Starting phenix.real_space_refine on Sun Sep 13 12:51:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6u8s_20691/09_2026/6u8s_20691.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u8s_20691/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6u8s_20691/09_2026/6u8s_20691.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6u8s_20691/09_2026/6u8s_20691.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u8s_20691/09_2026/6u8s_20691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u8s_20691/09_2026/6u8s_20691.map" model { file = "/net/cci-nas-00/data/ceres_data/6u8s_20691/09_2026/6u8s_20691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u8s_20691/09_2026/6u8s_20691.cif" } 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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 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: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 4.57, 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: 1.80 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: 0.57 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: 4.71 Time building geometry restraints manager: 2.47 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: 30726 3.27 - 6.54: 879 6.54 - 9.82: 115 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: 12812 17.68 - 35.36: 636 35.36 - 53.04: 296 53.04 - 70.72: 88 70.72 - 88.41: 16 Dihedral angle restraints: 13848 sinusoidal: 5344 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 13845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2747 0.071 - 0.142: 785 0.142 - 0.212: 92 0.212 - 0.283: 16 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: 0.09 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: 2.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 20.310 Find NCS groups from input model: 0.230 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 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= 0.594 Angle : 1.378 16.360 31792 Z= 0.681 Chirality : 0.067 0.354 3656 Planarity : 0.007 0.056 4000 Dihedral : 14.272 88.405 8456 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/Z covalent geometry : bond 0.01242 / 0.59 (23480) covalent geometry : angle 1.37789 / 0.68 (31792) hydrogen bonds : bond 0.20259 / 13.20 ( 841) hydrogen bonds : angle 8.62652 / 5.94 ( 2427) Misc. bond : bond 0.00121 / 0.06 ( 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 : 0.581 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: 0.1448 time to fit residues: 306.4445 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 : 0.806 ------------------------------------------------------------------------------- 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... A 22 GLN A 25 ASN A 48 GLN A 93 HIS A 243 GLN 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 243 GLN ** 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 G 48 GLN G 243 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: 52 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.108276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.087738 restraints weight = 41440.113| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 4.04 r_work: 0.2851 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2529 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= 0.165 Angle : 0.746 8.148 31792 Z= 0.370 Chirality : 0.048 0.162 3656 Planarity : 0.005 0.042 4000 Dihedral : 11.756 89.733 3525 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 7.01 % Allowed : 18.37 % Favored : 74.62 % 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: -3.20 (0.13), residues: 2960 helix: -2.25 (0.12), residues: 1120 sheet: -2.67 (0.18), residues: 464 loop : -1.63 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 407 TYR 0.019 0.002 TYR G 400 PHE 0.018 0.001 PHE E 401 HIS 0.003 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.17 (23480) covalent geometry : angle 0.74638 / 0.37 (31792) hydrogen bonds : bond 0.04115 / 2.70 ( 841) hydrogen bonds : angle 6.05861 / 4.14 ( 2427) Misc. bond : bond 0.00057 / 0.03 ( 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 1221 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 167 poor density : 1054 time to evaluate : 0.727 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: 0.8830 (m-30) cc_final: 0.8516 (m-30) REVERT: A 50 ASP cc_start: 0.9031 (t0) cc_final: 0.8796 (t0) REVERT: A 105 ARG cc_start: 0.9161 (mtm110) cc_final: 0.8927 (mtm110) REVERT: A 109 LYS cc_start: 0.9410 (mttp) cc_final: 0.8779 (tptt) REVERT: A 276 SER cc_start: 0.8764 (p) cc_final: 0.8513 (p) REVERT: A 285 ASN cc_start: 0.9443 (m-40) cc_final: 0.9071 (m-40) REVERT: A 352 GLU cc_start: 0.9161 (tm-30) cc_final: 0.8861 (tm-30) REVERT: A 395 GLU cc_start: 0.8769 (mp0) cc_final: 0.8155 (mp0) REVERT: A 399 GLU cc_start: 0.8982 (pm20) cc_final: 0.8709 (mp0) REVERT: A 404 ASP cc_start: 0.9120 (t0) cc_final: 0.8812 (t0) REVERT: A 512 ARG cc_start: 0.7786 (ttm-80) cc_final: 0.7503 (ptm160) REVERT: B 25 ASN cc_start: 0.9101 (m-40) cc_final: 0.8834 (p0) REVERT: B 28 ASP cc_start: 0.8870 (m-30) cc_final: 0.8540 (m-30) REVERT: B 50 ASP cc_start: 0.9044 (t70) cc_final: 0.8743 (t0) REVERT: B 58 LYS cc_start: 0.9450 (mmtp) cc_final: 0.9188 (mmmm) REVERT: B 66 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8237 (p) REVERT: B 105 ARG cc_start: 0.9199 (mtm110) cc_final: 0.8881 (mtm110) REVERT: B 109 LYS cc_start: 0.9417 (mttp) cc_final: 0.9029 (mttp) REVERT: B 276 SER cc_start: 0.8838 (p) cc_final: 0.8569 (p) REVERT: B 281 ILE cc_start: 0.8915 (tp) cc_final: 0.8577 (tt) REVERT: B 285 ASN cc_start: 0.9437 (m-40) cc_final: 0.9209 (m-40) REVERT: B 352 GLU cc_start: 0.9227 (tm-30) cc_final: 0.8961 (tm-30) REVERT: B 385 MET cc_start: 0.8907 (ttm) cc_final: 0.8425 (ttp) REVERT: B 395 GLU cc_start: 0.8860 (mp0) cc_final: 0.8365 (mp0) REVERT: B 399 GLU cc_start: 0.9056 (pm20) cc_final: 0.8822 (mp0) REVERT: B 400 TYR cc_start: 0.8420 (m-80) cc_final: 0.7510 (m-80) REVERT: B 404 ASP cc_start: 0.9148 (t0) cc_final: 0.8875 (t0) REVERT: B 407 ARG cc_start: 0.8787 (ttt-90) cc_final: 0.7741 (ttt-90) REVERT: B 449 ASP cc_start: 0.9272 (p0) cc_final: 0.9006 (p0) REVERT: B 461 ILE cc_start: 0.9156 (pp) cc_final: 0.8946 (pp) REVERT: B 512 ARG cc_start: 0.7801 (ttm-80) cc_final: 0.7531 (ptm160) REVERT: C 28 ASP cc_start: 0.8897 (m-30) cc_final: 0.8535 (m-30) REVERT: C 50 ASP cc_start: 0.9028 (t70) cc_final: 0.8717 (t0) REVERT: C 58 LYS cc_start: 0.9362 (mmtp) cc_final: 0.9097 (mmmm) REVERT: C 66 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8243 (p) REVERT: C 105 ARG cc_start: 0.9158 (mtm110) cc_final: 0.8893 (mtm110) REVERT: C 109 LYS cc_start: 0.9411 (mttp) cc_final: 0.9013 (mttp) REVERT: C 276 SER cc_start: 0.8710 (p) cc_final: 0.8427 (p) REVERT: C 285 ASN cc_start: 0.9469 (m-40) cc_final: 0.9162 (m-40) REVERT: C 322 ARG cc_start: 0.8270 (ppp80) cc_final: 0.7868 (ptm160) REVERT: C 352 GLU cc_start: 0.9121 (tm-30) cc_final: 0.8847 (tm-30) REVERT: C 385 MET cc_start: 0.8937 (ttm) cc_final: 0.8416 (ttp) REVERT: C 395 GLU cc_start: 0.8843 (mp0) cc_final: 0.8313 (mp0) REVERT: C 399 GLU cc_start: 0.8963 (pm20) cc_final: 0.8689 (mp0) REVERT: C 400 TYR cc_start: 0.8623 (m-80) cc_final: 0.7477 (m-10) REVERT: C 407 ARG cc_start: 0.8943 (ttt-90) cc_final: 0.7978 (ttt-90) REVERT: C 449 ASP cc_start: 0.9318 (p0) cc_final: 0.8905 (p0) REVERT: C 512 ARG cc_start: 0.7777 (ttm-80) cc_final: 0.7574 (ptm160) REVERT: D 1 MET cc_start: 0.6004 (ptp) cc_final: 0.5767 (ptp) REVERT: D 28 ASP cc_start: 0.8857 (m-30) cc_final: 0.8514 (m-30) REVERT: D 47 ASP cc_start: 0.9146 (p0) cc_final: 0.8885 (p0) REVERT: D 50 ASP cc_start: 0.9020 (t70) cc_final: 0.8716 (t0) REVERT: D 58 LYS cc_start: 0.9437 (mmtp) cc_final: 0.9179 (mmmm) REVERT: D 105 ARG cc_start: 0.9267 (mtm110) cc_final: 0.8757 (mtm110) REVERT: D 108 LYS cc_start: 0.9579 (OUTLIER) cc_final: 0.9322 (tppt) REVERT: D 258 TYR cc_start: 0.9209 (t80) cc_final: 0.8997 (t80) REVERT: D 275 SER cc_start: 0.9045 (t) cc_final: 