mtm) cc_final: 0.8817 (mtm) REVERT: E 395 GLU cc_start: 0.8814 (mp0) cc_final: 0.8210 (mp0) REVERT: E 399 GLU cc_start: 0.8978 (pm20) cc_final: 0.8692 (pm20) REVERT: E 400 TYR cc_start: 0.8505 (m-80) cc_final: 0.7728 (m-10) REVERT: E 407 ARG cc_start: 0.9125 (ttt-90) cc_final: 0.8580 (ttt-90) REVERT: F 28 ASP cc_start: 0.8903 (m-30) cc_final: 0.8604 (m-30) REVERT: F 51 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8927 (pp) REVERT: F 105 ARG cc_start: 0.9225 (mtm110) cc_final: 0.8795 (mtm110) REVERT: F 108 LYS cc_start: 0.9506 (OUTLIER) cc_final: 0.9226 (ttpt) REVERT: F 258 TYR cc_start: 0.9204 (t80) cc_final: 0.8995 (t80) REVERT: F 276 SER cc_start: 0.8747 (p) cc_final: 0.8415 (p) REVERT: F 281 ILE cc_start: 0.9007 (tp) cc_final: 0.8753 (tt) REVERT: F 285 ASN cc_start: 0.9453 (m-40) cc_final: 0.9198 (m-40) REVERT: F 322 ARG cc_start: 0.8363 (ppp80) cc_final: 0.7712 (ptm160) REVERT: F 352 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8975 (tm-30) REVERT: F 355 ARG cc_start: 0.9489 (ptm-80) cc_final: 0.9178 (ptm-80) REVERT: F 385 MET cc_start: 0.8918 (ttm) cc_final: 0.8581 (ttp) REVERT: F 395 GLU cc_start: 0.8890 (mp0) cc_final: 0.8206 (mp0) REVERT: F 399 GLU cc_start: 0.9029 (pm20) cc_final: 0.8775 (pm20) REVERT: F 404 ASP cc_start: 0.9224 (t0) cc_final: 0.8986 (t0) REVERT: F 407 ARG cc_start: 0.9055 (ttt90) cc_final: 0.8733 (tmt90) REVERT: G 28 ASP cc_start: 0.8944 (m-30) cc_final: 0.8717 (m-30) REVERT: G 50 ASP cc_start: 0.9016 (t70) cc_final: 0.8712 (t0) REVERT: G 51 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9093 (pp) REVERT: G 105 ARG cc_start: 0.9094 (mtm110) cc_final: 0.8523 (mtm110) REVERT: G 108 LYS cc_start: 0.9559 (OUTLIER) cc_final: 0.9318 (mttm) REVERT: G 109 LYS cc_start: 0.9357 (mttp) cc_final: 0.9135 (mttt) REVERT: G 258 TYR cc_start: 0.9162 (t80) cc_final: 0.8946 (t80) REVERT: G 299 VAL cc_start: 0.9427 (m) cc_final: 0.9164 (p) REVERT: G 352 GLU cc_start: 0.9254 (tm-30) cc_final: 0.9016 (tm-30) REVERT: G 385 MET cc_start: 0.8869 (ttm) cc_final: 0.8364 (ttm) REVERT: G 395 GLU cc_start: 0.8813 (mp0) cc_final: 0.8189 (mp0) REVERT: G 399 GLU cc_start: 0.9076 (pm20) cc_final: 0.8776 (pm20) REVERT: G 400 TYR cc_start: 0.8441 (m-80) cc_final: 0.8010 (m-80) REVERT: G 407 ARG cc_start: 0.8891 (ttt-90) cc_final: 0.8308 (ptm-80) REVERT: G 449 ASP cc_start: 0.9326 (p0) cc_final: 0.9076 (p0) REVERT: G 510 GLU cc_start: 0.8064 (tp30) cc_final: 0.7822 (tp30) REVERT: H 28 ASP cc_start: 0.8943 (m-30) cc_final: 0.8688 (m-30) REVERT: H 50 ASP cc_start: 0.9068 (t70) cc_final: 0.8845 (t0) REVERT: H 51 LEU cc_start: 0.9309 (OUTLIER) cc_final: 0.9016 (pp) REVERT: H 66 VAL cc_start: 0.8417 (OUTLIER) cc_final: 0.8030 (p) REVERT: H 105 ARG cc_start: 0.9235 (mtm110) cc_final: 0.8867 (mtm110) REVERT: H 258 TYR cc_start: 0.9083 (t80) cc_final: 0.8842 (t80) REVERT: H 276 SER cc_start: 0.8693 (p) cc_final: 0.8452 (p) REVERT: H 285 ASN cc_start: 0.9456 (m-40) cc_final: 0.9193 (m-40) REVERT: H 352 GLU cc_start: 0.9296 (tm-30) cc_final: 0.9059 (tm-30) REVERT: H 395 GLU cc_start: 0.8798 (mp0) cc_final: 0.8156 (mp0) REVERT: H 399 GLU cc_start: 0.8923 (pm20) cc_final: 0.8679 (pm20) outliers start: 130 outliers final: 71 residues processed: 1025 average time/residue: 0.1498 time to fit residues: 241.6905 Evaluate side-chains 967 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 881 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 290 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 225 optimal weight: 0.4980 chunk 145 optimal weight: 0.9990 chunk 21 optimal weight: 0.1980 chunk 280 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 229 optimal weight: 0.9990 chunk 228 optimal weight: 0.5980 chunk 214 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 GLN D 303 ASN D 312 ASN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 ASN ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 498 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.107484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.086526 restraints weight = 41409.793| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.99 r_work: 0.2836 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23488 Z= 0.140 Angle : 0.657 8.394 31792 Z= 0.332 Chirality : 0.046 0.156 3656 Planarity : 0.004 0.040 4000 Dihedral : 11.514 89.809 3769 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 5.33 % Allowed : 22.94 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.14), residues: 2960 helix: -1.36 (0.14), residues: 1120 sheet: -2.12 (0.20), residues: 464 loop : -1.14 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 407 TYR 0.016 0.001 TYR H 400 PHE 0.014 0.001 PHE E 401 HIS 0.003 0.000 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00329 (23480) covalent geometry : angle 0.65667 (31792) hydrogen bonds : bond 0.03450 ( 841) hydrogen bonds : angle 5.36193 ( 2427) Misc. bond : bond 0.00075 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 992 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8738 (m-30) cc_final: 0.8474 (m-30) REVERT: A 66 VAL cc_start: 0.8165 (OUTLIER) cc_final: 0.7750 (p) REVERT: A 105 ARG cc_start: 0.9177 (mtm110) cc_final: 0.8671 (mtm110) REVERT: A 109 LYS cc_start: 0.9404 (mttp) cc_final: 0.9176 (mptt) REVERT: A 242 LYS cc_start: 0.7992 (tttt) cc_final: 0.7563 (tttt) REVERT: A 258 TYR cc_start: 0.9104 (t80) cc_final: 0.8849 (t80) REVERT: A 274 ASP cc_start: 0.9120 (t0) cc_final: 0.8918 (t0) REVERT: A 276 SER cc_start: 0.8839 (p) cc_final: 0.8574 (p) REVERT: A 285 ASN cc_start: 0.9473 (m-40) cc_final: 0.9168 (m-40) REVERT: A 352 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8957 (tm-30) REVERT: A 355 ARG cc_start: 0.9345 (ptm-80) cc_final: 0.9133 (ptm-80) REVERT: A 362 ILE cc_start: 0.8156 (mt) cc_final: 0.7897 (mt) REVERT: A 395 GLU cc_start: 0.8842 (mp0) cc_final: 0.8251 (mp0) REVERT: A 399 GLU cc_start: 0.8991 (pm20) cc_final: 0.8750 (mp0) REVERT: A 400 TYR cc_start: 0.8461 (m-80) cc_final: 0.7838 (m-10) REVERT: A 404 ASP cc_start: 0.9206 (t0) cc_final: 0.8916 (t70) REVERT: A 407 ARG cc_start: 0.8946 (ttt-90) cc_final: 0.8338 (ttt-90) REVERT: A 438 LYS cc_start: 0.8977 (mttt) cc_final: 0.8515 (mmtt) REVERT: A 455 LYS cc_start: 0.9180 (mppt) cc_final: 0.8749 (mppt) REVERT: A 510 GLU cc_start: 0.8051 (tp30) cc_final: 0.7845 (tp30) REVERT: B 25 ASN cc_start: 0.9042 (m-40) cc_final: 0.8755 (p0) REVERT: B 28 ASP cc_start: 0.8786 (m-30) cc_final: 0.8509 (m-30) REVERT: B 50 ASP cc_start: 0.9038 (t70) cc_final: 0.8756 (t0) REVERT: B 51 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8989 (pp) REVERT: B 105 ARG cc_start: 0.9206 (mtm110) cc_final: 0.8732 (mtm110) REVERT: B 109 LYS cc_start: 0.9445 (mttp) cc_final: 0.9212 (mptt) REVERT: B 276 SER cc_start: 0.8785 (p) cc_final: 0.8488 (p) REVERT: B 285 ASN cc_start: 0.9444 (m-40) cc_final: 0.9218 (m-40) REVERT: B 352 GLU cc_start: 0.9197 (tm-30) cc_final: 0.8957 (tm-30) REVERT: B 395 GLU cc_start: 0.8856 (mp0) cc_final: 0.8255 (mp0) REVERT: B 399 GLU cc_start: 0.9077 (pm20) cc_final: 0.8825 (pm20) REVERT: B 404 ASP cc_start: 0.9183 (t0) cc_final: 0.8893 (t0) REVERT: B 438 LYS cc_start: 0.9009 (mttt) cc_final: 0.8748 (tttt) REVERT: C 28 ASP cc_start: 0.8755 (m-30) cc_final: 0.8480 (m-30) REVERT: C 50 ASP cc_start: 0.9159 (t70) cc_final: 0.8886 (t0) REVERT: C 51 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9003 (pp) REVERT: C 66 VAL cc_start: 0.8212 (OUTLIER) cc_final: 0.7713 (p) REVERT: C 75 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8157 (mm-30) REVERT: C 105 ARG cc_start: 0.9150 (mtm110) cc_final: 0.8673 (mtm110) REVERT: C 109 LYS cc_start: 0.9422 (mttp) cc_final: 0.9156 (mptt) REVERT: C 258 TYR cc_start: 0.9062 (t80) cc_final: 0.8721 (t80) REVERT: C 276 SER cc_start: 0.8493 (p) cc_final: 0.8219 (p) REVERT: C 279 ASN cc_start: 0.9165 (t0) cc_final: 0.8879 (t0) REVERT: C 285 ASN cc_start: 0.9504 (m-40) cc_final: 0.9303 (m-40) REVERT: C 352 GLU cc_start: 0.9194 (tm-30) cc_final: 0.8907 (tm-30) REVERT: C 355 ARG cc_start: 0.9516 (ptm-80) cc_final: 0.9301 (ptm-80) REVERT: C 395 GLU cc_start: 0.8864 (mp0) cc_final: 0.8334 (mp0) REVERT: C 400 TYR cc_start: 0.8280 (m-10) cc_final: 0.7908 (m-10) REVERT: C 409 LYS cc_start: 0.8758 (ttmp) cc_final: 0.8231 (tttt) REVERT: C 438 LYS cc_start: 0.8995 (mttt) cc_final: 0.8524 (mmtt) REVERT: C 510 GLU cc_start: 0.8142 (tp30) cc_final: 0.7840 (tp30) REVERT: D 25 ASN cc_start: 0.9211 (m-40) cc_final: 0.8954 (p0) REVERT: D 28 ASP cc_start: 0.8852 (m-30) cc_final: 0.8551 (m-30) REVERT: D 51 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9090 (pp) REVERT: D 105 ARG cc_start: 0.9256 (mtm110) cc_final: 0.9015 (mtm110) REVERT: D 109 LYS cc_start: 0.9417 (mttt) cc_final: 0.8982 (mttm) REVERT: D 256 ASP cc_start: 0.9324 (m-30) cc_final: 0.8845 (p0) REVERT: D 258 TYR cc_start: 0.9172 (t80) cc_final: 0.8955 (t80) REVERT: D 276 SER cc_start: 0.8694 (p) cc_final: 0.8387 (p) REVERT: D 285 ASN cc_start: 0.9466 (m-40) cc_final: 0.9165 (m-40) REVERT: D 332 ILE cc_start: 0.8932 (pp) cc_final: 0.8648 (pp) REVERT: D 352 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8901 (tm-30) REVERT: D 355 ARG cc_start: 0.9296 (ptm-80) cc_final: 0.9094 (ptm-80) REVERT: D 395 GLU cc_start: 0.8882 (mp0) cc_final: 0.8227 (mp0) REVERT: D 399 GLU cc_start: 0.8929 (pm20) cc_final: 0.8614 (pm20) REVERT: D 404 ASP cc_start: 0.9201 (t0) cc_final: 0.8938 (t0) REVERT: D 407 ARG cc_start: 0.8809 (tmt90) cc_final: 0.8555 (ttt90) REVERT: D 409 LYS cc_start: 0.8700 (ttmp) cc_final: 0.7996 (tttt) REVERT: D 438 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8144 (mmtm) REVERT: E 28 ASP cc_start: 0.8817 (m-30) cc_final: 0.8515 (m-30) REVERT: E 51 LEU cc_start: 0.9339 (pp) cc_final: 0.9034 (pp) REVERT: E 105 ARG cc_start: 0.9148 (mtm110) cc_final: 0.8641 (mtm110) REVERT: E 109 LYS cc_start: 0.9416 (mttp) cc_final: 0.9160 (mptt) REVERT: E 258 TYR cc_start: 0.9085 (t80) cc_final: 0.8869 (t80) REVERT: E 274 ASP cc_start: 0.9125 (t0) cc_final: 0.8908 (t0) REVERT: E 276 SER cc_start: 0.8747 (p) cc_final: 0.8464 (p) REVERT: E 285 ASN cc_start: 0.9456 (m-40) cc_final: 0.9249 (m-40) REVERT: E 352 GLU cc_start: 0.9229 (tm-30) cc_final: 0.8975 (tm-30) REVERT: E 395 GLU cc_start: 0.8834 (mp0) cc_final: 0.8269 (mp0) REVERT: E 399 GLU cc_start: 0.9001 (pm20) cc_final: 0.8744 (pm20) REVERT: E 510 GLU cc_start: 0.8306 (tp30) cc_final: 0.8013 (tp30) REVERT: F 28 ASP cc_start: 0.8886 (m-30) cc_final: 0.8633 (m-30) REVERT: F 51 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8777 (pp) REVERT: F 105 ARG cc_start: 0.9123 (mtm110) cc_final: 0.8876 (mtm110) REVERT: F 108 LYS cc_start: 0.9513 (OUTLIER) cc_final: 0.9218 (tppt) REVERT: F 109 LYS cc_start: 0.9475 (mptt) cc_final: 0.9153 (mttm) REVERT: F 258 TYR cc_start: 0.9204 (t80) cc_final: 0.8939 (t80) REVERT: F 276 SER cc_start: 0.8601 (p) cc_final: 0.8291 (p) REVERT: F 279 ASN cc_start: 0.8972 (t0) cc_final: 0.8164 (t0) REVERT: F 281 ILE cc_start: 0.9016 (tp) cc_final: 0.8718 (tt) REVERT: F 285 ASN cc_start: 0.9463 (m-40) cc_final: 0.9210 (m-40) REVERT: F 332 ILE cc_start: 0.8764 (OUTLIER) cc_final: 0.8514 (pp) REVERT: F 352 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8949 (tm-30) REVERT: F 355 ARG cc_start: 0.9440 (ptm-80) cc_final: 0.9119 (ptm-80) REVERT: F 385 MET cc_start: 0.8896 (ttm) cc_final: 0.8499 (ttm) REVERT: F 393 THR cc_start: 0.9172 (p) cc_final: 0.8239 (p) REVERT: F 395 GLU cc_start: 0.8880 (mp0) cc_final: 0.8018 (mp0) REVERT: F 404 ASP cc_start: 0.9235 (t0) cc_final: 0.8956 (t70) REVERT: F 409 LYS cc_start: 0.8699 (ttmp) cc_final: 0.7960 (tttt) REVERT: G 21 GLN cc_start: 0.8987 (pt0) cc_final: 0.8531 (tm-30) REVERT: G 28 ASP cc_start: 0.8920 (m-30) cc_final: 0.8707 (m-30) REVERT: G 50 ASP cc_start: 0.9093 (t70) cc_final: 0.8819 (t0) REVERT: G 51 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8859 (pp) REVERT: G 98 GLU cc_start: 0.9397 (mp0) cc_final: 0.9193 (mp0) REVERT: G 108 LYS cc_start: 0.9539 (OUTLIER) cc_final: 0.9253 (mttm) REVERT: G 109 LYS cc_start: 0.9353 (mttp) cc_final: 0.9049 (mttm) REVERT: G 256 ASP cc_start: 0.9316 (m-30) cc_final: 0.8945 (p0) REVERT: G 258 TYR cc_start: 0.9163 (t80) cc_final: 0.8889 (t80) REVERT: G 279 ASN cc_start: 0.8970 (t0) cc_final: 0.8377 (t0) REVERT: G 299 VAL cc_start: 0.9406 (m) cc_final: 0.9158 (p) REVERT: G 352 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8962 (tm-30) REVERT: G 385 MET cc_start: 0.8833 (ttm) cc_final: 0.8364 (ttm) REVERT: G 395 GLU cc_start: 0.8836 (mp0) cc_final: 0.8326 (mp0) REVERT: G 399 GLU cc_start: 0.9097 (pm20) cc_final: 0.8809 (pm20) REVERT: G 400 TYR cc_start: 0.8388 (m-80) cc_final: 0.7923 (m-80) REVERT: G 407 ARG cc_start: 0.8939 (ttt-90) cc_final: 0.8596 (ptm-80) REVERT: G 510 GLU cc_start: 0.8133 (tp30) cc_final: 0.7763 (tp30) REVERT: H 25 ASN cc_start: 0.9036 (m-40) cc_final: 0.8751 (p0) REVERT: H 28 ASP cc_start: 0.8904 (m-30) cc_final: 0.8635 (m-30) REVERT: H 51 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8785 (pp) REVERT: H 66 VAL cc_start: 0.8159 (OUTLIER) cc_final: 0.7866 (p) REVERT: H 105 ARG cc_start: 0.9180 (mtm110) cc_final: 0.8871 (mtm110) REVERT: H 276 SER cc_start: 0.8699 (p) cc_final: 0.8405 (p) REVERT: H 285 ASN cc_start: 0.9451 (m-40) cc_final: 0.9202 (m-40) REVERT: H 352 GLU cc_start: 0.9258 (tm-30) cc_final: 0.9016 (tm-30) REVERT: H 355 ARG cc_start: 0.9384 (ptm-80) cc_final: 0.9095 (ptm-80) REVERT: H 385 MET cc_start: 0.8916 (ttm) cc_final: 0.8456 (ttm) REVERT: H 395 GLU cc_start: 0.8812 (mp0) cc_final: 0.8236 (mp0) REVERT: H 399 GLU cc_start: 0.8908 (pm20) cc_final: 0.8694 (pm20) REVERT: H 512 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.7568 (ptm160) outliers start: 127 outliers final: 74 residues processed: 1044 average time/residue: 0.1479 time to fit residues: 244.8012 Evaluate side-chains 1012 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 926 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 282 optimal weight: 0.0770 chunk 142 optimal weight: 4.9990 chunk 177 optimal weight: 8.9990 chunk 141 optimal weight: 7.9990 chunk 144 optimal weight: 5.9990 chunk 261 optimal weight: 0.5980 chunk 173 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 198 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.1344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 ASN ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.104962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.084673 restraints weight = 41303.763| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 3.86 r_work: 0.2800 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23488 Z= 0.180 Angle : 0.673 8.373 31792 Z= 0.342 Chirality : 0.047 0.166 3656 Planarity : 0.004 0.039 4000 Dihedral : 11.133 89.871 3760 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 6.42 % Allowed : 23.66 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.15), residues: 2960 helix: -1.16 (0.15), residues: 1120 sheet: -2.02 (0.21), residues: 480 loop : -1.08 (0.17), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 105 TYR 0.018 0.001 TYR D 400 PHE 0.013 0.001 PHE E 401 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00425 (23480) covalent geometry : angle 0.67336 (31792) hydrogen bonds : bond 0.03523 ( 841) hydrogen bonds : angle 5.27070 ( 2427) Misc. bond : bond 0.00108 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 955 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9035 (pp) REVERT: A 105 ARG cc_start: 0.9165 (mtm110) cc_final: 0.8650 (mtm110) REVERT: A 109 LYS cc_start: 0.9428 (mttp) cc_final: 0.9177 (mptt) REVERT: A 274 ASP cc_start: 0.9167 (t0) cc_final: 0.8875 (t0) REVERT: A 276 SER cc_start: 0.8859 (p) cc_final: 0.8563 (p) REVERT: A 285 ASN cc_start: 0.9483 (m-40) cc_final: 0.9268 (m-40) REVERT: A 352 GLU cc_start: 0.9234 (tm-30) cc_final: 0.8986 (tm-30) REVERT: A 385 MET cc_start: 0.8945 (ttm) cc_final: 0.8510 (ttm) REVERT: A 395 GLU cc_start: 0.8868 (mp0) cc_final: 0.8294 (mp0) REVERT: A 399 GLU cc_start: 0.8995 (pm20) cc_final: 0.8776 (mp0) REVERT: A 404 ASP cc_start: 0.9238 (t0) cc_final: 0.8918 (t70) REVERT: A 406 ILE cc_start: 0.9073 (mp) cc_final: 0.8836 (mp) REVERT: A 438 LYS cc_start: 0.9047 (mttt) cc_final: 0.8536 (mmtt) REVERT: A 455 LYS cc_start: 0.9164 (mppt) cc_final: 0.8741 (mppt) REVERT: A 510 GLU cc_start: 0.8078 (tp30) cc_final: 0.7872 (tp30) REVERT: B 28 ASP cc_start: 0.8767 (m-30) cc_final: 0.8560 (m-30) REVERT: B 50 ASP cc_start: 0.9024 (t70) cc_final: 0.8778 (t0) REVERT: B 51 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8996 (pp) REVERT: B 105 ARG cc_start: 0.9221 (mtm110) cc_final: 0.8769 (mtm110) REVERT: B 258 TYR cc_start: 0.9087 (t80) cc_final: 0.8822 (t80) REVERT: B 276 SER cc_start: 0.8903 (p) cc_final: 0.8620 (p) REVERT: B 285 ASN cc_start: 0.9453 (m-40) cc_final: 0.9220 (m-40) REVERT: B 332 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8754 (pp) REVERT: B 352 GLU cc_start: 0.9234 (tm-30) cc_final: 0.9024 (tm-30) REVERT: B 395 GLU cc_start: 0.8876 (mp0) cc_final: 0.8287 (mp0) REVERT: B 399 GLU cc_start: 0.8978 (pm20) cc_final: 0.8747 (pm20) REVERT: B 404 ASP cc_start: 0.9258 (t0) cc_final: 0.8992 (t70) REVERT: B 410 LYS cc_start: 0.8728 (ptmt) cc_final: 0.8480 (ptmt) REVERT: B 438 LYS cc_start: 0.9090 (mttt) cc_final: 0.8829 (tttt) REVERT: C 50 ASP cc_start: 0.9174 (t70) cc_final: 0.8879 (t0) REVERT: C 51 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9100 (pp) REVERT: C 66 VAL cc_start: 0.8170 (OUTLIER) cc_final: 0.7599 (m) REVERT: C 105 ARG cc_start: 0.9173 (mtm110) cc_final: 0.8692 (mtm110) REVERT: C 109 LYS cc_start: 0.9431 (mttp) cc_final: 0.9168 (mptt) REVERT: C 258 TYR cc_start: 0.9065 (t80) cc_final: 0.8732 (t80) REVERT: C 276 SER cc_start: 0.8705 (p) cc_final: 0.8421 (p) REVERT: C 279 ASN cc_start: 0.9227 (t0) cc_final: 0.8201 (t0) REVERT: C 332 ILE cc_start: 0.9028 (OUTLIER) cc_final: 0.8787 (pp) REVERT: C 352 GLU cc_start: 0.9231 (tm-30) cc_final: 0.8948 (tm-30) REVERT: C 355 ARG cc_start: 0.9529 (ptm-80) cc_final: 0.9282 (ptm-80) REVERT: C 385 MET cc_start: 0.9085 (ttm) cc_final: 0.8618 (ttm) REVERT: C 395 GLU cc_start: 0.8951 (mp0) cc_final: 0.8394 (mp0) REVERT: C 407 ARG cc_start: 0.8993 (ttt90) cc_final: 0.8786 (ttt90) REVERT: C 409 LYS cc_start: 0.8807 (ttmp) cc_final: 0.8480 (ttmt) REVERT: C 438 LYS cc_start: 0.8995 (mttt) cc_final: 0.8479 (mmtm) REVERT: C 510 GLU cc_start: 0.8138 (tp30) cc_final: 0.7845 (tp30) REVERT: D 25 ASN cc_start: 0.9238 (m-40) cc_final: 0.8976 (p0) REVERT: D 28 ASP cc_start: 0.8788 (m-30) cc_final: 0.8580 (m-30) REVERT: D 51 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9129 (pp) REVERT: D 105 ARG cc_start: 0.9255 (mtm110) cc_final: 0.8966 (mtm110) REVERT: D 256 ASP cc_start: 0.9305 (m-30) cc_final: 0.8808 (p0) REVERT: D 258 TYR cc_start: 0.9186 (t80) cc_final: 0.8931 (t80) REVERT: D 276 SER cc_start: 0.8833 (p) cc_final: 0.8563 (p) REVERT: D 285 ASN cc_start: 0.9476 (m-40) cc_final: 0.9246 (m-40) REVERT: D 332 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8743 (pp) REVERT: D 352 GLU cc_start: 0.9208 (tm-30) cc_final: 0.8963 (tm-30) REVERT: D 395 GLU cc_start: 0.8910 (mp0) cc_final: 0.8232 (mp0) REVERT: D 399 GLU cc_start: 0.9060 (pm20) cc_final: 0.8686 (mp0) REVERT: D 400 TYR cc_start: 0.8349 (m-10) cc_final: 0.7495 (m-10) REVERT: D 404 ASP cc_start: 0.9201 (t0) cc_final: 0.8945 (t0) REVERT: D 407 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8511 (ttt-90) REVERT: D 409 LYS cc_start: 0.8756 (ttmp) cc_final: 0.8207 (tttt) REVERT: E 21 GLN cc_start: 0.9129 (pt0) cc_final: 0.8677 (tm-30) REVERT: E 28 ASP cc_start: 0.8807 (m-30) cc_final: 0.8586 (m-30) REVERT: E 51 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8948 (pp) REVERT: E 105 ARG cc_start: 0.9180 (mtm110) cc_final: 0.8683 (mtm110) REVERT: E 109 LYS cc_start: 0.9431 (mttp) cc_final: 0.9181 (mptt) REVERT: E 258 TYR cc_start: 0.9134 (t80) cc_final: 0.8893 (t80) REVERT: E 259 ARG cc_start: 0.9305 (ttm-80) cc_final: 0.9073 (ttm-80) REVERT: E 276 SER cc_start: 0.8831 (p) cc_final: 0.8530 (p) REVERT: E 285 ASN cc_start: 0.9458 (m-40) cc_final: 0.9253 (m-40) REVERT: E 332 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8751 (pp) REVERT: E 352 GLU cc_start: 0.9267 (tm-30) cc_final: 0.9024 (tm-30) REVERT: E 395 GLU cc_start: 0.8875 (mp0) cc_final: 0.8318 (mp0) REVERT: E 399 GLU cc_start: 0.8966 (pm20) cc_final: 0.8727 (pm20) REVERT: F 21 GLN cc_start: 0.9089 (pt0) cc_final: 0.8778 (tm-30) REVERT: F 51 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8978 (pp) REVERT: F 105 ARG cc_start: 0.9188 (mtm110) cc_final: 0.8668 (mtm110) REVERT: F 108 LYS cc_start: 0.9542 (OUTLIER) cc_final: 0.9300 (tppt) REVERT: F 109 LYS cc_start: 0.9443 (mptt) cc_final: 0.9088 (mttt) REVERT: F 258 TYR cc_start: 0.9202 (t80) cc_final: 0.8913 (t80) REVERT: F 276 SER cc_start: 0.8630 (p) cc_final: 0.8310 (p) REVERT: F 279 ASN cc_start: 0.9068 (t0) cc_final: 0.8224 (t0) REVERT: F 285 ASN cc_start: 0.9460 (m-40) cc_final: 0.9213 (m-40) REVERT: F 332 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8582 (pp) REVERT: F 352 GLU cc_start: 0.9211 (tm-30) cc_final: 0.8974 (tm-30) REVERT: F 362 ILE cc_start: 0.8153 (mt) cc_final: 0.7904 (mt) REVERT: F 385 MET cc_start: 0.8958 (ttm) cc_final: 0.8532 (ttm) REVERT: F 395 GLU cc_start: 0.8889 (mp0) cc_final: 0.8299 (mp0) REVERT: F 404 ASP cc_start: 0.9250 (t0) cc_final: 0.8995 (t70) REVERT: F 407 ARG cc_start: 0.8891 (ttt90) cc_final: 0.8582 (ttt90) REVERT: G 21 GLN cc_start: 0.9083 (pt0) cc_final: 0.8705 (tm-30) REVERT: G 50 ASP cc_start: 0.9116 (t70) cc_final: 0.8846 (t0) REVERT: G 51 LEU cc_start: 0.9298 (OUTLIER) cc_final: 0.8936 (pp) REVERT: G 78 MET cc_start: 0.8739 (OUTLIER) cc_final: 0.8223 (ptm) REVERT: G 258 TYR cc_start: 0.9150 (t80) cc_final: 0.8827 (t80) REVERT: G 279 ASN cc_start: 0.9091 (t0) cc_final: 0.8490 (t0) REVERT: G 299 VAL cc_start: 0.9393 (m) cc_final: 0.9130 (p) REVERT: G 332 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8777 (pp) REVERT: G 352 GLU cc_start: 0.9241 (tm-30) cc_final: 0.9006 (tm-30) REVERT: G 385 MET cc_start: 0.8962 (ttm) cc_final: 0.8462 (ttm) REVERT: G 395 GLU cc_start: 0.8810 (mp0) cc_final: 0.8320 (mp0) REVERT: G 399 GLU cc_start: 0.9117 (pm20) cc_final: 0.8838 (pm20) REVERT: G 400 TYR cc_start: 0.8354 (m-80) cc_final: 0.7914 (m-80) REVERT: G 407 ARG cc_start: 0.9063 (ttt-90) cc_final: 0.8774 (ttt-90) REVERT: H 25 ASN cc_start: 0.9078 (m-40) cc_final: 0.8760 (p0) REVERT: H 28 ASP cc_start: 0.8921 (m-30) cc_final: 0.8716 (m-30) REVERT: H 51 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8903 (pp) REVERT: H 66 VAL cc_start: 0.8062 (OUTLIER) cc_final: 0.7835 (p) REVERT: H 105 ARG cc_start: 0.9199 (mtm110) cc_final: 0.8879 (mtm110) REVERT: H 276 SER cc_start: 0.8772 (p) cc_final: 0.8406 (p) REVERT: H 332 ILE cc_start: 0.9062 (OUTLIER) cc_final: 0.8832 (pp) REVERT: H 352 GLU cc_start: 0.9280 (tm-30) cc_final: 0.9041 (tm-30) REVERT: H 385 MET cc_start: 0.8951 (ttm) cc_final: 0.8500 (ttm) REVERT: H 395 GLU cc_start: 0.8887 (mp0) cc_final: 0.8323 (mp0) REVERT: H 410 LYS cc_start: 0.8748 (ptmt) cc_final: 0.8457 (ptmt) outliers start: 153 outliers final: 90 residues processed: 1019 average time/residue: 0.1494 time to fit residues: 241.3888 Evaluate side-chains 1018 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 908 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 471 ILE Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 407 ARG Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 147 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 242 optimal weight: 3.9990 chunk 277 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 ASN ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.099405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.078967 restraints weight = 42116.995| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 3.86 r_work: 0.2723 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 23488 Z= 0.264 Angle : 0.729 8.426 31792 Z= 0.373 Chirality : 0.049 0.162 3656 Planarity : 0.004 0.052 4000 Dihedral : 10.983 89.739 3750 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 7.05 % Allowed : 24.54 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.15), residues: 2960 helix: -1.14 (0.15), residues: 1128 sheet: -2.09 (0.23), residues: 376 loop : -1.11 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 105 TYR 0.021 0.002 TYR A 400 PHE 0.011 0.001 PHE E 401 HIS 0.003 0.001 HIS G 507 Details of bonding type rmsd covalent geometry : bond 0.00620 (23480) covalent geometry : angle 0.72864 (31792) hydrogen bonds : bond 0.03699 ( 841) hydrogen bonds : angle 5.31580 ( 2427) Misc. bond : bond 0.00201 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1084 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 916 time to evaluate : 0.808 Fit side-chains REVERT: A 1 MET cc_start: 0.4681 (ptp) cc_final: 0.3857 (ptm) REVERT: A 51 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9115 (pp) REVERT: A 84 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8338 (mm) REVERT: A 105 ARG cc_start: 0.9169 (mtm110) cc_final: 0.8680 (mtm110) REVERT: A 109 LYS cc_start: 0.9450 (mttp) cc_final: 0.9223 (mptt) REVERT: A 274 ASP cc_start: 0.9208 (t0) cc_final: 0.8983 (t0) REVERT: A 352 GLU cc_start: 0.9268 (tm-30) cc_final: 0.9050 (tm-30) REVERT: A 385 MET cc_start: 0.9015 (ttm) cc_final: 0.8592 (ttm) REVERT: A 395 GLU cc_start: 0.8928 (mp0) cc_final: 0.8307 (mp0) REVERT: A 399 GLU cc_start: 0.9058 (pm20) cc_final: 0.8810 (pm20) REVERT: A 400 TYR cc_start: 0.8304 (m-10) cc_final: 0.7833 (m-10) REVERT: A 404 ASP cc_start: 0.9342 (t0) cc_final: 0.9088 (t70) REVERT: A 407 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8154 (ttt-90) REVERT: A 409 LYS cc_start: 0.8676 (ttmp) cc_final: 0.8311 (ttmt) REVERT: A 438 LYS cc_start: 0.9035 (mttt) cc_final: 0.8516 (mmtt) REVERT: A 455 LYS cc_start: 0.9190 (mppt) cc_final: 0.8770 (mppt) REVERT: B 50 ASP cc_start: 0.9041 (t70) cc_final: 0.8780 (t0) REVERT: B 51 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9093 (pp) REVERT: B 105 ARG cc_start: 0.9185 (mtm110) cc_final: 0.8836 (mtm110) REVERT: B 258 TYR cc_start: 0.9139 (t80) cc_final: 0.8934 (t80) REVERT: B 276 SER cc_start: 0.8960 (p) cc_final: 0.8662 (p) REVERT: B 332 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8496 (pp) REVERT: B 335 GLU cc_start: 0.8605 (tm-30) cc_final: 0.7860 (tm-30) REVERT: B 352 GLU cc_start: 0.9278 (tm-30) cc_final: 0.9069 (tm-30) REVERT: B 369 ASN cc_start: 0.8425 (p0) cc_final: 0.8142 (p0) REVERT: B 395 GLU cc_start: 0.8947 (mp0) cc_final: 0.8309 (mp0) REVERT: B 404 ASP cc_start: 0.9303 (t0) cc_final: 0.9050 (t70) REVERT: B 407 ARG cc_start: 0.8992 (ttt90) cc_final: 0.8695 (ttt90) REVERT: B 438 LYS cc_start: 0.9096 (mttt) cc_final: 0.8589 (mmtt) REVERT: C 50 ASP cc_start: 0.9171 (t70) cc_final: 0.8878 (t0) REVERT: C 51 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8956 (pp) REVERT: C 66 VAL cc_start: 0.8093 (OUTLIER) cc_final: 0.7869 (p) REVERT: C 80 ILE cc_start: 0.9291 (pp) cc_final: 0.9055 (pp) REVERT: C 84 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8426 (mm) REVERT: C 258 TYR cc_start: 0.9101 (t80) cc_final: 0.8733 (t80) REVERT: C 276 SER cc_start: 0.8798 (p) cc_final: 0.8484 (p) REVERT: C 279 ASN cc_start: 0.9281 (t0) cc_final: 0.8988 (t0) REVERT: C 332 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8801 (pp) REVERT: C 369 ASN cc_start: 0.8401 (p0) cc_final: 0.8081 (p0) REVERT: C 395 GLU cc_start: 0.9007 (mp0) cc_final: 