0.8828 (t) REVERT: D 276 SER cc_start: 0.8717 (p) cc_final: 0.8512 (p) REVERT: D 285 ASN cc_start: 0.9441 (m-40) cc_final: 0.9069 (m-40) REVERT: D 312 ASN cc_start: 0.9059 (OUTLIER) cc_final: 0.8833 (t0) REVERT: D 352 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8841 (tm-30) REVERT: D 355 ARG cc_start: 0.9601 (ptm-80) cc_final: 0.9286 (ptm-80) REVERT: D 385 MET cc_start: 0.9006 (ttm) cc_final: 0.8685 (ttp) REVERT: D 395 GLU cc_start: 0.8843 (mp0) cc_final: 0.8230 (mp0) REVERT: D 399 GLU cc_start: 0.9047 (pm20) cc_final: 0.8773 (pm20) REVERT: D 404 ASP cc_start: 0.9104 (t0) cc_final: 0.8809 (t0) REVERT: E 28 ASP cc_start: 0.8883 (m-30) cc_final: 0.8517 (m-30) REVERT: E 58 LYS cc_start: 0.9320 (mmtp) cc_final: 0.9013 (mmmm) REVERT: E 105 ARG cc_start: 0.9155 (mtm110) cc_final: 0.8909 (mtm110) REVERT: E 109 LYS cc_start: 0.9390 (mttp) cc_final: 0.8710 (tptt) REVERT: E 274 ASP cc_start: 0.9098 (t0) cc_final: 0.8891 (t0) REVERT: E 276 SER cc_start: 0.8721 (p) cc_final: 0.8441 (p) REVERT: E 281 ILE cc_start: 0.8794 (tp) cc_final: 0.8082 (tt) REVERT: E 285 ASN cc_start: 0.9412 (m-40) cc_final: 0.9039 (m-40) REVERT: E 322 ARG cc_start: 0.8206 (ppp80) cc_final: 0.7726 (ptm160) REVERT: E 352 GLU cc_start: 0.9154 (tm-30) cc_final: 0.8935 (tm-30) REVERT: E 385 MET cc_start: 0.8919 (ttm) cc_final: 0.8258 (ttp) REVERT: E 386 MET cc_start: 0.9333 (mtm) cc_final: 0.8992 (mtm) REVERT: E 395 GLU cc_start: 0.8732 (mp0) cc_final: 0.8078 (mp0) REVERT: E 399 GLU cc_start: 0.8941 (pm20) cc_final: 0.8664 (pm20) REVERT: E 400 TYR cc_start: 0.8649 (m-80) cc_final: 0.7661 (m-10) REVERT: E 407 ARG cc_start: 0.9022 (ttt-90) cc_final: 0.8284 (ttt-90) REVERT: E 438 LYS cc_start: 0.8168 (mmtt) cc_final: 0.7874 (mttp) REVERT: E 512 ARG cc_start: 0.7808 (ttm-80) cc_final: 0.7526 (ttm-80) REVERT: F 28 ASP cc_start: 0.8879 (m-30) cc_final: 0.8518 (m-30) REVERT: F 47 ASP cc_start: 0.9158 (p0) cc_final: 0.8933 (p0) REVERT: F 105 ARG cc_start: 0.9227 (mtm110) cc_final: 0.8947 (mtm110) REVERT: F 108 LYS cc_start: 0.9580 (OUTLIER) cc_final: 0.9306 (tppt) REVERT: F 109 LYS cc_start: 0.9394 (mttp) cc_final: 0.9168 (mtmm) REVERT: F 274 ASP cc_start: 0.8995 (t0) cc_final: 0.8791 (t0) REVERT: F 276 SER cc_start: 0.8759 (p) cc_final: 0.8485 (p) REVERT: F 279 ASN cc_start: 0.8913 (t0) cc_final: 0.8664 (t0) REVERT: F 281 ILE cc_start: 0.8918 (tp) cc_final: 0.8596 (tt) REVERT: F 285 ASN cc_start: 0.9399 (m-40) cc_final: 0.9155 (m110) REVERT: F 312 ASN cc_start: 0.9015 (t160) cc_final: 0.8811 (t0) REVERT: F 352 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8913 (tm-30) REVERT: F 395 GLU cc_start: 0.8853 (mp0) cc_final: 0.8157 (mp0) REVERT: F 399 GLU cc_start: 0.9064 (pm20) cc_final: 0.8767 (pm20) REVERT: F 404 ASP cc_start: 0.9186 (t0) cc_final: 0.8933 (t0) REVERT: F 512 ARG cc_start: 0.7666 (ttm-80) cc_final: 0.7116 (ptm160) REVERT: G 28 ASP cc_start: 0.8957 (m-30) cc_final: 0.8669 (m-30) REVERT: G 50 ASP cc_start: 0.9015 (t70) cc_final: 0.8730 (t0) REVERT: G 51 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9095 (pp) REVERT: G 105 ARG cc_start: 0.9175 (mtm110) cc_final: 0.8539 (mtm110) REVERT: G 108 LYS cc_start: 0.9624 (OUTLIER) cc_final: 0.9420 (mttm) REVERT: G 109 LYS cc_start: 0.9345 (mttp) cc_final: 0.9123 (mttt) REVERT: G 275 SER cc_start: 0.8966 (t) cc_final: 0.8729 (t) REVERT: G 285 ASN cc_start: 0.9337 (m-40) cc_final: 0.8955 (m-40) REVERT: G 312 ASN cc_start: 0.9102 (OUTLIER) cc_final: 0.8900 (t0) REVERT: G 352 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8918 (tm-30) REVERT: G 395 GLU cc_start: 0.8756 (mp0) cc_final: 0.8157 (mp0) REVERT: G 399 GLU cc_start: 0.9005 (pm20) cc_final: 0.8691 (pm20) REVERT: G 400 TYR cc_start: 0.8480 (m-80) cc_final: 0.8019 (m-80) REVERT: G 407 ARG cc_start: 0.8940 (ttt-90) cc_final: 0.8388 (ptm-80) REVERT: G 512 ARG cc_start: 0.7580 (ttm-80) cc_final: 0.7361 (ptm160) REVERT: H 25 ASN cc_start: 0.9113 (m-40) cc_final: 0.8851 (p0) REVERT: H 28 ASP cc_start: 0.8979 (m-30) cc_final: 0.8626 (m-30) REVERT: H 50 ASP cc_start: 0.9024 (t70) cc_final: 0.8709 (t0) REVERT: H 58 LYS cc_start: 0.9449 (mmtp) cc_final: 0.9179 (mmmm) REVERT: H 105 ARG cc_start: 0.9263 (mtm110) cc_final: 0.8783 (mtm110) REVERT: H 109 LYS cc_start: 0.9399 (mttp) cc_final: 0.9195 (mttt) REVERT: H 274 ASP cc_start: 0.9068 (t0) cc_final: 0.8833 (t0) REVERT: H 276 SER cc_start: 0.8684 (p) cc_final: 0.8438 (p) REVERT: H 285 ASN cc_start: 0.9464 (m-40) cc_final: 0.9208 (m-40) REVERT: H 322 ARG cc_start: 0.8370 (ppp80) cc_final: 0.7990 (ptm160) REVERT: H 352 GLU cc_start: 0.9282 (tm-30) cc_final: 0.9027 (tm-30) REVERT: H 355 ARG cc_start: 0.9582 (ptm-80) cc_final: 0.9177 (ptm-80) REVERT: H 395 GLU cc_start: 0.8738 (mp0) cc_final: 0.8233 (mp0) REVERT: H 399 GLU cc_start: 0.8979 (pm20) cc_final: 0.8738 (pm20) outliers start: 167 outliers final: 76 residues processed: 1118 average time/residue: 0.1513 time to fit residues: 265.2876 Evaluate side-chains 1013 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 929 time to evaluate : 0.832 ------------------------------------------------------------------------------- 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 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 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 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 312 ASN 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: 0.8980 chunk 57 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 153 optimal weight: 4.9990 chunk 262 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 248 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 93 HIS ** 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 93 HIS ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 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 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.104119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.083841 restraints weight = 41784.717| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 3.86 r_work: 0.2778 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 23488 Z= 0.225 Angle : 0.735 7.447 31792 Z= 0.369 Chirality : 0.049 0.162 3656 Planarity : 0.005 0.045 4000 Dihedral : 10.129 89.728 3401 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.54 % Allowed : 21.14 % Favored : 73.32 % 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: -2.54 (0.14), residues: 2960 helix: -1.65 (0.14), residues: 1120 sheet: -2.32 (0.20), residues: 464 loop : -1.31 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 407 TYR 0.021 0.002 TYR H 400 PHE 0.013 0.001 PHE H 401 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.22 (23480) covalent geometry : angle 0.73524 / 0.37 (31792) hydrogen bonds : bond 0.03934 / 2.56 ( 841) hydrogen bonds : angle 5.58023 / 3.81 ( 2427) Misc. bond : bond 0.00142 / 0.07 ( 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 1085 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 953 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8789 (m-30) cc_final: 0.8484 (m-30) REVERT: A 50 ASP cc_start: 0.9090 (t0) cc_final: 0.8847 (t0) REVERT: A 51 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9013 (pp) REVERT: A 66 VAL cc_start: 0.8322 (OUTLIER) cc_final: 0.8075 (p) REVERT: A 105 ARG cc_start: 0.9192 (mtm110) cc_final: 0.8701 (mtm110) REVERT: A 109 LYS cc_start: 0.9415 (mttp) cc_final: 0.9169 (mptt) REVERT: A 242 LYS cc_start: 0.8190 (mtpt) cc_final: 0.7982 (mttt) REVERT: A 258 TYR cc_start: 0.9105 (t80) cc_final: 0.8890 (t80) REVERT: A 276 SER cc_start: 0.9091 (p) cc_final: 0.8836 (p) REVERT: A 285 ASN cc_start: 0.9459 (m-40) cc_final: 0.9150 (m-40) REVERT: A 352 GLU cc_start: 0.9276 (tm-30) cc_final: 0.9020 (tm-30) REVERT: A 385 MET cc_start: 0.8945 (ttm) cc_final: 0.8531 (ttm) REVERT: A 395 GLU cc_start: 0.8861 (mp0) cc_final: 0.8113 (mp0) REVERT: A 399 GLU cc_start: 0.9000 (pm20) cc_final: 0.8737 (mp0) REVERT: A 400 TYR cc_start: 0.8584 (m-80) cc_final: 0.8103 (m-10) REVERT: A 404 ASP cc_start: 0.9161 (t0) cc_final: 0.8854 (t70) REVERT: A 407 ARG cc_start: 0.9023 (ttt-90) cc_final: 0.8300 (ttt-90) REVERT: A 438 LYS cc_start: 0.8973 (mttt) cc_final: 0.8476 (mmtt) REVERT: A 449 ASP cc_start: 0.9406 (p0) cc_final: 0.9142 (p0) REVERT: A 455 LYS cc_start: 0.9177 (mppt) cc_final: 0.8717 (mppt) REVERT: B 28 ASP cc_start: 0.8860 (m-30) cc_final: 0.8563 (m-30) REVERT: B 50 ASP cc_start: 0.9040 (t70) cc_final: 0.8831 (t0) REVERT: B 51 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9079 (pp) REVERT: B 66 VAL cc_start: 0.8413 (OUTLIER) cc_final: 0.8183 (p) REVERT: B 105 ARG cc_start: 0.9221 (mtm110) cc_final: 0.8755 (mtm110) REVERT: B 109 LYS cc_start: 0.9440 (mttp) cc_final: 0.9199 (mptt) REVERT: B 258 TYR cc_start: 0.9098 (t80) cc_final: 0.8888 (t80) REVERT: B 276 SER cc_start: 0.9094 (p) cc_final: 0.8851 (p) REVERT: B 285 ASN cc_start: 0.9454 (m-40) cc_final: 0.9229 (m-40) REVERT: B 352 GLU cc_start: 0.9254 (tm-30) cc_final: 0.9010 (tm-30) REVERT: B 385 MET cc_start: 0.8967 (ttm) cc_final: 0.8674 (ttm) REVERT: B 395 GLU cc_start: 0.8910 (mp0) cc_final: 0.8358 (mp0) REVERT: B 399 GLU cc_start: 0.9063 (pm20) cc_final: 0.8813 (mp0) REVERT: B 404 ASP cc_start: 0.9179 (t0) cc_final: 0.8912 (t0) REVERT: B 414 MET cc_start: 0.9365 (mpt) cc_final: 0.9161 (mpt) REVERT: B 438 LYS cc_start: 0.9025 (mttt) cc_final: 0.8807 (tttt) REVERT: C 28 ASP cc_start: 0.8819 (m-30) cc_final: 0.8511 (m-30) REVERT: C 50 ASP cc_start: 0.9124 (t70) cc_final: 0.8868 (t0) REVERT: C 51 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9039 (pp) REVERT: C 66 VAL cc_start: 0.8274 (OUTLIER) cc_final: 0.8017 (p) REVERT: C 105 ARG cc_start: 0.9166 (mtm110) cc_final: 0.8703 (mtm110) REVERT: C 109 LYS cc_start: 0.9402 (mttp) cc_final: 0.9144 (mptt) REVERT: C 258 TYR cc_start: 0.9067 (t80) cc_final: 0.8785 (t80) REVERT: C 276 SER cc_start: 0.8858 (p) cc_final: 0.8571 (p) REVERT: C 279 ASN cc_start: 0.9139 (t0) cc_final: 0.8044 (t0) REVERT: C 281 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8839 (tt) REVERT: C 352 GLU cc_start: 0.9270 (tm-30) cc_final: 0.8998 (tm-30) REVERT: C 355 ARG cc_start: 0.9598 (ptm-80) cc_final: 0.9386 (ptm-80) REVERT: C 395 GLU cc_start: 0.8918 (mp0) cc_final: 0.8351 (mp0) REVERT: C 438 LYS cc_start: 0.9025 (mttt) cc_final: 0.8600 (mmtt) REVERT: D 25 ASN cc_start: 0.9173 (m-40) cc_final: 0.8901 (p0) REVERT: D 28 ASP cc_start: 0.8835 (m-30) cc_final: 0.8508 (m-30) REVERT: D 50 ASP cc_start: 0.9101 (t70) cc_final: 0.8763 (t0) REVERT: D 51 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9050 (pp) REVERT: D 105 ARG cc_start: 0.9189 (mtm110) cc_final: 0.8911 (mtm110) REVERT: D 109 LYS cc_start: 0.9441 (mttt) cc_final: 0.9182 (mttt) REVERT: D 258 TYR cc_start: 0.9210 (t80) cc_final: 0.8985 (t80) REVERT: D 276 SER cc_start: 0.8924 (p) cc_final: 0.8660 (p) REVERT: D 285 ASN cc_start: 0.9456 (m-40) cc_final: 0.9202 (m-40) REVERT: D 332 ILE cc_start: 0.8965 (pp) cc_final: 0.8674 (pp) REVERT: D 352 GLU cc_start: 0.9248 (tm-30) cc_final: 0.8972 (tm-30) REVERT: D 355 ARG cc_start: 0.9563 (ptm-80) cc_final: 0.9363 (ptm-80) REVERT: D 385 MET cc_start: 0.9027 (ttm) cc_final: 0.8547 (ttp) REVERT: D 395 GLU cc_start: 0.8889 (mp0) cc_final: 0.8233 (mp0) REVERT: D 399 GLU cc_start: 0.9010 (pm20) cc_final: 0.8759 (pm20) REVERT: D 404 ASP cc_start: 0.9159 (t0) cc_final: 0.8881 (t0) REVERT: D 438 LYS cc_start: 0.8425 (mmtt) cc_final: 0.8064 (mmtm) REVERT: E 28 ASP cc_start: 0.8863 (m-30) cc_final: 0.8529 (m-30) REVERT: E 51 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9077 (pp) REVERT: E 105 ARG cc_start: 0.9175 (mtm110) cc_final: 0.8919 (mtm110) REVERT: E 109 LYS cc_start: 0.9418 (mttp) cc_final: 0.8951 (tmtt) REVERT: E 258 TYR cc_start: 0.9093 (t80) cc_final: 0.8876 (t80) REVERT: E 274 ASP cc_start: 0.9087 (t0) cc_final: 0.8856 (t0) REVERT: E 276 SER cc_start: 0.8972 (p) cc_final: 0.8681 (p) REVERT: E 281 ILE cc_start: 0.8911 (tp) cc_final: 0.8566 (tt) REVERT: E 285 ASN cc_start: 0.9444 (m-40) cc_final: 0.9223 (m-40) REVERT: E 352 GLU cc_start: 0.9293 (tm-30) cc_final: 0.9022 (tm-30) REVERT: E 385 MET cc_start: 0.8982 (ttm) cc_final: 0.8458 (ttm) REVERT: E 386 MET cc_start: 0.9272 (mtm) cc_final: 0.8833 (mtm) REVERT: E 395 GLU cc_start: 0.8813 (mp0) cc_final: 0.8213 (mp0) REVERT: E 399 GLU cc_start: 0.8979 (pm20) cc_final: 0.8700 (pm20) REVERT: E 400 TYR cc_start: 0.8502 (m-80) cc_final: 0.7708 (m-10) REVERT: E 407 ARG cc_start: 0.9119 (ttt-90) cc_final: 0.8562 (ttt-90) REVERT: F 28 ASP cc_start: 0.8900 (m-30) cc_final: 0.8603 (m-30) REVERT: F 51 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8940 (pp) REVERT: F 108 LYS cc_start: 0.9508 (OUTLIER) cc_final: 0.9227 (mttm) REVERT: F 109 LYS cc_start: 0.9426 (mttp) cc_final: 0.9164 (mtmm) REVERT: F 274 ASP cc_start: 0.9024 (t0) cc_final: 0.8797 (t0) REVERT: F 276 SER cc_start: 0.8987 (p) cc_final: 0.8728 (p) REVERT: F 281 ILE cc_start: 0.9021 (tp) cc_final: 0.8766 (tt) REVERT: F 285 ASN cc_start: 0.9447 (m-40) cc_final: 0.9190 (m-40) REVERT: F 352 GLU cc_start: 0.9240 (tm-30) cc_final: 0.8998 (tm-30) REVERT: F 355 ARG cc_start: 0.9509 (ptm-80) cc_final: 0.9189 (ptm-80) REVERT: F 385 MET cc_start: 0.8858 (ttm) cc_final: 0.8329 (ttm) REVERT: F 395 GLU cc_start: 0.8907 (mp0) cc_final: 0.8207 (mp0) REVERT: F 399 GLU cc_start: 0.9035 (pm20) cc_final: 0.8766 (pm20) REVERT: F 404 ASP cc_start: 0.9221 (t0) cc_final: 0.8979 (t0) REVERT: F 407 ARG cc_start: 0.9101 (ttt90) cc_final: 0.8846 (ttt90) REVERT: F 438 LYS cc_start: 0.8266 (mptt) cc_final: 0.8048 (mmtm) REVERT: G 28 ASP cc_start: 0.8954 (m-30) cc_final: 0.8729 (m-30) REVERT: G 50 ASP cc_start: 0.9026 (t70) cc_final: 0.8722 (t0) REVERT: G 51 LEU cc_start: 0.9409 (OUTLIER) cc_final: 0.9104 (pp) REVERT: G 105 ARG cc_start: 0.9074 (mtm110) cc_final: 0.8759 (mtm110) REVERT: G 108 LYS cc_start: 0.9561 (OUTLIER) cc_final: 0.9301 (mttm) REVERT: G 109 LYS cc_start: 0.9364 (mttp) cc_final: 0.9091 (mttm) REVERT: G 258 TYR cc_start: 0.9172 (t80) cc_final: 0.8960 (t80) REVERT: G 279 ASN cc_start: 0.9093 (t0) cc_final: 0.8790 (t0) REVERT: G 299 VAL cc_start: 0.9435 (m) cc_final: 0.9174 (p) REVERT: G 352 GLU cc_start: 0.9258 (tm-30) cc_final: 0.9019 (tm-30) REVERT: G 385 MET cc_start: 0.8866 (ttm) cc_final: 0.8525 (ttm) REVERT: G 395 GLU cc_start: 0.8830 (mp0) cc_final: 0.8211 (mp0) REVERT: G 399 GLU cc_start: 0.9079 (pm20) cc_final: 0.8787 (pm20) REVERT: G 400 TYR cc_start: 0.8425 (m-80) cc_final: 0.7985 (m-80) REVERT: G 407 ARG cc_start: 0.8894 (ttt-90) cc_final: 0.8289 (ptm-80) REVERT: G 449 ASP cc_start: 0.9334 (p0) cc_final: 0.9051 (p0) REVERT: G 510 GLU cc_start: 0.8064 (tp30) cc_final: 0.7824 (tp30) REVERT: H 28 ASP cc_start: 0.8951 (m-30) cc_final: 0.8698 (m-30) REVERT: H 50 ASP cc_start: 0.9067 (t70) cc_final: 0.8848 (t0) REVERT: H 51 LEU cc_start: 0.9302 (OUTLIER) cc_final: 0.9011 (pp) REVERT: H 105 ARG cc_start: 0.9235 (mtm110) cc_final: 0.8864 (mtm110) REVERT: H 276 SER cc_start: 0.8912 (p) cc_final: 0.8617 (p) REVERT: H 285 ASN cc_start: 0.9449 (m-40) cc_final: 0.9199 (m-40) REVERT: H 352 GLU cc_start: 0.9300 (tm-30) cc_final: 0.9062 (tm-30) REVERT: H 355 ARG cc_start: 0.9550 (ptm-80) cc_final: 0.9335 (ptm-80) REVERT: H 385 MET cc_start: 0.8972 (ttm) cc_final: 0.8720 (ttm) REVERT: H 395 GLU cc_start: 0.8807 (mp0) cc_final: 0.8167 (mp0) REVERT: H 399 GLU cc_start: 0.8888 (pm20) cc_final: 0.8634 (pm20) outliers start: 132 outliers final: 75 residues processed: 1000 average time/residue: 0.1497 time to fit residues: 235.4974 Evaluate side-chains 961 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 872 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 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 367 ILE 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 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 313 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 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 56 THR 