0.8441 (mp0) REVERT: C 400 TYR cc_start: 0.8131 (m-10) cc_final: 0.7697 (m-10) REVERT: C 407 ARG cc_start: 0.9015 (ttt90) cc_final: 0.8800 (ttt90) REVERT: C 438 LYS cc_start: 0.9139 (mttt) cc_final: 0.8542 (mmtm) REVERT: C 510 GLU cc_start: 0.8146 (tp30) cc_final: 0.7876 (tp30) REVERT: D 25 ASN cc_start: 0.9263 (m-40) cc_final: 0.8997 (p0) REVERT: D 51 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8946 (pp) REVERT: D 84 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8314 (mm) REVERT: D 105 ARG cc_start: 0.9292 (mtm110) cc_final: 0.8960 (mtm110) REVERT: D 256 ASP cc_start: 0.9282 (m-30) cc_final: 0.8723 (p0) REVERT: D 258 TYR cc_start: 0.9218 (t80) cc_final: 0.8872 (t80) REVERT: D 275 SER cc_start: 0.9129 (t) cc_final: 0.8894 (t) REVERT: D 276 SER cc_start: 0.8946 (p) cc_final: 0.8660 (p) REVERT: D 279 ASN cc_start: 0.7991 (m110) cc_final: 0.7786 (m-40) REVERT: D 332 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8823 (pp) REVERT: D 352 GLU cc_start: 0.9269 (tm-30) cc_final: 0.9029 (tm-30) REVERT: D 369 ASN cc_start: 0.8450 (p0) cc_final: 0.8194 (p0) REVERT: D 395 GLU cc_start: 0.8981 (mp0) cc_final: 0.8332 (mp0) REVERT: D 400 TYR cc_start: 0.8219 (m-10) cc_final: 0.7105 (m-10) REVERT: D 404 ASP cc_start: 0.9273 (t0) cc_final: 0.9043 (t0) REVERT: D 407 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8348 (ttt-90) REVERT: E 21 GLN cc_start: 0.9220 (pt0) cc_final: 0.8805 (tm-30) REVERT: E 51 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8953 (pp) REVERT: E 105 ARG cc_start: 0.9201 (mtm110) cc_final: 0.8718 (mtm110) REVERT: E 109 LYS cc_start: 0.9457 (mttp) cc_final: 0.9197 (mptt) REVERT: E 258 TYR cc_start: 0.9175 (t80) cc_final: 0.8881 (t80) REVERT: E 259 ARG cc_start: 0.9302 (ttm-80) cc_final: 0.9094 (ttm-80) REVERT: E 285 ASN cc_start: 0.9475 (m-40) cc_final: 0.9240 (m-40) REVERT: E 352 GLU cc_start: 0.9294 (tm-30) cc_final: 0.9074 (tm-30) REVERT: E 395 GLU cc_start: 0.8958 (mp0) cc_final: 0.8365 (mp0) REVERT: E 407 ARG cc_start: 0.9067 (ttt90) cc_final: 0.8853 (ttt90) REVERT: E 510 GLU cc_start: 0.8242 (tp30) cc_final: 0.8002 (tp30) REVERT: F 21 GLN cc_start: 0.9182 (pt0) cc_final: 0.8866 (tm-30) REVERT: F 51 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8951 (pp) REVERT: F 80 ILE cc_start: 0.9273 (pp) cc_final: 0.9068 (pp) REVERT: F 84 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8502 (mm) REVERT: F 108 LYS cc_start: 0.9575 (ttpp) cc_final: 0.9339 (tppt) REVERT: F 109 LYS cc_start: 0.9442 (mptt) cc_final: 0.8999 (mttp) REVERT: F 258 TYR cc_start: 0.9224 (t80) cc_final: 0.8905 (t80) REVERT: F 276 SER cc_start: 0.8702 (p) cc_final: 0.8348 (p) REVERT: F 332 ILE cc_start: 0.8886 (OUTLIER) cc_final: 0.8650 (pp) REVERT: F 352 GLU cc_start: 0.9271 (tm-30) cc_final: 0.9031 (tm-30) REVERT: F 355 ARG cc_start: 0.9293 (ptm-80) cc_final: 0.8860 (ptm-80) REVERT: F 369 ASN cc_start: 0.8378 (p0) cc_final: 0.8102 (p0) REVERT: F 385 MET cc_start: 0.9041 (ttm) cc_final: 0.8518 (ttm) REVERT: F 395 GLU cc_start: 0.8939 (mp0) cc_final: 0.8325 (mp0) REVERT: F 404 ASP cc_start: 0.9314 (t0) cc_final: 0.9082 (t70) REVERT: F 407 ARG cc_start: 0.8950 (ttt90) cc_final: 0.8280 (ttt-90) REVERT: G 21 GLN cc_start: 0.9175 (pt0) cc_final: 0.8789 (tm-30) REVERT: G 50 ASP cc_start: 0.9131 (t70) cc_final: 0.8851 (t0) REVERT: G 51 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8980 (pp) REVERT: G 84 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8397 (mm) REVERT: G 109 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.9014 (tmtt) REVERT: G 258 TYR cc_start: 0.9184 (t80) cc_final: 0.8864 (t80) REVERT: G 299 VAL cc_start: 0.9311 (m) cc_final: 0.9074 (p) REVERT: G 332 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8760 (pp) REVERT: G 352 GLU cc_start: 0.9291 (tm-30) cc_final: 0.9071 (tm-30) REVERT: G 385 MET cc_start: 0.9079 (ttm) cc_final: 0.8583 (ttm) REVERT: G 395 GLU cc_start: 0.8806 (mp0) cc_final: 0.8268 (mp0) REVERT: G 399 GLU cc_start: 0.9175 (pm20) cc_final: 0.8911 (pm20) REVERT: G 400 TYR cc_start: 0.8293 (m-80) cc_final: 0.6865 (m-80) REVERT: G 407 ARG cc_start: 0.9112 (ttt-90) cc_final: 0.8151 (ttt-90) REVERT: G 510 GLU cc_start: 0.8293 (tp30) cc_final: 0.8029 (tp30) REVERT: H 51 LEU cc_start: 0.9201 (OUTLIER) cc_final: 0.8853 (pp) REVERT: H 66 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.7970 (p) REVERT: H 84 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8221 (mm) REVERT: H 105 ARG cc_start: 0.9230 (mtm110) cc_final: 0.8914 (mtm110) REVERT: H 332 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8851 (pp) REVERT: H 352 GLU cc_start: 0.9328 (tm-30) cc_final: 0.9100 (tm-30) REVERT: H 355 ARG cc_start: 0.9272 (ptm-80) cc_final: 0.8837 (ptm-80) REVERT: H 369 ASN cc_start: 0.8415 (p0) cc_final: 0.8079 (p0) REVERT: H 385 MET cc_start: 0.8970 (ttm) cc_final: 0.8586 (ttm) REVERT: H 395 GLU cc_start: 0.8914 (mp0) cc_final: 0.8318 (mp0) outliers start: 168 outliers final: 111 residues processed: 1000 average time/residue: 0.1459 time to fit residues: 231.7687 Evaluate side-chains 1013 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 877 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 455 LYS Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 407 ARG Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 499 VAL Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 282 PHE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 109 LYS Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 207 optimal weight: 0.7980 chunk 233 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 63 optimal weight: 0.3980 chunk 80 optimal weight: 0.4980 chunk 115 optimal weight: 5.9990 chunk 295 optimal weight: 4.9990 chunk 281 optimal weight: 0.6980 chunk 252 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN D 368 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 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 = 0.3315 r_free = 0.3315 target = 0.105950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.085107 restraints weight = 41163.228| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 3.93 r_work: 0.2808 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.3965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23488 Z= 0.147 Angle : 0.695 9.939 31792 Z= 0.353 Chirality : 0.047 0.186 3656 Planarity : 0.004 0.038 4000 Dihedral : 10.663 89.533 3738 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.79 % Allowed : 26.68 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.95 (0.15), residues: 2960 helix: -1.19 (0.15), residues: 1144 sheet: -1.86 (0.24), residues: 368 loop : -1.08 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 105 TYR 0.021 0.001 TYR A 258 PHE 0.012 0.001 PHE C 401 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00351 (23480) covalent geometry : angle 0.69537 (31792) hydrogen bonds : bond 0.03489 ( 841) hydrogen bonds : angle 5.26592 ( 2427) Misc. bond : bond 0.00071 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 979 time to evaluate : 0.818 Fit side-chains REVERT: A 1 MET cc_start: 0.4571 (ptp) cc_final: 0.4018 (ptm) REVERT: A 21 GLN cc_start: 0.9084 (pt0) cc_final: 0.8542 (tm-30) REVERT: A 51 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9044 (pp) REVERT: A 105 ARG cc_start: 0.9151 (mtm110) cc_final: 0.8592 (mtm110) REVERT: A 109 LYS cc_start: 0.9455 (mttp) cc_final: 0.9175 (mptt) REVERT: A 274 ASP cc_start: 0.9209 (t0) cc_final: 0.8955 (t0) REVERT: A 276 SER cc_start: 0.8962 (p) cc_final: 0.8591 (p) REVERT: A 352 GLU cc_start: 0.9216 (tm-30) cc_final: 0.8979 (tm-30) REVERT: A 385 MET cc_start: 0.8924 (ttm) cc_final: 0.8569 (ttm) REVERT: A 395 GLU cc_start: 0.8959 (mp0) cc_final: 0.8294 (mp0) REVERT: A 399 GLU cc_start: 0.9060 (pm20) cc_final: 0.8784 (pm20) REVERT: A 404 ASP cc_start: 0.9305 (t0) cc_final: 0.9052 (t0) REVERT: A 409 LYS cc_start: 0.8698 (ttmp) cc_final: 0.8430 (ttmt) REVERT: A 438 LYS cc_start: 0.9085 (mttt) cc_final: 0.8486 (mmtm) REVERT: B 21 GLN cc_start: 0.9126 (pt0) cc_final: 0.8618 (tm-30) REVERT: B 38 LEU cc_start: 0.9324 (mp) cc_final: 0.9106 (mp) REVERT: B 50 ASP cc_start: 0.9068 (t70) cc_final: 0.8802 (t0) REVERT: B 51 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.8956 (pp) REVERT: B 258 TYR cc_start: 0.9102 (t80) cc_final: 0.8892 (t80) REVERT: B 276 SER cc_start: 0.8899 (p) cc_final: 0.8659 (p) REVERT: B 332 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8356 (pp) REVERT: B 335 GLU cc_start: 0.8550 (tm-30) cc_final: 0.7834 (tm-30) REVERT: B 352 GLU cc_start: 0.9247 (tm-30) cc_final: 0.9003 (tm-30) REVERT: B 395 GLU cc_start: 0.8955 (mp0) cc_final: 0.8302 (mp0) REVERT: B 404 ASP cc_start: 0.9276 (t0) cc_final: 0.9030 (t70) REVERT: B 438 LYS cc_start: 0.9074 (mttt) cc_final: 0.8572 (mmtm) REVERT: C 21 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8235 (tm-30) REVERT: C 50 ASP cc_start: 0.9197 (t70) cc_final: 0.8910 (t0) REVERT: C 51 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8810 (pp) REVERT: C 66 VAL cc_start: 0.7669 (OUTLIER) cc_final: 0.6605 (t) REVERT: C 109 LYS cc_start: 0.9559 (mmmt) cc_final: 0.9010 (tptt) REVERT: C 258 TYR cc_start: 0.9099 (t80) cc_final: 0.8781 (t80) REVERT: C 276 SER cc_start: 0.8655 (p) cc_final: 0.8344 (p) REVERT: C 279 ASN cc_start: 0.9276 (t0) cc_final: 0.8986 (t0) REVERT: C 332 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8449 (pp) REVERT: C 335 GLU cc_start: 0.8516 (tm-30) cc_final: 0.7739 (tm-30) REVERT: C 362 ILE cc_start: 0.8140 (mt) cc_final: 0.7929 (mt) REVERT: C 385 MET cc_start: 0.8871 (ttm) cc_final: 0.8536 (ttm) REVERT: C 393 THR cc_start: 0.9424 (p) cc_final: 0.8730 (p) REVERT: C 395 GLU cc_start: 0.8996 (mp0) cc_final: 0.8304 (mp0) REVERT: C 400 TYR cc_start: 0.8373 (m-10) cc_final: 0.8155 (m-10) REVERT: C 407 ARG cc_start: 0.8967 (ttt90) cc_final: 0.8751 (ttt90) REVERT: C 438 LYS cc_start: 0.9087 (mttt) cc_final: 0.8517 (mmtm) REVERT: C 510 GLU cc_start: 0.8152 (tp30) cc_final: 0.7866 (tp30) REVERT: D 25 ASN cc_start: 0.9229 (m-40) cc_final: 0.8971 (p0) REVERT: D 50 ASP cc_start: 0.9114 (t70) cc_final: 0.8888 (t0) REVERT: D 51 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8908 (pp) REVERT: D 105 ARG cc_start: 0.9276 (mtm110) cc_final: 0.8946 (mtm110) REVERT: D 258 TYR cc_start: 0.9210 (t80) cc_final: 0.8935 (t80) REVERT: D 276 SER cc_start: 0.8766 (p) cc_final: 0.8462 (p) REVERT: D 332 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8762 (pp) REVERT: D 352 GLU cc_start: 0.9229 (tm-30) cc_final: 0.9018 (tm-30) REVERT: D 395 GLU cc_start: 0.8951 (mp0) cc_final: 0.8297 (mp0) REVERT: D 400 TYR cc_start: 0.8393 (m-10) cc_final: 0.7389 (m-10) REVERT: D 404 ASP cc_start: 0.9259 (t0) cc_final: 0.9013 (t0) REVERT: D 407 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8271 (ttt-90) REVERT: E 21 GLN cc_start: 0.9163 (pt0) cc_final: 0.8575 (tm-30) REVERT: E 25 ASN cc_start: 0.9303 (m-40) cc_final: 0.8960 (m-40) REVERT: E 51 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8811 (pp) REVERT: E 105 ARG cc_start: 0.9113 (mtm110) cc_final: 0.8877 (mtm110) REVERT: E 258 TYR cc_start: 0.9171 (t80) cc_final: 0.8934 (t80) REVERT: E 276 SER cc_start: 0.8954 (p) cc_final: 0.8563 (p) REVERT: E 285 ASN cc_start: 0.9489 (m-40) cc_final: 0.9266 (m-40) REVERT: E 352 GLU cc_start: 0.9262 (tm-30) cc_final: 0.9027 (tm-30) REVERT: E 355 ARG cc_start: 0.9243 (ptm-80) cc_final: 0.8983 (ptm-80) REVERT: E 395 GLU cc_start: 0.8888 (mp0) cc_final: 0.8290 (mp0) REVERT: E 510 GLU cc_start: 0.8273 (tp30) cc_final: 0.8018 (tp30) REVERT: F 21 GLN cc_start: 0.9064 (pt0) cc_final: 0.8715 (tm-30) REVERT: F 51 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8903 (pp) REVERT: F 105 ARG cc_start: 0.9187 (mtm110) cc_final: 0.8677 (mtm110) REVERT: F 109 LYS cc_start: 0.9447 (mptt) cc_final: 0.9197 (mttt) REVERT: F 258 TYR cc_start: 0.9208 (t80) cc_final: 0.8929 (t80) REVERT: F 276 SER cc_start: 0.8586 (p) cc_final: 0.8247 (p) REVERT: F 279 ASN cc_start: 0.8887 (t0) cc_final: 0.8272 (t0) REVERT: F 332 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8537 (pp) REVERT: F 352 GLU cc_start: 0.9243 (tm-30) cc_final: 0.8998 (tm-30) REVERT: F 355 ARG cc_start: 0.9288 (ptm-80) cc_final: 0.8900 (ptm-80) REVERT: F 385 MET cc_start: 0.8978 (ttm) cc_final: 0.8474 (ttm) REVERT: F 395 GLU cc_start: 0.8916 (mp0) cc_final: 0.8278 (mp0) REVERT: F 404 ASP cc_start: 0.9291 (t0) cc_final: 0.9040 (t70) REVERT: F 407 ARG cc_start: 0.8957 (ttt90) cc_final: 0.8448 (ttt-90) REVERT: G 21 GLN cc_start: 0.9181 (pt0) cc_final: 0.8739 (tm-30) REVERT: G 50 ASP cc_start: 0.9161 (t70) cc_final: 0.8937 (t0) REVERT: G 51 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8930 (pp) REVERT: G 78 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8084 (ptm) REVERT: G 109 LYS cc_start: 0.9381 (OUTLIER) cc_final: 0.8987 (tmtt) REVERT: G 258 TYR cc_start: 0.9145 (t80) cc_final: 0.8823 (t80) REVERT: G 279 ASN cc_start: 0.9003 (t0) cc_final: 0.8454 (t0) REVERT: G 332 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8679 (pp) REVERT: G 352 GLU cc_start: 0.9244 (tm-30) cc_final: 0.8987 (tm-30) REVERT: G 355 ARG cc_start: 0.9242 (ptm-80) cc_final: 0.8941 (ptm-80) REVERT: G 385 MET cc_start: 0.8986 (ttm) cc_final: 0.8549 (ttm) REVERT: G 395 GLU cc_start: 0.8750 (mp0) cc_final: 0.8241 (mp0) REVERT: G 399 GLU cc_start: 0.9169 (pm20) cc_final: 0.8909 (pm20) REVERT: G 400 TYR cc_start: 0.8302 (m-80) cc_final: 0.8041 (m-80) REVERT: G 510 GLU cc_start: 0.8305 (tp30) cc_final: 0.8047 (tp30) REVERT: H 25 ASN cc_start: 0.9086 (m-40) cc_final: 0.8779 (p0) REVERT: H 51 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8706 (pp) REVERT: H 256 ASP cc_start: 0.9260 (m-30) cc_final: 0.8766 (p0) REVERT: H 259 ARG cc_start: 0.9337 (ttm-80) cc_final: 0.9090 (ttm-80) REVERT: H 276 SER cc_start: 0.8931 (p) cc_final: 0.8533 (p) REVERT: H 285 ASN cc_start: 0.9275 (m-40) cc_final: 0.9068 (m-40) REVERT: H 332 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8815 (pp) REVERT: H 352 GLU cc_start: 0.9262 (tm-30) cc_final: 0.9035 (tm-30) REVERT: H 355 ARG cc_start: 0.9256 (ptm-80) cc_final: 0.8861 (ptm-80) REVERT: H 385 MET cc_start: 0.8860 (ttm) cc_final: 0.8454 (ttm) REVERT: H 395 GLU cc_start: 0.8906 (mp0) cc_final: 0.8280 (mp0) outliers start: 138 outliers final: 78 residues processed: 1042 average time/residue: 0.1487 time to fit residues: 245.7075 Evaluate side-chains 1016 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 920 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 407 ARG Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 282 PHE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 109 LYS Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 180 optimal weight: 0.8980 chunk 23 optimal weight: 0.0980 chunk 227 optimal weight: 4.9990 chunk 225 optimal weight: 0.9980 chunk 287 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 146 optimal weight: 0.9990 chunk 247 optimal weight: 0.6980 chunk 292 optimal weight: 0.6980 chunk 185 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN B 498 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 ASN ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 HIS ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.107061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.086811 restraints weight = 40569.369| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.82 r_work: 0.2835 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23488 Z= 0.149 Angle : 0.717 10.169 31792 Z= 0.362 Chirality : 0.047 0.197 3656 Planarity : 0.004 0.052 4000 Dihedral : 10.436 89.968 3735 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.37 % Allowed : 27.52 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.15), residues: 2960 helix: -1.17 (0.15), residues: 1144 sheet: -2.07 (0.26), residues: 320 loop : -1.06 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 105 TYR 0.026 0.001 TYR A 258 PHE 0.012 0.001 PHE C 401 HIS 0.005 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00355 (23480) covalent geometry : angle 0.71742 (31792) hydrogen bonds : bond 0.03433 ( 841) hydrogen bonds : angle 5.20744 ( 2427) Misc. bond : bond 0.00072 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1101 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 973 time to evaluate : 0.744 Fit side-chains REVERT: A 1 MET cc_start: 0.4501 (ptp) cc_final: 0.3956 (ptm) REVERT: A 21 GLN cc_start: 0.9096 (pt0) cc_final: 0.8688 (tm-30) REVERT: A 25 ASN cc_start: 0.9183 (m-40) cc_final: 0.8805 (m-40) REVERT: A 51 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8742 (pp) REVERT: A 105 ARG cc_start: 0.9157 (mtm110) cc_final: 0.8855 (mtm110) REVERT: A 109 LYS cc_start: 0.9442 (mttp) cc_final: 0.9097 (mptt) REVERT: A 274 ASP cc_start: 0.9183 (t0) cc_final: 0.8934 (t0) REVERT: A 276 SER cc_start: 0.8969 (p) cc_final: 0.8567 (p) REVERT: A 352 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8961 (tm-30) REVERT: A 355 ARG cc_start: 0.9181 (ptm-80) cc_final: 0.8883 (ptm-80) REVERT: A 385 MET cc_start: 0.8902 (ttm) cc_final: 0.8532 (ttm) REVERT: A 395 GLU cc_start: 0.8960 (mp0) cc_final: 0.8356 (mp0) REVERT: A 399 GLU cc_start: 0.9094 (pm20) cc_final: 0.8851 (pm20) REVERT: A 404 ASP cc_start: 0.9289 (t0) cc_final: 0.9082 (t0) REVERT: A 409 LYS cc_start: 0.8767 (ttmp) cc_final: 0.8318 (tttt) REVERT: A 438 LYS cc_start: 0.9128 (mttt) cc_final: 0.8586 (mmtt) REVERT: B 21 GLN cc_start: 0.9118 (pt0) cc_final: 0.8577 (tm-30) REVERT: B 50 ASP cc_start: 0.9053 (t70) cc_final: 0.8797 (t0) REVERT: B 51 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.8973 (pp) REVERT: B 105 ARG cc_start: 0.9176 (mtm110) cc_final: 0.8857 (mtm110) REVERT: B 276 SER cc_start: 0.8885 (p) cc_final: 0.8648 (p) REVERT: B 332 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8325 (pp) REVERT: B 335 GLU cc_start: 0.8583 (tm-30) cc_final: 0.7819 (tm-30) REVERT: B 352 GLU cc_start: 0.9211 (tm-30) cc_final: 0.8984 (tm-30) REVERT: B 355 ARG cc_start: 0.9174 (ptm-80) cc_final: 0.8887 (ptm-80) REVERT: B 395 GLU cc_start: 0.8967 (mp0) cc_final: 0.8354 (mp0) REVERT: B 404 ASP cc_start: 0.9281 (t0) cc_final: 0.9039 (t70) REVERT: B 407 ARG cc_start: 0.9043 (ttt90) cc_final: 0.8833 (ttt90) REVERT: B 438 LYS cc_start: 0.9079 (mttt) cc_final: 0.8581 (mmtm) REVERT: C 21 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8278 (tm-30) REVERT: C 50 ASP cc_start: 0.9192 (t70) cc_final: 0.8965 (t0) REVERT: C 51 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8949 (pp) REVERT: C 66 VAL cc_start: 0.7637 (OUTLIER) cc_final: 0.6664 (t) REVERT: C 109 LYS cc_start: 0.9596 (mmmt) cc_final: 0.9033 (tptt) REVERT: C 258 TYR cc_start: 0.9088 (t80) cc_final: 0.8797 (t80) REVERT: C 276 SER cc_start: 0.8629 (p) cc_final: 0.8323 (p) REVERT: C 279 ASN cc_start: 0.9265 (t0) cc_final: 0.8972 (t0) REVERT: C 332 ILE cc_start: 0.8972 (OUTLIER) cc_final: 0.8494 (pp) REVERT: C 335 GLU cc_start: 0.8511 (tm-30) cc_final: 0.7772 (tm-30) REVERT: C 362 ILE cc_start: 0.8094 (mt) cc_final: 0.7885 (mt) REVERT: C 385 MET cc_start: 0.8843 (ttm) cc_final: 0.8473 (ttm) REVERT: C 395 GLU cc_start: 0.8956 (mp0) cc_final: 0.8262 (mp0) REVERT: C 400 TYR cc_start: 0.8403 (m-10) cc_final: 0.7375 (m-10) REVERT: C 407 ARG cc_start: 0.8985 (ttt90) cc_final: 0.8445 (ttt-90) REVERT: C 438 LYS cc_start: 0.9099 (mttt) cc_final: 0.8595 (mmtt) REVERT: C 510 GLU cc_start: 0.8207 (tp30) cc_final: 0.7927 (tp30) REVERT: D 21 GLN cc_start: 0.9114 (pt0) cc_final: 0.8658 (tm-30) REVERT: D 25 ASN cc_start: 0.9223 (m-40) cc_final: 0.8909 (p0) REVERT: D 50 ASP cc_start: 0.9137 (t70) cc_final: 0.8893 (t0) REVERT: D 51 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8732 (pp) REVERT: D 105 ARG cc_start: 0.9264 (mtm110) cc_final: 0.8921 (mtm110) REVERT: D 258 TYR cc_start: 0.9194 (t80) cc_final: 0.8917 (t80) REVERT: D 276 SER cc_start: 0.8792 (p) cc_final: 0.8512 (p) REVERT: D 279 ASN cc_start: 0.8997 (m-40) cc_final: 0.8757 (m110) REVERT: D 285 ASN cc_start: 0.9294 (m-40) cc_final: 0.9069 (m-40) REVERT: D 332 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8761 (pp) REVERT: D 352 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8774 (tm-30) REVERT: D 395 GLU cc_start: 0.8972 (mp0) cc_final: 0.8359 (mp0) REVERT: D 400 TYR cc_start: 0.8461 (m-10) cc_final: 0.7442 (m-10) REVERT: D 407 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8361 (ttt-90) REVERT: E 21 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8712 (tm-30) REVERT: E 51 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8785 (pp) REVERT: E 109 LYS cc_start: 0.9628 (mmmt) cc_final: 0.8992 (tptt) REVERT: E 258 TYR cc_start: 0.9224 (t80) cc_final: 0.8967 (t80) REVERT: E 259 ARG cc_start: 0.9299 (ttm-80) cc_final: 0.8853 (ttm170) REVERT: E 276 SER cc_start: 0.8942 (p) cc_final: 0.8549 (p) REVERT: E 285 ASN cc_start: 0.9489 (m-40) cc_final: 0.9179 (m-40) REVERT: E 352 GLU cc_start: 0.9233 (tm-30) cc_final: 0.8987 (tm-30) REVERT: E 355 ARG cc_start: 0.9214 (ptm-80) cc_final: 0.8788 (ptm-80) REVERT: E 395 GLU cc_start: 0.8916 (mp0) cc_final: 0.8258 (mp0) REVERT: E 400 TYR cc_start: 0.8377 (m-10) cc_final: 0.8004 (m-10) REVERT: E 510 GLU cc_start: 0.8300 (tp30) cc_final: 0.8053 (tp30) REVERT: F 21 GLN cc_start: 0.9104 (pt0) cc_final: 0.8780 (tm-30) REVERT: F 51 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8755 (pp) REVERT: F 108 LYS cc_start: 0.9279 (tppt) cc_final: 0.9022 (mmtp) REVERT: F 109 LYS cc_start: 0.9437 (mptt) cc_final: 0.9168 (mttt) REVERT: F 258 TYR cc_start: 0.9213 (t80) cc_final: 0.8925 (t80) REVERT: F 276 SER cc_start: 0.8511 (p) cc_final: 0.8178 (p) REVERT: F 279 ASN cc_start: 0.8866 (t0) cc_final: 0.8269 (t0) REVERT: F 332 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8525 (pp) REVERT: F 352 GLU cc_start: 0.9244 (tm-30) cc_final: 0.8997 (tm-30) REVERT: F 355 ARG cc_start: 0.9271 (ptm-80) cc_final: 0.8896 (ptm-80) REVERT: F 385 MET cc_start: 0.8941 (ttm) cc_final: 0.8468 (ttm) REVERT: F 393 THR cc_start: 0.9223 (p) cc_final: 0.8503 (p) REVERT: F 395 GLU cc_start: 0.8873 (mp0) cc_final: 0.8286 (mp0) REVERT: F 404 ASP cc_start: 0.9291 (t0) cc_final: 0.9051 (t70) REVERT: F 407 ARG cc_start: 0.8959 (ttt90) cc_final: 0.8437 (ttt-90) REVERT: G 21 GLN cc_start: 0.9177 (pt0) cc_final: 0.8790 (tm-30) REVERT: G 50 ASP cc_start: 0.9172 (t70) cc_final: 0.8970 (t0) REVERT: G 51 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8748 (pp) REVERT: G 78 MET cc_start: 0.8437 (OUTLIER) cc_final: 0.8142 (ptm) REVERT: G 105 ARG cc_start: 0.8982 (mtm110) cc_final: 0.8560 (mtm110) REVERT: G 109 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9148 (mttt) REVERT: G 279 ASN cc_start: 0.8948 (t0) cc_final: 0.8429 (t0) REVERT: G 332 ILE cc_start: 0.8946 (OUTLIER) cc_final: 0.8389 (pp) REVERT: G 335 GLU cc_start: 0.8559 (tm-30) cc_final: 0.7814 (tm-30) REVERT: G 352 GLU cc_start: 0.9244 (tm-30) cc_final: 0.9016 (tm-30) REVERT: G 385 MET cc_start: 0.9027 (ttm) cc_final: 0.8570 (ttm) REVERT: G 395 GLU cc_start: 0.8760 (mp0) cc_final: 0.8247 (mp0) REVERT: G 399 GLU cc_start: 0.9177 (pm20) cc_final: 0.8948 (pm20) REVERT: G 400 TYR cc_start: 0.8324 (m-80) cc_final: 0.8091 (m-80) REVERT: G 510 GLU cc_start: 0.8366 (tp30) cc_final: 0.7928 (tp30) REVERT: H 21 GLN cc_start: 0.9119 (pt0) cc_final: 0.8791 (tm-30) REVERT: H 25 ASN cc_start: 0.9104 (m-40) cc_final: 0.8640 (p0) REVERT: H 51 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8819 (pp) REVERT: H 105 ARG cc_start: 0.9179 (mtm110) cc_final: 0.8915 (mtm110) REVERT: H 109 LYS cc_start: 0.9459 (mttt) cc_final: 0.9081 (mttm) REVERT: H 256 ASP cc_start: 0.9258 (m-30) cc_final: 0.8777 (p0) REVERT: H 259 ARG cc_start: 0.9357 (ttm-80) cc_final: 0.9118 (ttm-80) REVERT: H 275 SER cc_start: 0.8988 (t) cc_final: 0.8782 (t) REVERT: H 276 SER cc_start: 0.8885 (p) cc_final: 0.8518 (p) REVERT: H 285 ASN cc_start: 0.9261 (m-40) cc_final: 0.9030 (m-40) REVERT: H 325 MET cc_start: 0.8568 (ptm) cc_final: 0.8246 (ptt) REVERT: H 332 ILE cc_start: 0.8987 (OUTLIER) cc_final: 0.8769 (pp) REVERT: H 352 GLU cc_start: 0.9271 (tm-30) cc_final: 0.9038 (tm-30) REVERT: H 355 ARG cc_start: 0.9218 (ptm-80) cc_final: 0.8838 (ptm-80) REVERT: H 385 MET cc_start: 0.8904 (ttm) cc_final: 0.8609 (ttm) REVERT: H 395 GLU cc_start: 0.8898 (mp0) cc_final: 0.8352 (mp0) outliers start: 128 outliers final: 83 residues processed: 1032 average time/residue: 0.1446 time to fit residues: 238.5615 Evaluate side-chains 1024 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 922 time to evaluate : 0.761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 407 ARG Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 282 PHE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 282 PHE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 109 LYS Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 282 PHE Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 510 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 0 optimal weight: 6.9990 chunk 192 optimal weight: 0.8980 chunk 239 optimal weight: 1.9990 chunk 262 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 253 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 225 optimal weight: 0.5980 chunk 200 optimal weight: 3.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 HIS H 309 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.107359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.086627 restraints weight = 40951.443| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.90 r_work: 0.2832 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23488 Z= 0.161 Angle : 0.734 9.692 31792 Z= 0.369 Chirality : 0.047 0.200 3656 Planarity : 0.004 0.063 4000 Dihedral : 10.305 89.426 3735 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 5.29 % Allowed : 28.40 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.15), residues: 2960 helix: -1.12 (0.15), residues: 1144 sheet: -2.03 (0.27), residues: 320 loop : -1.03 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 105 TYR 0.023 0.001 TYR A 258 PHE 0.012 0.001 PHE C 401 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00386 (23480) covalent geometry : angle 0.73370 (31792) hydrogen bonds : bond 0.03467 ( 841) hydrogen bonds : angle 5.19149 ( 2427) Misc. bond : bond 0.00092 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 960 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4518 (ptp) cc_final: 0.3973 (ptm) REVERT: A 21 GLN cc_start: 0.9105 (pt0) cc_final: 0.8733 (tm-30) REVERT: A 25 ASN cc_start: 0.9175 (m-40) cc_final: 0.8818 (m-40) REVERT: A 51 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8985 (pp) REVERT: A 105 ARG cc_start: 0.9110 (mtm110) cc_final: 0.8541 (mtm110) REVERT: A 274 ASP cc_start: 0.9240 (t0) cc_final: 0.8973 (t0) REVERT: A 279 ASN cc_start: 0.8480 (m-40) cc_final: 0.8279 (m-40) REVERT: A 303 ASN cc_start: 0.9333 (m-40) cc_final: 0.9071 (m-40) REVERT: A 352 GLU cc_start: 0.9200 (tm-30) cc_final: 0.8964 (tm-30) REVERT: A 355 ARG cc_start: 0.9195 (ptm-80) cc_final: 0.8901 (ptm-80) REVERT: A 385 MET cc_start: 0.8943 (ttm) cc_final: 0.8553 (ttm) REVERT: A 395 GLU cc_start: 0.8988 (mp0) cc_final: 0.8310 (mp0) REVERT: A 409 LYS cc_start: 0.8795 (ttmp) cc_final: 0.8460 (tttt) REVERT: A 438 LYS cc_start: 0.9137 (mttt) cc_final: 0.8602 (mmtt) REVERT: B 21 GLN cc_start: 0.9140 (pt0) cc_final: 0.8849 (tm-30) REVERT: B 25 ASN cc_start: 0.9141 (m-40) cc_final: 0.8533 (p0) REVERT: B 50 ASP cc_start: 0.9057 (t70) cc_final: 0.8829 (t0) REVERT: B 51 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8907 (pp) REVERT: B 276 SER cc_start: 0.8968 (p) cc_final: 0.8682 (p) REVERT: B 332 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8305 (pp) REVERT: B 335 GLU cc_start: 0.8570 (tm-30) cc_final: 0.7802 (tm-30) REVERT: B 352 GLU cc_start: 0.9223 (tm-30) cc_final: 0.8994 (tm-30) REVERT: B 355 ARG cc_start: 0.9180 (ptm-80) cc_final: 0.8893 (ptm-80) REVERT: B 369 ASN cc_start: 0.8440 (p0) cc_final: 0.8084 (p0) REVERT: B 395 GLU cc_start: 0.8919 (mp0) cc_final: 0.8414 (mp0) REVERT: B 400 TYR cc_start: 0.8404 (m-10) cc_final: 0.8126 (m-10) REVERT: B 404 ASP cc_start: 0.9290 (t0) cc_final: 0.9044 (t70) REVERT: B 407 ARG cc_start: 0.9059 (ttt90) cc_final: 0.8820 (ttt90) REVERT: B 438 LYS cc_start: 0.9069 (mttt) cc_final: 0.8656 (mmtt) REVERT: B 510 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8035 (tp30) REVERT: C 21 GLN cc_start: 0.8866 (tm-30) cc_final: 0.8234 (tm-30) REVERT: C 50 ASP cc_start: 0.9218 (t70) cc_final: 0.8988 (t0) REVERT: C 51 LEU cc_start: 0.9079 (OUTLIER) cc_final: 0.8763 (pp) REVERT: C 66 VAL cc_start: 0.7502 (OUTLIER) cc_final: 0.6545 (t) REVERT: C 109 LYS cc_start: 0.9588 (mmmt) cc_final: 0.9044 (tptt) REVERT: C 258 TYR cc_start: 0.9093 (t80) cc_final: 0.8777 (t80) REVERT: C 276 SER cc_start: 0.8637 (p) cc_final: 0.8314 (p) REVERT: C 279 ASN cc_start: 0.9259 (t0) cc_final: 0.8956 (t0) REVERT: C 335 GLU cc_start: 0.8521 (tm-30) cc_final: 0.7767 (tm-30) REVERT: C 362 ILE cc_start: 0.8134 (mt) cc_final: 0.7928 (mt) REVERT: C 385 MET cc_start: 0.8856 (ttm) cc_final: 0.8497 (ttm) REVERT: C 395 GLU cc_start: 0.8847 (mp0) cc_final: 0.8401 (mp0) REVERT: C 400 TYR cc_start: 0.8360 (m-10) cc_final: 0.8124 (m-10) REVERT: C 407 ARG cc_start: 0.9076 (ttt90) cc_final: 0.8797 (ttt-90) REVERT: C 438 LYS cc_start: 0.9118 (mttt) cc_final: 0.8643 (mptt) REVERT: C 510 GLU cc_start: 0.8181 (tp30) cc_final: 0.7904 (tp30) REVERT: D 21 GLN cc_start: 0.9154 (pt0) cc_final: 0.8686 (tm-30) REVERT: D 25 ASN cc_start: 0.9222 (m-40) cc_final: 0.8903 (p0) REVERT: D 51 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8783 (pp) REVERT: D 70 MET cc_start: 0.9100 (mtm) cc_final: 0.8770 (mpp) REVERT: D 84 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8189 (mm) REVERT: D 258 TYR cc_start: 0.9189 (t80) cc_final: 0.8912 (t80) REVERT: D 276 SER cc_start: 0.8832 (p) cc_final: 0.8541 (p) REVERT: D 285 ASN cc_start: 0.9285 (m-40) cc_final: 0.9029 (m-40) REVERT: D 332 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8756 (pp) REVERT: D 352 GLU cc_start: 0.9203 (tm-30) cc_final: 0.8781 (tm-30) REVERT: D 393 THR cc_start: 0.9263 (p) cc_final: 0.8489 (p) REVERT: D 395 GLU cc_start: 0.8982 (mp0) cc_final: 0.8262 (mp0) REVERT: D 400 TYR cc_start: 0.8524 (m-10) cc_final: 0.7486 (m-10) REVERT: D 407 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8333 (ttt-90) REVERT: E 21 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8613 (tm-30) REVERT: E 51 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8802 (pp) REVERT: E 105 ARG cc_start: 0.9229 (ttp80) cc_final: 0.9007 (ttp-110) REVERT: E 109 LYS cc_start: 0.9679 (mmmt) cc_final: 0.9007 (tptt) REVERT: E 258 TYR cc_start: 0.9225 (t80) cc_final: 0.8943 (t80) REVERT: E 276 SER cc_start: 0.8957 (p) cc_final: 0.8565 (p) REVERT: E 285 ASN cc_start: 0.9527 (m-40) cc_final: 0.9309 (m-40) REVERT: E 352 GLU cc_start: 0.9227 (tm-30) cc_final: 0.8978 (tm-30) REVERT: E 355 ARG cc_start: 0.9233 (ptm-80) cc_final: 0.8814 (ptm-80) REVERT: E 395 GLU cc_start: 0.8856 (mp0) cc_final: 0.8418 (mp0) REVERT: E 400 TYR cc_start: 0.8098 (m-10) cc_final: 0.7477 (m-10) REVERT: E 407 ARG cc_start: 0.9161 (ttt90) cc_final: 0.8780 (ttt-90) REVERT: E 510 GLU cc_start: 0.8300 (tp30) cc_final: 0.8050 (tp30) REVERT: F 21 GLN cc_start: 0.9119 (pt0) cc_final: 0.8800 (tm-30) REVERT: F 51 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8818 (pp) REVERT: F 108 LYS cc_start: 0.9325 (tppt) cc_final: 0.9066 (mmtp) REVERT: F 258 TYR cc_start: 0.9198 (t80) cc_final: 0.8976 (t80) REVERT: F 276 SER cc_start: 0.8574 (p) cc_final: 0.8247 (p) REVERT: F 279 ASN cc_start: 0.8881 (t0) cc_final: 0.8245 (t0) REVERT: F 332 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8580 (pp) REVERT: F 352 GLU cc_start: 0.9241 (tm-30) cc_final: 0.8995 (tm-30) REVERT: F 355 ARG cc_start: 0.9274 (ptm-80) cc_final: 0.8927 (ptm-80) REVERT: F 385 MET cc_start: 0.8914 (ttm) cc_final: 0.8441 (ttm) REVERT: F 393 THR cc_start: 0.9199 (p) cc_final: 0.8497 (p) REVERT: F 395 GLU cc_start: 0.8888 (mp0) cc_final: 0.8360 (mp0) REVERT: F 404 ASP cc_start: 0.9283 (t0) cc_final: 0.9039 (t70) REVERT: G 21 GLN cc_start: 0.9175 (pt0) cc_final: 0.8792 (tm-30) REVERT: G 50 ASP cc_start: 0.9141 (t70) cc_final: 0.8914 (t0) REVERT: G 51 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8930 (pp) REVERT: G 105 ARG cc_start: 0.9029 (mtm110) cc_final: 0.8599 (mtm110) REVERT: G 109 LYS cc_start: 0.9354 (OUTLIER) cc_final: 0.8916 (tmtt) REVERT: G 258 TYR cc_start: 0.9150 (t80) cc_final: 0.8843 (t80) REVERT: G 279 ASN cc_start: 0.8903 (t0) cc_final: 0.8334 (t0) REVERT: G 332 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8380 (pp) REVERT: G 335 GLU cc_start: 0.8561 (tm-30) cc_final: 0.7818 (tm-30) REVERT: G 352 GLU cc_start: 0.9253 (tm-30) cc_final: 0.9024 (tm-30) REVERT: G 355 ARG cc_start: 0.9245 (ptm-80) cc_final: 0.8878 (ptm-80) REVERT: G 385 MET cc_start: 0.8975 (ttm) cc_final: 0.8554 (ttm) REVERT: G 395 GLU cc_start: 0.8780 (mp0) cc_final: 0.8279 (mp0) REVERT: G 399 GLU cc_start: 0.9185 (pm20) cc_final: 0.8970 (pm20) REVERT: G 400 TYR cc_start: 0.8351 (m-80) cc_final: 0.6936 (m-80) REVERT: G 407 ARG cc_start: 0.9142 (ttt-90) cc_final: 0.8221 (ttt-90) REVERT: G 510 GLU cc_start: 0.8313 (tp30) cc_final: 0.7853 (tp30) REVERT: H 21 GLN cc_start: 0.9132 (pt0) cc_final: 0.8806 (tm-30) REVERT: H 25 ASN cc_start: 0.9128 (m-40) cc_final: 0.8669 (p0) REVERT: H 51 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8843 (pp) REVERT: H 84 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8115 (mm) REVERT: H 109 LYS cc_start: 0.9498 (mttt) cc_final: 0.9212 (mttt) REVERT: H 256 ASP cc_start: 0.9234 (m-30) cc_final: 0.8716 (p0) REVERT: H 259 ARG cc_start: 0.9342 (ttm-80) cc_final: 0.9117 (ttm-80) REVERT: H 285 ASN cc_start: 0.9282 (m-40) cc_final: 0.9018 (m-40) REVERT: H 332 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8459 (pp) REVERT: H 335 GLU cc_start: 0.8564 (tm-30) cc_final: 0.7838 (tm-30) REVERT: H 352 GLU cc_start: 0.9268 (tm-30) cc_final: 0.9040 (tm-30) REVERT: H 355 ARG cc_start: 0.9224 (ptm-80) cc_final: 0.8863 (ptm-80) REVERT: H 385 MET cc_start: 0.8866 (ttm) cc_final: 0.8512 (ttm) REVERT: H 395 GLU cc_start: 0.8942 (mp0) cc_final: 0.8472 (mp0) outliers start: 126 outliers final: 87 residues processed: 1024 average time/residue: 0.1467 time to fit residues: 238.6239 Evaluate side-chains 1041 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 934 time to evaluate : 0.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 407 ARG Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 282 PHE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 109 LYS Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 510 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 168 optimal weight: 3.9990 chunk 218 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 283 optimal weight: 0.7980 chunk 165 optimal weight: 0.8980 chunk 141 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 128 optimal weight: 0.0970 chunk 145 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 ASN ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.107670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.087138 restraints weight = 41032.454| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 3.88 r_work: 0.2843 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23488 Z= 0.161 Angle : 0.761 10.175 31792 Z= 0.381 Chirality : 0.047 0.191 3656 Planarity : 0.004 0.062 4000 Dihedral : 10.164 89.873 3734 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.53 % Allowed : 29.36 % Favored : 66.