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 347 VAL 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: 2.9990 chunk 275 optimal weight: 3.9990 chunk 225 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 280 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 229 optimal weight: 0.6980 chunk 228 optimal weight: 0.5980 chunk 214 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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** ** 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 = 0.107391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.086339 restraints weight = 41406.491| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.98 r_work: 0.2829 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23488 Z= 0.138 Angle : 0.670 8.329 31792 Z= 0.334 Chirality : 0.046 0.148 3656 Planarity : 0.004 0.040 4000 Dihedral : 9.707 89.412 3370 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.49 % Allowed : 22.57 % Favored : 71.94 % 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: -1.34 (0.14), residues: 1120 sheet: -2.10 (0.21), residues: 464 loop : -1.17 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 105 TYR 0.017 0.001 TYR H 258 PHE 0.014 0.001 PHE E 401 HIS 0.003 0.000 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (23480) covalent geometry : angle 0.67032 / 0.33 (31792) hydrogen bonds : bond 0.03476 / 2.26 ( 841) hydrogen bonds : angle 5.37580 / 3.66 ( 2427) Misc. bond : bond 0.00057 / 0.03 ( 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 1118 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 987 time to evaluate : 0.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8757 (m-30) cc_final: 0.8497 (m-30) REVERT: A 66 VAL cc_start: 0.8327 (OUTLIER) cc_final: 0.7938 (p) REVERT: A 105 ARG cc_start: 0.9179 (mtm110) cc_final: 0.8678 (mtm110) REVERT: A 109 LYS cc_start: 0.9412 (mttp) cc_final: 0.9181 (mptt) REVERT: A 258 TYR cc_start: 0.9110 (t80) cc_final: 0.8861 (t80) REVERT: A 276 SER cc_start: 0.9032 (p) cc_final: 0.8784 (p) REVERT: A 285 ASN cc_start: 0.9466 (m-40) cc_final: 0.9157 (m-40) REVERT: A 352 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8971 (tm-30) REVERT: A 355 ARG cc_start: 0.9353 (ptm-80) cc_final: 0.9145 (ptm-80) REVERT: A 385 MET cc_start: 0.8933 (ttm) cc_final: 0.8566 (ttm) REVERT: A 395 GLU cc_start: 0.8830 (mp0) cc_final: 0.8241 (mp0) REVERT: A 399 GLU cc_start: 0.9021 (pm20) cc_final: 0.8782 (mp0) REVERT: A 400 TYR cc_start: 0.8464 (m-80) cc_final: 0.7892 (m-10) REVERT: A 404 ASP cc_start: 0.9169 (t0) cc_final: 0.8871 (t70) REVERT: A 407 ARG cc_start: 0.8955 (ttt-90) cc_final: 0.8333 (ttt-90) REVERT: A 438 LYS cc_start: 0.8976 (mttt) cc_final: 0.8522 (mmtt) REVERT: A 455 LYS cc_start: 0.9189 (mppt) cc_final: 0.8746 (mppt) REVERT: B 25 ASN cc_start: 0.9041 (m-40) cc_final: 0.8762 (p0) REVERT: B 28 ASP cc_start: 0.8791 (m-30) cc_final: 0.8516 (m-30) REVERT: B 50 ASP cc_start: 0.9047 (t70) cc_final: 0.8777 (t0) REVERT: B 51 LEU cc_start: 0.9224 (OUTLIER) cc_final: 0.8890 (pp) REVERT: B 66 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.7944 (p) REVERT: B 105 ARG cc_start: 0.9204 (mtm110) cc_final: 0.8743 (mtm110) REVERT: B 109 LYS cc_start: 0.9435 (mttp) cc_final: 0.9225 (mttt) REVERT: B 276 SER cc_start: 0.9050 (p) cc_final: 0.8791 (p) REVERT: B 285 ASN cc_start: 0.9455 (m-40) cc_final: 0.9249 (m-40) REVERT: B 352 GLU cc_start: 0.9208 (tm-30) cc_final: 0.8970 (tm-30) REVERT: B 385 MET cc_start: 0.8972 (ttm) cc_final: 0.8619 (ttm) REVERT: B 395 GLU cc_start: 0.8852 (mp0) cc_final: 0.8262 (mp0) REVERT: B 399 GLU cc_start: 0.8989 (pm20) cc_final: 0.8741 (pm20) REVERT: B 400 TYR cc_start: 0.8598 (m-80) cc_final: 0.8153 (m-80) REVERT: B 404 ASP cc_start: 0.9174 (t0) cc_final: 0.8898 (t0) REVERT: B 407 ARG cc_start: 0.9110 (ttt-90) cc_final: 0.8667 (ttt-90) REVERT: B 438 LYS cc_start: 0.9031 (mttt) cc_final: 0.8776 (tttt) REVERT: B 449 ASP cc_start: 0.9407 (p0) cc_final: 0.9206 (p0) REVERT: C 28 ASP cc_start: 0.8759 (m-30) cc_final: 0.8489 (m-30) REVERT: C 50 ASP cc_start: 0.9173 (t70) cc_final: 0.8931 (t0) REVERT: C 51 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.8895 (pp) REVERT: C 66 VAL cc_start: 0.8210 (OUTLIER) cc_final: 0.7680 (p) REVERT: C 75 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8164 (mm-30) REVERT: C 105 ARG cc_start: 0.9154 (mtm110) cc_final: 0.8681 (mtm110) REVERT: C 109 LYS cc_start: 0.9418 (mttp) cc_final: 0.9149 (mptt) REVERT: C 258 TYR cc_start: 0.9083 (t80) cc_final: 0.8757 (t80) REVERT: C 276 SER cc_start: 0.8668 (p) cc_final: 0.8360 (p) REVERT: C 279 ASN cc_start: 0.9209 (t0) cc_final: 0.8212 (t0) REVERT: C 322 ARG cc_start: 0.8649 (ptm-80) cc_final: 0.7908 (ptm160) REVERT: C 352 GLU cc_start: 0.9197 (tm-30) cc_final: 0.8914 (tm-30) REVERT: C 355 ARG cc_start: 0.9520 (ptm-80) cc_final: 0.9302 (ptm-80) REVERT: C 395 GLU cc_start: 0.8869 (mp0) cc_final: 0.8346 (mp0) REVERT: C 409 LYS cc_start: 0.8786 (ttmp) cc_final: 0.8254 (tttt) REVERT: C 438 LYS cc_start: 0.9013 (mttt) cc_final: 0.8548 (mmtt) REVERT: C 510 GLU cc_start: 0.8103 (tp30) cc_final: 0.7810 (tp30) REVERT: C 512 ARG cc_start: 0.7894 (ttm-80) cc_final: 0.7616 (ptm160) REVERT: D 25 ASN cc_start: 0.9209 (m-40) cc_final: 0.8953 (p0) REVERT: D 28 ASP cc_start: 0.8842 (m-30) cc_final: 0.8542 (m-30) REVERT: D 51 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.8952 (pp) REVERT: D 105 ARG cc_start: 0.9241 (mtm110) cc_final: 0.8953 (mtm110) REVERT: D 109 LYS cc_start: 0.9429 (mttt) cc_final: 0.9201 (mttt) REVERT: D 256 ASP cc_start: 0.9346 (m-30) cc_final: 0.8899 (p0) REVERT: D 258 TYR cc_start: 0.9171 (t80) cc_final: 0.8954 (t80) REVERT: D 276 SER cc_start: 0.8869 (p) cc_final: 0.8607 (p) REVERT: D 285 ASN cc_start: 0.9459 (m-40) cc_final: 0.9163 (m-40) REVERT: D 332 ILE cc_start: 0.8943 (pp) cc_final: 0.8652 (pp) REVERT: D 352 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8885 (tm-30) REVERT: D 355 ARG cc_start: 0.9473 (ptm-80) cc_final: 0.9265 (ptm-80) REVERT: D 385 MET cc_start: 0.8981 (ttm) cc_final: 0.8748 (ttp) REVERT: D 395 GLU cc_start: 0.8865 (mp0) cc_final: 0.8229 (mp0) REVERT: D 399 GLU cc_start: 0.8977 (pm20) cc_final: 0.8672 (pm20) REVERT: D 404 ASP cc_start: 0.9172 (t0) cc_final: 0.8901 (t0) REVERT: D 409 LYS cc_start: 0.8685 (ttmp) cc_final: 0.7985 (tttt) REVERT: D 438 LYS cc_start: 0.8506 (mmtt) cc_final: 0.8152 (mmtm) REVERT: E 28 ASP cc_start: 0.8820 (m-30) cc_final: 0.8523 (m-30) REVERT: E 51 LEU cc_start: 0.9335 (pp) cc_final: 0.9028 (pp) REVERT: E 75 GLU cc_start: 0.8327 (mm-30) cc_final: 0.8108 (mm-30) REVERT: E 105 ARG cc_start: 0.9155 (mtm110) cc_final: 0.8657 (mtm110) REVERT: E 109 LYS cc_start: 0.9420 (mttp) cc_final: 0.9170 (mptt) REVERT: E 258 TYR cc_start: 0.9081 (t80) cc_final: 0.8872 (t80) REVERT: E 274 ASP cc_start: 0.9091 (t0) cc_final: 0.8863 (t0) REVERT: E 276 SER cc_start: 0.8956 (p) cc_final: 0.8700 (p) REVERT: E 352 GLU cc_start: 0.9236 (tm-30) cc_final: 0.8989 (tm-30) REVERT: E 385 MET cc_start: 0.8929 (ttm) cc_final: 0.8319 (ttm) REVERT: E 395 GLU cc_start: 0.8837 (mp0) cc_final: 0.8261 (mp0) REVERT: E 399 GLU cc_start: 0.8998 (pm20) cc_final: 0.8712 (pm20) REVERT: F 28 ASP cc_start: 0.8893 (m-30) cc_final: 0.8641 (m-30) REVERT: F 51 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8787 (pp) REVERT: F 105 ARG cc_start: 0.9215 (mtm110) cc_final: 0.8987 (mtm110) REVERT: F 108 LYS cc_start: 0.9485 (OUTLIER) cc_final: 0.9119 (tppt) REVERT: F 256 ASP cc_start: 0.9295 (m-30) cc_final: 0.8886 (p0) REVERT: F 259 ARG cc_start: 0.9422 (ttm-80) cc_final: 0.9170 (ttm-80) REVERT: F 274 ASP cc_start: 0.9022 (t0) cc_final: 0.8821 (t0) REVERT: F 276 SER cc_start: 0.8802 (p) cc_final: 0.8506 (p) REVERT: F 279 ASN cc_start: 0.9006 (t0) cc_final: 0.8201 (t0) REVERT: F 281 ILE cc_start: 0.9023 (tp) cc_final: 0.8717 (tt) REVERT: F 285 ASN cc_start: 0.9463 (m-40) cc_final: 0.9205 (m-40) REVERT: F 332 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8566 (pp) REVERT: F 352 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8948 (tm-30) REVERT: F 355 ARG cc_start: 0.9439 (ptm-80) cc_final: 0.9120 (ptm-80) REVERT: F 385 MET cc_start: 0.8845 (ttm) cc_final: 0.8410 (ttm) REVERT: F 395 GLU cc_start: 0.8910 (mp0) cc_final: 0.8236 (mp0) REVERT: F 399 GLU cc_start: 0.8987 (pm20) cc_final: 0.8744 (pm20) REVERT: F 400 TYR cc_start: 0.8343 (m-10) cc_final: 0.8112 (m-10) REVERT: F 404 ASP cc_start: 0.9211 (t0) cc_final: 0.8949 (t70) REVERT: F 407 ARG cc_start: 0.8977 (ttt90) cc_final: 0.8732 (ttt90) REVERT: G 28 ASP cc_start: 0.8933 (m-30) cc_final: 0.8705 (m-30) REVERT: G 50 ASP cc_start: 0.9120 (t70) cc_final: 0.8850 (t0) REVERT: G 51 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8846 (pp) REVERT: G 108 LYS cc_start: 0.9556 (OUTLIER) cc_final: 0.9269 (mttm) REVERT: G 109 LYS cc_start: 0.9373 (mttp) cc_final: 0.9081 (mttm) REVERT: G 256 ASP cc_start: 0.9324 (m-30) cc_final: 0.8927 (p0) REVERT: G 258 TYR cc_start: 0.9157 (t80) cc_final: 0.8894 (t80) REVERT: G 299 VAL cc_start: 0.9426 (m) cc_final: 0.9187 (p) REVERT: G 352 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8974 (tm-30) REVERT: G 385 MET cc_start: 0.8838 (ttm) cc_final: 0.8351 (ttm) REVERT: G 395 GLU cc_start: 0.8821 (mp0) cc_final: 0.8314 (mp0) REVERT: G 399 GLU cc_start: 0.9084 (pm20) cc_final: 0.8801 (pm20) REVERT: G 400 TYR cc_start: 0.8407 (m-80) cc_final: 0.7633 (m-80) REVERT: G 449 ASP cc_start: 0.9262 (p0) cc_final: 0.8999 (t0) REVERT: H 25 ASN cc_start: 0.9010 (m-40) cc_final: 0.8764 (p0) REVERT: H 28 ASP cc_start: 0.8907 (m-30) cc_final: 0.8642 (m-30) REVERT: H 51 LEU cc_start: 0.9203 (OUTLIER) cc_final: 0.8851 (pp) REVERT: H 66 VAL cc_start: 0.8429 (OUTLIER) cc_final: 0.8037 (p) REVERT: H 105 ARG cc_start: 0.9175 (mtm110) cc_final: 0.8865 (mtm110) REVERT: H 259 ARG cc_start: 0.9301 (ttm-80) cc_final: 0.9090 (ttm-80) REVERT: H 276 SER cc_start: 0.8847 (p) cc_final: 0.8550 (p) REVERT: H 285 ASN cc_start: 0.9438 (m-40) cc_final: 0.9184 (m-40) REVERT: H 352 GLU cc_start: 0.9253 (tm-30) cc_final: 0.9015 (tm-30) REVERT: H 355 ARG cc_start: 0.9484 (ptm-80) cc_final: 0.9278 (ptm-80) REVERT: H 385 MET cc_start: 0.8942 (ttm) cc_final: 0.8575 (ttm) REVERT: H 395 GLU cc_start: 0.8807 (mp0) cc_final: 0.8258 (mp0) REVERT: H 512 ARG cc_start: 0.7901 (ttm-80) cc_final: 0.7542 (ptm160) outliers start: 131 outliers final: 65 residues processed: 1038 average time/residue: 0.1503 time to fit residues: 247.3053 Evaluate side-chains 994 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 916 time to evaluate : 0.872 ------------------------------------------------------------------------------- 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 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 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 260 LEU 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 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 367 ILE Chi-restraints excluded: chain D residue 373 ILE 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 297 LEU Chi-restraints excluded: chain E residue 313 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 108 LYS 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 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 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: 0.6980 chunk 142 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 144 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 173 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 334 GLN ** 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 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 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.106638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.085584 restraints weight = 41102.620| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.99 r_work: 0.2827 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23488 Z= 0.150 Angle : 0.682 8.272 31792 Z= 0.337 Chirality : 0.047 0.155 3656 Planarity : 0.004 0.038 4000 Dihedral : 9.301 87.852 3360 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 6.04 % Allowed : 24.12 % Favored : 69.84 % 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: -2.05 (0.15), residues: 2960 helix: -1.17 (0.15), residues: 1120 sheet: -2.04 (0.21), residues: 464 loop : -1.09 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 105 TYR 0.020 0.001 TYR G 400 PHE 0.012 0.001 PHE E 401 HIS 0.002 0.000 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (23480) covalent geometry : angle 0.68196 / 0.34 (31792) hydrogen bonds : bond 0.03428 / 2.24 ( 841) hydrogen bonds : angle 5.26211 / 3.59 ( 2427) Misc. bond : bond 0.00073 / 0.04 ( 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 1114 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 970 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8739 (m-30) cc_final: 0.8531 (m-30) REVERT: A 51 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9011 (pp) REVERT: A 105 ARG cc_start: 0.9186 (mtm110) cc_final: 0.8679 (mtm110) REVERT: A 109 LYS cc_start: 0.9420 (mttp) cc_final: 0.9160 (mptt) REVERT: A 258 TYR cc_start: 0.9122 (t80) cc_final: 0.8905 (t80) REVERT: A 276 SER cc_start: 0.9016 (p) cc_final: 0.8760 (p) REVERT: A 285 ASN cc_start: 0.9473 (m-40) cc_final: 0.9254 (m-40) REVERT: A 325 MET cc_start: 0.8630 (ptm) cc_final: 0.8370 (ptt) REVERT: A 352 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8966 (tm-30) REVERT: A 385 MET cc_start: 0.8925 (ttm) cc_final: 0.8437 (ttm) REVERT: A 395 GLU cc_start: 0.8851 (mp0) cc_final: 0.8268 (mp0) REVERT: A 399 GLU cc_start: 0.9032 (pm20) cc_final: 0.8818 (mp0) REVERT: A 404 ASP cc_start: 0.9217 (t0) cc_final: 0.8891 (t70) REVERT: A 406 ILE cc_start: 0.9045 (mp) cc_final: 0.8750 (mp) REVERT: A 438 LYS cc_start: 0.9009 (mttt) cc_final: 0.8526 (mmtt) REVERT: A 510 GLU cc_start: 0.8067 (tp30) cc_final: 0.7859 (tp30) REVERT: B 25 ASN cc_start: 0.9092 (m-40) cc_final: 0.8751 (p0) REVERT: B 28 ASP cc_start: 0.8759 (m-30) cc_final: 0.8536 (m-30) REVERT: B 50 ASP cc_start: 0.9049 (t70) cc_final: 0.8819 (t0) REVERT: B 51 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8890 (pp) REVERT: B 66 VAL cc_start: 0.8047 (OUTLIER) cc_final: 0.7800 (p) REVERT: B 105 ARG cc_start: 0.9215 (mtm110) cc_final: 0.8764 (mtm110) REVERT: B 258 TYR cc_start: 0.9061 (t80) cc_final: 0.8788 (t80) REVERT: B 276 SER cc_start: 0.9035 (p) cc_final: 0.8780 (p) REVERT: B 285 ASN cc_start: 0.9457 (m-40) cc_final: 0.9239 (m-40) REVERT: B 332 ILE cc_start: 0.8980 (OUTLIER) cc_final: 0.8719 (pp) REVERT: B 352 GLU cc_start: 0.9229 (tm-30) cc_final: 0.9016 (tm-30) REVERT: B 385 MET cc_start: 0.8989 (ttm) cc_final: 0.8569 (ttm) REVERT: B 395 GLU cc_start: 0.8892 (mp0) cc_final: 0.8307 (mp0) REVERT: B 399 GLU cc_start: 0.9018 (pm20) cc_final: 0.8777 (mp0) REVERT: B 404 ASP cc_start: 0.9222 (t0) cc_final: 0.8929 (t0) REVERT: B 438 LYS cc_start: 0.9095 (mttt) cc_final: 0.8830 (tttt) REVERT: C 28 ASP cc_start: 0.8743 (m-30) cc_final: 0.8509 (m-30) REVERT: C 50 ASP cc_start: 0.9175 (t70) cc_final: 0.8933 (t0) REVERT: C 51 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8993 (pp) REVERT: C 66 VAL cc_start: 0.8031 (OUTLIER) cc_final: 0.7799 (p) REVERT: C 78 MET cc_start: 0.8684 (OUTLIER) cc_final: 0.8478 (ptm) REVERT: C 105 ARG cc_start: 0.9155 (mtm110) cc_final: 0.8672 (mtm110) REVERT: C 109 LYS cc_start: 0.9408 (mttp) cc_final: 0.9153 (mptt) REVERT: C 258 TYR cc_start: 0.9064 (t80) cc_final: 0.8701 (t80) REVERT: C 276 SER cc_start: 0.8703 (p) cc_final: 0.8412 (p) REVERT: C 279 ASN cc_start: 0.9231 (t0) cc_final: 0.8234 (t0) REVERT: C 322 ARG cc_start: 0.8704 (ptm-80) cc_final: 0.7712 (ptm160) REVERT: C 332 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8704 (pp) REVERT: C 352 GLU cc_start: 0.9185 (tm-30) cc_final: 0.8887 (tm-30) REVERT: C 355 ARG cc_start: 0.9512 (ptm-80) cc_final: 0.9286 (ptm-80) REVERT: C 385 MET cc_start: 0.8774 (ttm) cc_final: 0.7874 (ttm) REVERT: C 395 