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.15), residues: 2960 helix: -1.06 (0.15), residues: 1144 sheet: -2.01 (0.27), residues: 320 loop : -1.05 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 105 TYR 0.018 0.001 TYR H 258 PHE 0.011 0.001 PHE C 401 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00387 (23480) covalent geometry : angle 0.76096 (31792) hydrogen bonds : bond 0.03433 ( 841) hydrogen bonds : angle 5.20721 ( 2427) Misc. bond : bond 0.00084 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 961 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4679 (ptp) cc_final: 0.4131 (ptm) REVERT: A 21 GLN cc_start: 0.9110 (pt0) cc_final: 0.8737 (tm-30) REVERT: A 25 ASN cc_start: 0.9181 (m-40) cc_final: 0.8813 (m-40) REVERT: A 51 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8992 (pp) REVERT: A 109 LYS cc_start: 0.9618 (mmmt) cc_final: 0.9019 (tptt) REVERT: A 274 ASP cc_start: 0.9230 (t0) cc_final: 0.8979 (t0) REVERT: A 279 ASN cc_start: 0.8674 (m-40) cc_final: 0.8436 (m-40) REVERT: A 303 ASN cc_start: 0.9355 (m-40) cc_final: 0.9118 (m-40) REVERT: A 352 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8973 (tm-30) REVERT: A 355 ARG cc_start: 0.9209 (ptm-80) cc_final: 0.8755 (ptm-80) REVERT: A 385 MET cc_start: 0.8914 (ttm) cc_final: 0.8535 (ttm) REVERT: A 395 GLU cc_start: 0.8957 (mp0) cc_final: 0.8413 (mp0) REVERT: A 409 LYS cc_start: 0.8828 (ttmp) cc_final: 0.8589 (ttmt) REVERT: A 438 LYS cc_start: 0.9120 (mttt) cc_final: 0.8614 (mmtt) REVERT: B 21 GLN cc_start: 0.9137 (pt0) cc_final: 0.8860 (tm-30) REVERT: B 25 ASN cc_start: 0.9151 (m-40) cc_final: 0.8545 (p0) REVERT: B 51 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8758 (pp) REVERT: B 105 ARG cc_start: 0.9169 (mtm110) cc_final: 0.8721 (mtm110) REVERT: B 276 SER cc_start: 0.8971 (p) cc_final: 0.8677 (p) REVERT: B 332 ILE cc_start: 0.8864 (OUTLIER) cc_final: 0.8298 (pp) REVERT: B 335 GLU cc_start: 0.8557 (tm-30) cc_final: 0.7802 (tm-30) REVERT: B 352 GLU cc_start: 0.9217 (tm-30) cc_final: 0.8996 (tm-30) REVERT: B 355 ARG cc_start: 0.9173 (ptm-80) cc_final: 0.8913 (ptm-80) REVERT: B 369 ASN cc_start: 0.8398 (p0) cc_final: 0.8098 (p0) REVERT: B 395 GLU cc_start: 0.8935 (mp0) cc_final: 0.8352 (mp0) REVERT: B 404 ASP cc_start: 0.9287 (t0) cc_final: 0.9028 (t70) REVERT: B 438 LYS cc_start: 0.9068 (mttt) cc_final: 0.8670 (mmtt) REVERT: B 510 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8032 (tp30) REVERT: C 21 GLN cc_start: 0.8821 (tm-30) cc_final: 0.8252 (tm-30) REVERT: C 50 ASP cc_start: 0.9239 (t70) cc_final: 0.9008 (t0) REVERT: C 51 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8901 (pp) REVERT: C 66 VAL cc_start: 0.7469 (OUTLIER) cc_final: 0.6568 (t) REVERT: C 109 LYS cc_start: 0.9603 (mmmt) cc_final: 0.9040 (tptt) REVERT: C 258 TYR cc_start: 0.9092 (t80) cc_final: 0.8779 (t80) REVERT: C 276 SER cc_start: 0.8636 (p) cc_final: 0.8313 (p) REVERT: C 279 ASN cc_start: 0.9254 (t0) cc_final: 0.8948 (t0) REVERT: C 335 GLU cc_start: 0.8545 (tm-30) cc_final: 0.7779 (tm-30) REVERT: C 362 ILE cc_start: 0.8108 (mt) cc_final: 0.7892 (mt) REVERT: C 385 MET cc_start: 0.8791 (ttm) cc_final: 0.8465 (ttm) REVERT: C 395 GLU cc_start: 0.8887 (mp0) cc_final: 0.8443 (mp0) REVERT: C 400 TYR cc_start: 0.8386 (m-10) cc_final: 0.7340 (m-10) REVERT: C 407 ARG cc_start: 0.9083 (ttt90) cc_final: 0.8557 (ttt-90) REVERT: C 438 LYS cc_start: 0.9144 (mttt) cc_final: 0.8669 (mptt) REVERT: C 510 GLU cc_start: 0.8176 (tp30) cc_final: 0.7898 (tp30) REVERT: D 21 GLN cc_start: 0.9159 (pt0) cc_final: 0.8704 (tm-30) REVERT: D 25 ASN cc_start: 0.9220 (m-40) cc_final: 0.8935 (p0) REVERT: D 51 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8616 (pp) REVERT: D 70 MET cc_start: 0.9094 (mtm) cc_final: 0.8761 (mpp) REVERT: D 105 ARG cc_start: 0.9228 (mtm110) cc_final: 0.8820 (mtm110) REVERT: D 244 LEU cc_start: 0.8761 (mt) cc_final: 0.8454 (mt) REVERT: D 258 TYR cc_start: 0.9180 (t80) cc_final: 0.8905 (t80) REVERT: D 276 SER cc_start: 0.8860 (p) cc_final: 0.8571 (p) REVERT: D 332 ILE cc_start: 0.8969 (OUTLIER) cc_final: 0.8743 (pp) REVERT: D 352 GLU cc_start: 0.9196 (tm-30) cc_final: 0.8777 (tm-30) REVERT: D 393 THR cc_start: 0.9246 (p) cc_final: 0.8487 (p) REVERT: D 395 GLU cc_start: 0.8952 (mp0) cc_final: 0.8297 (mp0) REVERT: D 400 TYR cc_start: 0.8458 (m-10) cc_final: 0.8094 (m-10) REVERT: D 407 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8541 (ttt-90) REVERT: E 21 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8531 (tm-30) REVERT: E 25 ASN cc_start: 0.9331 (m-40) cc_final: 0.8827 (m-40) REVERT: E 51 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8806 (pp) REVERT: E 105 ARG cc_start: 0.9210 (ttp80) cc_final: 0.8999 (ttp80) REVERT: E 109 LYS cc_start: 0.9661 (mmmt) cc_final: 0.9017 (tptt) REVERT: E 258 TYR cc_start: 0.9222 (t80) cc_final: 0.8955 (t80) REVERT: E 352 GLU cc_start: 0.9226 (tm-30) cc_final: 0.8984 (tm-30) REVERT: E 355 ARG cc_start: 0.9227 (ptm-80) cc_final: 0.8811 (ptm-80) REVERT: E 395 GLU cc_start: 0.8872 (mp0) cc_final: 0.8403 (mp0) REVERT: E 407 ARG cc_start: 0.9197 (ttt90) cc_final: 0.8994 (ttt90) REVERT: E 510 GLU cc_start: 0.8303 (tp30) cc_final: 0.8067 (tp30) REVERT: F 21 GLN cc_start: 0.9139 (pt0) cc_final: 0.8803 (tm-30) REVERT: F 51 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8784 (pp) REVERT: F 108 LYS cc_start: 0.9430 (tppt) cc_final: 0.9129 (tmtt) REVERT: F 109 LYS cc_start: 0.9514 (mptt) cc_final: 0.9205 (mttt) REVERT: F 244 LEU cc_start: 0.8879 (mt) cc_final: 0.8627 (mt) REVERT: F 276 SER cc_start: 0.8567 (p) cc_final: 0.8241 (p) REVERT: F 279 ASN cc_start: 0.8843 (t0) cc_final: 0.8218 (t0) REVERT: F 332 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8591 (pp) REVERT: F 352 GLU cc_start: 0.9250 (tm-30) cc_final: 0.9004 (tm-30) REVERT: F 355 ARG cc_start: 0.9263 (ptm-80) cc_final: 0.8921 (ptm-80) REVERT: F 385 MET cc_start: 0.8907 (ttm) cc_final: 0.8393 (ttm) REVERT: F 393 THR cc_start: 0.9170 (p) cc_final: 0.8478 (p) REVERT: F 395 GLU cc_start: 0.8898 (mp0) cc_final: 0.8364 (mp0) REVERT: F 404 ASP cc_start: 0.9294 (t0) cc_final: 0.9028 (t70) REVERT: F 406 ILE cc_start: 0.8967 (mp) cc_final: 0.8658 (mp) REVERT: G 21 GLN cc_start: 0.9169 (pt0) cc_final: 0.8811 (tm-30) REVERT: G 50 ASP cc_start: 0.9171 (t70) cc_final: 0.8954 (t0) REVERT: G 51 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8746 (pp) REVERT: G 105 ARG cc_start: 0.9003 (mtm110) cc_final: 0.8583 (mtm110) REVERT: G 109 LYS cc_start: 0.9347 (OUTLIER) cc_final: 0.8914 (tmtt) REVERT: G 258 TYR cc_start: 0.9157 (t80) cc_final: 0.8859 (t80) REVERT: G 279 ASN cc_start: 0.8922 (t0) cc_final: 0.8373 (t0) REVERT: G 332 ILE cc_start: 0.8932 (OUTLIER) cc_final: 0.8384 (pp) REVERT: G 335 GLU cc_start: 0.8568 (tm-30) cc_final: 0.7833 (tm-30) REVERT: G 385 MET cc_start: 0.8958 (ttm) cc_final: 0.8556 (ttm) REVERT: G 395 GLU cc_start: 0.8781 (mp0) cc_final: 0.8302 (mp0) REVERT: G 399 GLU cc_start: 0.9200 (pm20) cc_final: 0.8983 (pm20) REVERT: G 400 TYR cc_start: 0.8350 (m-80) cc_final: 0.6997 (m-80) REVERT: G 407 ARG cc_start: 0.9146 (ttt-90) cc_final: 0.8228 (ttt-90) REVERT: G 438 LYS cc_start: 0.7953 (mmtt) cc_final: 0.7617 (mmtt) REVERT: G 510 GLU cc_start: 0.8279 (tp30) cc_final: 0.7826 (tp30) REVERT: H 21 GLN cc_start: 0.9132 (pt0) cc_final: 0.8832 (tm-30) REVERT: H 25 ASN cc_start: 0.9132 (m-40) cc_final: 0.8550 (p0) REVERT: H 51 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8849 (pp) REVERT: H 70 MET cc_start: 0.8940 (mpp) cc_final: 0.8679 (mpp) REVERT: H 84 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8108 (mm) REVERT: H 105 ARG cc_start: 0.9178 (mtm110) cc_final: 0.8784 (mtm110) REVERT: H 109 LYS cc_start: 0.9457 (mttt) cc_final: 0.9165 (mttt) REVERT: H 285 ASN cc_start: 0.9268 (m-40) cc_final: 0.8951 (m110) REVERT: H 332 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8463 (pp) REVERT: H 335 GLU cc_start: 0.8518 (tm-30) cc_final: 0.7802 (tm-30) REVERT: H 352 GLU cc_start: 0.9246 (tm-30) cc_final: 0.9020 (tm-30) REVERT: H 355 ARG cc_start: 0.9247 (ptm-80) cc_final: 0.8887 (ptm-80) REVERT: H 385 MET cc_start: 0.8899 (ttm) cc_final: 0.8553 (ttm) REVERT: H 395 GLU cc_start: 0.8931 (mp0) cc_final: 0.8401 (mp0) outliers start: 108 outliers final: 82 residues processed: 1009 average time/residue: 0.1460 time to fit residues: 233.8359 Evaluate side-chains 1045 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 944 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 499 VAL Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 407 ARG Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 282 PHE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 282 PHE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 109 LYS Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 510 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 99 optimal weight: 0.6980 chunk 80 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 256 optimal weight: 0.9980 chunk 179 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 170 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 285 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.107474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.087042 restraints weight = 40760.466| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 3.86 r_work: 0.2846 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23488 Z= 0.167 Angle : 0.771 10.701 31792 Z= 0.385 Chirality : 0.047 0.215 3656 Planarity : 0.004 0.066 4000 Dihedral : 10.050 88.383 3734 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.70 % Allowed : 29.70 % Favored : 65.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.15), residues: 2960 helix: -1.03 (0.15), residues: 1144 sheet: -2.00 (0.26), residues: 320 loop : -1.04 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 105 TYR 0.030 0.001 TYR A 258 PHE 0.011 0.001 PHE C 401 HIS 0.004 0.001 HIS C 92 Details of bonding type rmsd covalent geometry : bond 0.00401 (23480) covalent geometry : angle 0.77096 (31792) hydrogen bonds : bond 0.03421 ( 841) hydrogen bonds : angle 5.18098 ( 2427) Misc. bond : bond 0.00094 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6260.95 seconds wall clock time: 107 minutes 57.00 seconds (6477.00 seconds total)