GLU cc_start: 0.8913 (mp0) cc_final: 0.8399 (mp0) REVERT: C 400 TYR cc_start: 0.8238 (m-10) cc_final: 0.7183 (m-10) REVERT: C 407 ARG cc_start: 0.9039 (ttt-90) cc_final: 0.8658 (ttt-90) REVERT: C 409 LYS cc_start: 0.8795 (ttmp) cc_final: 0.8412 (tttt) REVERT: C 438 LYS cc_start: 0.9036 (mttt) cc_final: 0.8548 (mmtt) REVERT: C 510 GLU cc_start: 0.8116 (tp30) cc_final: 0.7823 (tp30) REVERT: D 25 ASN cc_start: 0.9233 (m-40) cc_final: 0.8977 (p0) REVERT: D 28 ASP cc_start: 0.8800 (m-30) cc_final: 0.8561 (m-30) REVERT: D 50 ASP cc_start: 0.9095 (t70) cc_final: 0.8839 (t0) REVERT: D 51 LEU cc_start: 0.9390 (OUTLIER) cc_final: 0.9149 (pp) REVERT: D 105 ARG cc_start: 0.9257 (mtm110) cc_final: 0.8992 (mtm110) REVERT: D 256 ASP cc_start: 0.9326 (m-30) cc_final: 0.8767 (p0) REVERT: D 258 TYR cc_start: 0.9181 (t80) cc_final: 0.8897 (t80) REVERT: D 276 SER cc_start: 0.8925 (p) cc_final: 0.8667 (p) REVERT: D 279 ASN cc_start: 0.8084 (m-40) cc_final: 0.7831 (m110) REVERT: D 285 ASN cc_start: 0.9469 (m-40) cc_final: 0.9171 (m-40) REVERT: D 332 ILE cc_start: 0.8959 (OUTLIER) cc_final: 0.8693 (pp) REVERT: D 352 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8902 (tm-30) REVERT: D 355 ARG cc_start: 0.9466 (ptm-80) cc_final: 0.9242 (ptm-80) REVERT: D 385 MET cc_start: 0.8985 (ttm) cc_final: 0.8740 (ttp) REVERT: D 395 GLU cc_start: 0.8899 (mp0) cc_final: 0.8268 (mp0) REVERT: D 399 GLU cc_start: 0.9026 (pm20) cc_final: 0.8647 (mp0) REVERT: D 400 TYR cc_start: 0.8426 (m-10) cc_final: 0.7402 (m-10) REVERT: D 404 ASP cc_start: 0.9186 (t0) cc_final: 0.8928 (t0) REVERT: D 407 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8275 (ttt-90) REVERT: D 409 LYS cc_start: 0.8754 (ttmp) cc_final: 0.8297 (tttt) REVERT: D 438 LYS cc_start: 0.8545 (mmtt) cc_final: 0.8197 (mmtm) REVERT: E 28 ASP cc_start: 0.8815 (m-30) cc_final: 0.8556 (m-30) REVERT: E 51 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8933 (pp) REVERT: E 105 ARG cc_start: 0.9168 (mtm110) cc_final: 0.8665 (mtm110) REVERT: E 109 LYS cc_start: 0.9415 (mttp) cc_final: 0.9171 (mptt) REVERT: E 258 TYR cc_start: 0.9122 (t80) cc_final: 0.8847 (t80) REVERT: E 259 ARG cc_start: 0.9299 (ttm-80) cc_final: 0.9062 (ttm-80) REVERT: E 274 ASP cc_start: 0.9107 (t0) cc_final: 0.8877 (t0) REVERT: E 276 SER cc_start: 0.8958 (p) cc_final: 0.8705 (p) REVERT: E 285 ASN cc_start: 0.9259 (m-40) cc_final: 0.9048 (m-40) REVERT: E 332 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8656 (pp) REVERT: E 352 GLU cc_start: 0.9243 (tm-30) cc_final: 0.9012 (tm-30) REVERT: E 385 MET cc_start: 0.8919 (ttm) cc_final: 0.8318 (ttm) REVERT: E 395 GLU cc_start: 0.8846 (mp0) cc_final: 0.8303 (mp0) REVERT: E 400 TYR cc_start: 0.8239 (m-10) cc_final: 0.7188 (m-10) REVERT: E 407 ARG cc_start: 0.9053 (ttt-90) cc_final: 0.8611 (ttt-90) REVERT: E 409 LYS cc_start: 0.8782 (ttmp) cc_final: 0.8045 (tttt) REVERT: F 28 ASP cc_start: 0.8871 (m-30) cc_final: 0.8662 (m-30) REVERT: F 51 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8932 (pp) REVERT: F 105 ARG cc_start: 0.9191 (mtm110) cc_final: 0.8947 (mtm110) REVERT: F 108 LYS cc_start: 0.9532 (OUTLIER) cc_final: 0.9277 (tppt) REVERT: F 109 LYS cc_start: 0.9450 (mptt) cc_final: 0.9131 (mttm) REVERT: F 259 ARG cc_start: 0.9433 (ttm-80) cc_final: 0.9229 (ttm-80) REVERT: F 274 ASP cc_start: 0.9076 (t0) cc_final: 0.8874 (t0) REVERT: F 276 SER cc_start: 0.8780 (p) cc_final: 0.8494 (p) REVERT: F 279 ASN cc_start: 0.9046 (t0) cc_final: 0.8238 (t0) REVERT: F 285 ASN cc_start: 0.9475 (m-40) cc_final: 0.9203 (m-40) REVERT: F 332 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8556 (pp) REVERT: F 352 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8954 (tm-30) REVERT: F 355 ARG cc_start: 0.9429 (ptm-80) cc_final: 0.9133 (ptm-80) REVERT: F 385 MET cc_start: 0.8793 (ttm) cc_final: 0.8337 (ttm) REVERT: F 395 GLU cc_start: 0.8942 (mp0) cc_final: 0.8222 (mp0) REVERT: F 399 GLU cc_start: 0.9014 (pm20) cc_final: 0.8755 (pm20) REVERT: F 404 ASP cc_start: 0.9221 (t0) cc_final: 0.8962 (t70) REVERT: F 407 ARG cc_start: 0.8940 (ttt90) cc_final: 0.8679 (ttt90) REVERT: F 409 LYS cc_start: 0.8712 (ttmp) cc_final: 0.8144 (tttt) REVERT: F 438 LYS cc_start: 0.8067 (mmtt) cc_final: 0.7829 (mmtm) REVERT: G 21 GLN cc_start: 0.9100 (pt0) cc_final: 0.8755 (tm-30) REVERT: G 50 ASP cc_start: 0.9115 (t70) cc_final: 0.8845 (t0) REVERT: G 51 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.8916 (pp) REVERT: G 70 MET cc_start: 0.9064 (mpp) cc_final: 0.8842 (mpp) REVERT: G 258 TYR cc_start: 0.9127 (t80) cc_final: 0.8801 (t80) REVERT: G 279 ASN cc_start: 0.8984 (t0) cc_final: 0.8413 (t0) REVERT: G 299 VAL cc_start: 0.9404 (m) cc_final: 0.9149 (p) REVERT: G 332 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8735 (pp) REVERT: G 352 GLU cc_start: 0.9219 (tm-30) cc_final: 0.8977 (tm-30) REVERT: G 385 MET cc_start: 0.8915 (ttm) cc_final: 0.8365 (ttm) REVERT: G 395 GLU cc_start: 0.8812 (mp0) cc_final: 0.8283 (mp0) REVERT: G 399 GLU cc_start: 0.9062 (pm20) cc_final: 0.8795 (pm20) REVERT: H 25 ASN cc_start: 0.9052 (m-40) cc_final: 0.8753 (p0) REVERT: H 28 ASP cc_start: 0.8883 (m-30) cc_final: 0.8654 (m-30) REVERT: H 51 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8801 (pp) REVERT: H 105 ARG cc_start: 0.9188 (mtm110) cc_final: 0.8832 (mtm110) REVERT: H 259 ARG cc_start: 0.9291 (ttm-80) cc_final: 0.9082 (ttm-80) REVERT: H 276 SER cc_start: 0.8847 (p) cc_final: 0.8578 (p) REVERT: H 285 ASN cc_start: 0.9424 (m-40) cc_final: 0.9174 (m-40) REVERT: H 332 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8750 (pp) REVERT: H 352 GLU cc_start: 0.9262 (tm-30) cc_final: 0.8989 (tm-30) REVERT: H 355 ARG cc_start: 0.9471 (ptm-80) cc_final: 0.9245 (ptm-80) REVERT: H 385 MET cc_start: 0.8960 (ttm) cc_final: 0.8537 (ttm) REVERT: H 395 GLU cc_start: 0.8887 (mp0) cc_final: 0.8294 (mp0) REVERT: H 512 ARG cc_start: 0.7901 (ttm-80) cc_final: 0.7613 (ptm160) outliers start: 144 outliers final: 88 residues processed: 1027 average time/residue: 0.1548 time to fit residues: 252.5519 Evaluate side-chains 1028 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 920 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 297 LEU 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 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 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 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 78 MET 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 250 ILE 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 367 ILE Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 377 LEU 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 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 78 MET 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 313 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 66 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 108 LYS 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 386 MET Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 471 ILE 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 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 377 LEU Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 471 ILE 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: 7.9990 chunk 175 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 191 optimal weight: 0.2980 chunk 223 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 269 optimal weight: 2.9990 chunk 242 optimal weight: 5.9990 chunk 277 optimal weight: 0.0040 chunk 104 optimal weight: 7.9990 chunk 41 optimal weight: 4.9990 overall best weight: 2.2598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** 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 279 ASN ** 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 312 ASN ** 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 ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN ** 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 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.098179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.077727 restraints weight = 42241.279| |-----------------------------------------------------------------------------| r_work (start): 0.2869 rms_B_bonded: 3.85 r_work: 0.2704 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 23488 Z= 0.306 Angle : 0.775 8.624 31792 Z= 0.389 Chirality : 0.051 0.169 3656 Planarity : 0.004 0.043 4000 Dihedral : 9.344 89.222 3351 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 7.21 % Allowed : 24.37 % 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: -2.02 (0.15), residues: 2960 helix: -1.13 (0.15), residues: 1128 sheet: -2.00 (0.21), residues: 464 loop : -1.10 (0.17), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 105 TYR 0.023 0.002 TYR A 400 PHE 0.011 0.002 PHE H 401 HIS 0.004 0.001 HIS E 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00715 / 0.31 (23480) covalent geometry : angle 0.77461 / 0.39 (31792) hydrogen bonds : bond 0.03785 / 2.47 ( 841) hydrogen bonds : angle 5.32909 / 3.64 ( 2427) Misc. bond : bond 0.00239 / 0.12 ( 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 1093 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 172 poor density : 921 time to evaluate : 0.891 Fit side-chains REVERT: A 1 MET cc_start: 0.4720 (ptp) cc_final: 0.3914 (ptm) REVERT: A 51 LEU cc_start: 0.9421 (OUTLIER) cc_final: 0.9132 (pp) REVERT: A 84 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8483 (mm) REVERT: A 105 ARG cc_start: 0.9217 (mtm110) cc_final: 0.8718 (mtm110) REVERT: A 109 LYS cc_start: 0.9432 (mttp) cc_final: 0.9193 (mptt) REVERT: A 258 TYR cc_start: 0.9158 (t80) cc_final: 0.8864 (t80) REVERT: A 352 GLU cc_start: 0.9297 (tm-30) cc_final: 0.9090 (tm-30) REVERT: A 385 MET cc_start: 0.9046 (ttm) cc_final: 0.8374 (ttm) REVERT: A 395 GLU cc_start: 0.8942 (mp0) cc_final: 0.8321 (mp0) REVERT: A 438 LYS cc_start: 0.9057 (mttt) cc_final: 0.8533 (mmtt) REVERT: A 455 LYS cc_start: 0.9175 (mppt) cc_final: 0.8744 (mppt) REVERT: B 50 ASP cc_start: 0.9037 (t70) cc_final: 0.8802 (t0) REVERT: B 51 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9128 (pp) REVERT: B 66 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8169 (p) REVERT: B 88 ILE cc_start: 0.9208 (tp) cc_final: 0.8889 (tp) REVERT: B 105 ARG cc_start: 0.9202 (mtm110) cc_final: 0.8872 (mtm110) REVERT: B 258 TYR cc_start: 0.9137 (t80) cc_final: 0.8936 (t80) REVERT: B 276 SER cc_start: 0.9169 (p) cc_final: 0.8883 (p) REVERT: B 285 ASN cc_start: 0.9472 (m-40) cc_final: 0.9256 (m-40) REVERT: B 319 ASP cc_start: 0.8884 (m-30) cc_final: 0.8676 (m-30) REVERT: B 332 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8831 (pp) REVERT: B 352 GLU cc_start: 0.9308 (tm-30) cc_final: 0.9087 (tm-30) REVERT: B 369 ASN cc_start: 0.8414 (p0) cc_final: 0.8131 (p0) REVERT: B 385 MET cc_start: 0.8983 (ttm) cc_final: 0.8371 (ttm) REVERT: B 395 GLU cc_start: 0.8960 (mp0) cc_final: 0.8382 (mp0) REVERT: B 404 ASP cc_start: 0.9295 (t0) cc_final: 0.9029 (t70) REVERT: B 438 LYS cc_start: 0.9106 (mttt) cc_final: 0.8652 (mmtt) REVERT: C 51 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9187 (pp) REVERT: C 66 VAL cc_start: 0.8191 (OUTLIER) cc_final: 0.7888 (p) REVERT: C 80 ILE cc_start: 0.9310 (pp) cc_final: 0.9078 (pp) REVERT: C 84 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8582 (mm) REVERT: C 258 TYR cc_start: 0.9130 (t80) cc_final: 0.8768 (t80) REVERT: C 276 SER cc_start: 0.8910 (p) cc_final: 0.8593 (p) REVERT: C 332 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8820 (pp) REVERT: C 369 ASN cc_start: 0.8429 (p0) cc_final: 0.8134 (p0) REVERT: C 385 MET cc_start: 0.9025 (ttm) cc_final: 0.8576 (ttm) REVERT: C 395 GLU cc_start: 0.8993 (mp0) cc_final: 0.8404 (mp0) REVERT: C 400 TYR cc_start: 0.8098 (m-10) cc_final: 0.7329 (m-10) REVERT: C 407 ARG cc_start: 0.9100 (ttt-90) cc_final: 0.8591 (ttt-90) REVERT: C 438 LYS cc_start: 0.9101 (mttt) cc_final: 0.8530 (mmtm) REVERT: C 510 GLU cc_start: 0.8103 (tp30) cc_final: 0.7830 (tp30) REVERT: D 28 ASP cc_start: 0.8739 (m-30) cc_final: 0.8395 (m-30) REVERT: D 50 ASP cc_start: 0.9100 (t70) cc_final: 0.8865 (t0) REVERT: D 80 ILE cc_start: 0.9331 (pp) cc_final: 0.9115 (pp) REVERT: D 84 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8495 (mm) REVERT: D 105 ARG cc_start: 0.9283 (mtm110) cc_final: 0.9036 (mtm110) REVERT: D 108 LYS cc_start: 0.9144 (tppt) cc_final: 0.8899 (mmtp) REVERT: D 109 LYS cc_start: 0.9517 (mttt) cc_final: 0.9248 (mttt) REVERT: D 258 TYR cc_start: 0.9193 (t80) cc_final: 0.8821 (t80) REVERT: D 276 SER cc_start: 0.9093 (p) cc_final: 0.8823 (p) REVERT: D 279 ASN cc_start: 0.8574 (m-40) cc_final: 0.8369 (m110) REVERT: D 332 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8813 (pp) REVERT: D 352 GLU cc_start: 0.9310 (tm-30) cc_final: 0.9066 (tm-30) REVERT: D 355 ARG cc_start: 0.9510 (ptm-80) cc_final: 0.9108 (ptm-80) REVERT: D 369 ASN cc_start: 0.8411 (p0) cc_final: 0.8082 (p0) REVERT: D 385 MET cc_start: 0.9028 (ttm) cc_final: 0.8535 (ttm) REVERT: D 395 GLU cc_start: 0.8994 (mp0) cc_final: 0.8317 (mp0) REVERT: D 399 GLU cc_start: 0.9119 (pm20) cc_final: 0.8897 (mp0) REVERT: D 400 TYR cc_start: 0.8308 (m-10) cc_final: 0.7944 (m-10) REVERT: D 404 ASP cc_start: 0.9293 (t0) cc_final: 0.9048 (t70) REVERT: E 21 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.8757 (tm-30) REVERT: E 51 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8971 (pp) REVERT: E 80 ILE cc_start: 0.9258 (pp) cc_final: 0.9024 (pp) REVERT: E 84 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8501 (mm) REVERT: E 105 ARG cc_start: 0.9212 (mtm110) cc_final: 0.8816 (mtm110) REVERT: E 235 LEU cc_start: 0.8865 (mt) cc_final: 0.8415 (mp) REVERT: E 258 TYR cc_start: 0.9183 (t80) cc_final: 0.8897 (t80) REVERT: E 259 ARG cc_start: 0.9310 (ttm-80) cc_final: 0.9086 (ttm-80) REVERT: E 274 ASP cc_start: 0.9134 (t0) cc_final: 0.8883 (t0) REVERT: E 352 GLU cc_start: 0.9311 (tm-30) cc_final: 0.9094 (tm-30) REVERT: E 385 MET cc_start: 0.9010 (ttm) cc_final: 0.8365 (ttm) REVERT: E 395 GLU cc_start: 0.8932 (mp0) cc_final: 0.8356 (mp0) REVERT: E 409 LYS cc_start: 0.8757 (ttmp) cc_final: 0.8293 (ttmt) REVERT: E 510 GLU cc_start: 0.8244 (tp30) cc_final: 0.8012 (tp30) REVERT: F 21 GLN cc_start: 0.9180 (pt0) cc_final: 0.8838 (tm-30) REVERT: F 51 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.8966 (pp) REVERT: F 84 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8521 (mm) REVERT: F 105 ARG cc_start: 0.9267 (mtm110) cc_final: 0.9015 (mtm110) REVERT: F 108 LYS cc_start: 0.9582 (ttpp) cc_final: 0.9360 (tppt) REVERT: F 109 LYS cc_start: 0.9421 (mptt) cc_final: 0.9141 (mttt) REVERT: F 258 TYR cc_start: 0.9168 (t80) cc_final: 0.8931 (t80) REVERT: F 274 ASP cc_start: 0.9101 (t0) cc_final: 0.8890 (t0) REVERT: F 276 SER cc_start: 0.9016 (p) cc_final: 0.8732 (p) REVERT: F 332 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8705 (pp) REVERT: F 352 GLU cc_start: 0.9320 (tm-30) cc_final: 0.9088 (tm-30) REVERT: F 369 ASN cc_start: 0.8347 (p0) cc_final: 0.8051 (p0) REVERT: F 385 MET cc_start: 0.8886 (ttm) cc_final: 0.8449 (ttm) REVERT: F 395 GLU cc_start: 0.8958 (mp0) cc_final: 0.8334 (mp0) REVERT: F 404 ASP cc_start: 0.9315 (t0) cc_final: 0.9083 (t70) REVERT: F 407 ARG cc_start: 0.8985 (ttt90) cc_final: 0.8761 (ttt90) REVERT: F 438 LYS cc_start: 0.8205 (mmtt) cc_final: 0.7981 (mmtm) REVERT: G 21 GLN cc_start: 0.9165 (pt0) cc_final: 0.8770 (tm-30) REVERT: G 50 ASP cc_start: 0.9123 (t70) cc_final: 0.8843 (t0) REVERT: G 51 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9019 (pp) REVERT: G 84 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8410 (mm) REVERT: G 109 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.8982 (mttm) REVERT: G 258 TYR cc_start: 0.9193 (t80) cc_final: 0.8876 (t80) REVERT: G 332 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8770 (pp) REVERT: G 352 GLU cc_start: 0.9287 (tm-30) cc_final: 0.9062 (tm-30) REVERT: G 385 MET cc_start: 0.8971 (ttm) cc_final: 0.8424 (ttm) REVERT: G 395 GLU cc_start: 0.8864 (mp0) cc_final: 0.8305 (mp0) REVERT: G 399 GLU cc_start: 0.9134 (pm20) cc_final: 0.8871 (pm20) REVERT: G 400 TYR cc_start: 0.8381 (m-80) cc_final: 0.8034 (m-10) REVERT: H 51 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9105 (pp) REVERT: H 84 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8301 (mm) REVERT: H 105 ARG cc_start: 0.9220 (mtm110) cc_final: 0.8901 (mtm110) REVERT: H 332 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8826 (pp) REVERT: H 352 GLU cc_start: 0.9344 (tm-30) cc_final: 0.8951 (tm-30) REVERT: H 355 ARG cc_start: 0.9511 (ptm-80) cc_final: 0.9105 (ptm-80) REVERT: H 369 ASN cc_start: 0.8421 (p0) cc_final: 0.8090 (p0) REVERT: H 385 MET cc_start: 0.8986 (ttm) cc_final: 0.8360 (ttm) REVERT: H 395 GLU cc_start: 0.8906 (mp0) cc_final: 0.8291 (mp0) outliers start: 172 outliers final: 106 residues processed: 1003 average time/residue: 0.1599 time to fit residues: 253.5090 Evaluate side-chains 1003 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 873 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 65 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 297 LEU Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 313 LEU 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 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 297 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 325 MET 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 500 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 45 THR 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 63 THR 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 377 LEU 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 36 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 63 THR 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 74 THR Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 280 SER 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 373 ILE 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 21 GLN 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 78 MET Chi-restraints excluded: chain E residue 84 LEU 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 281 ILE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 327 SER 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 36 LEU 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 84 LEU Chi-restraints excluded: chain F residue 107 VAL 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 386 MET Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 36 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 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 313 LEU Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 332 ILE 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 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 377 LEU Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 471 ILE 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: 0.0970 chunk 233 optimal weight: 0.0870 chunk 104 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 295 optimal weight: 4.9990 chunk 281 optimal weight: 0.5980 chunk 252 optimal weight: 4.9990 chunk 133 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN D 454 HIS ** 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 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 265 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.106050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.085334 restraints weight = 41208.997| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 3.96 r_work: 0.2818 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23488 Z= 0.139 Angle : 0.711 8.792 31792 Z= 0.353 Chirality : 0.047 0.181 3656 Planarity : 0.004 0.038 4000 Dihedral : 8.805 84.523 3339 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 5.29 % Allowed : 26.85 % Favored : 67.87 % 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: -1.96 (0.15), residues: 2960 helix: -1.13 (0.15), residues: 1128 sheet: -2.04 (0.26), residues: 320 loop : -1.17 (0.16), residues: 1512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 105 TYR 0.015 0.001 TYR G 353 PHE 0.013 0.001 PHE A 401 HIS 0.002 0.000 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (23480) covalent geometry : angle 0.71098 / 0.35 (31792) hydrogen bonds : bond 0.03459 / 2.26 ( 841) hydrogen bonds : angle 5.23993 / 3.56 ( 2427) Misc. bond : bond 0.00040 / 0.02 ( 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 1098 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 972 time to evaluate : 0.869 Fit side-chains REVERT: A 1 MET cc_start: 0.4364 (ptp) cc_final: 0.3844 (ptm) REVERT: A 21 GLN cc_start: 0.9083 (pt0) cc_final: 0.8514 (tm-30) REVERT: A 51 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.8959 (pp) REVERT: A 105 ARG cc_start: 0.9158 (mtm110) cc_final: 0.8589 (mtm110) REVERT: A 109 LYS cc_start: 0.9452 (mttp) cc_final: 0.9165 (mptt) REVERT: A 258 TYR cc_start: 0.9149 (t80) cc_final: 0.8870 (t80) REVERT: A 276 SER cc_start: 0.9102 (p) cc_final: 0.8836 (p) REVERT: A 325 MET cc_start: 0.8600 (ptm) cc_final: 0.8384 (ptt) REVERT: A 332 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8825 (pp) REVERT: A 352 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8979 (tm-30) REVERT: A 385 MET cc_start: 0.9014 (ttm) cc_final: 0.8386 (ttm) REVERT: A 395 GLU cc_start: 0.8940 (mp0) cc_final: 0.8265 (mp0) REVERT: A 406 ILE cc_start: 0.9167 (mm) cc_final: 0.8887 (mp) REVERT: A 438 LYS cc_start: 0.9074 (mttt) cc_final: 0.8543 (mmtt) REVERT: B 25 ASN cc_start: 0.9099 (m-40) cc_final: 0.8772 (p0) REVERT: B 50 ASP cc_start: 0.9068 (t70) cc_final: 0.8817 (t0) REVERT: B 51 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8983 (pp) REVERT: B 105 ARG cc_start: 0.9177 (mtm110) cc_final: 0.8830 (mtm110) REVERT: B 258 TYR cc_start: 0.9102 (t80) cc_final: 0.8892 (t80) REVERT: B 276 SER cc_start: 0.8993 (p) cc_final: 0.8742 (p) REVERT: B 285 ASN cc_start: 0.9478 (m-40) cc_final: 0.9252 (m-40) REVERT: B 332 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8712 (pp) REVERT: B 352 GLU cc_start: 0.9228 (tm-30) cc_final: 0.8979 (tm-30) REVERT: B 385 MET cc_start: 0.8950 (ttm) cc_final: 0.8480 (ttm) REVERT: B 395 GLU cc_start: 0.8869 (mp0) cc_final: 0.8249 (mp0) REVERT: B 399 GLU cc_start: 0.8899 (pm20) cc_final: 0.8695 (mp0) REVERT: B 400 TYR cc_start: 0.8433 (m-10) cc_final: 0.7162 (m-10) REVERT: B 404 ASP cc_start: 0.9239 (t0) cc_final: 0.8983 (t0) REVERT: B 407 ARG cc_start: 0.8939 (ttt-90) cc_final: 0.8693 (ttt-90) REVERT: B 410 LYS cc_start: 0.8727 (ptmt) cc_final: 0.8497 (ptmt) REVERT: B 438 LYS cc_start: 0.9098 (mttt) cc_final: 0.8623 (mmtt) REVERT: C 21 GLN cc_start: 0.9103 (pt0) cc_final: 0.8638 (tm-30) REVERT: C 51 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8974 (pp) REVERT: C 66 VAL cc_start: 0.7796 (OUTLIER) cc_final: 0.7526 (p) REVERT: C 109 LYS cc_start: 0.9633 (mmmt) cc_final: 0.9024 (tptt) REVERT: C 276 SER cc_start: 0.8683 (p) cc_final: 0.8354 (p) REVERT: C 279 ASN cc_start: 0.8973 (t0) cc_final: 0.8163 (t0) REVERT: C 332 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8726 (pp) REVERT: C 385 MET cc_start: 0.8968 (ttm) cc_final: 0.8551 (ttm) REVERT: C 395 GLU cc_start: 0.8969 (mp0) cc_final: 0.8399 (mp0) REVERT: C 400 TYR cc_start: 0.8058 (m-10) cc_final: 0.7196 (m-10) REVERT: C 407 ARG cc_start: 0.9077 (ttt-90) cc_final: 0.8515 (ttt-90) REVERT: C 438 LYS cc_start: 0.9105 (mttt) cc_final: 0.8526 (mmtm) REVERT: C 510 GLU cc_start: 0.8170 (tp30) cc_final: 0.7891 (tp30) REVERT: D 21 GLN cc_start: 0.9084 (pt0) cc_final: 0.8641 (tm-30) REVERT: D 25 ASN cc_start: 0.9077 (m-40) cc_final: 0.8754 (p0) REVERT: D 28 ASP cc_start: 0.8724 (m-30) cc_final: 0.8506 (m-30) REVERT: D 50 ASP cc_start: 0.9113 (t70) cc_final: 0.8875 (t0) REVERT: D 105 ARG cc_start: 0.9274 (mtm110) cc_final: 0.8965 (mtm110) REVERT: D 109 LYS cc_start: 0.9496 (mttt) cc_final: 0.9190 (mttt) REVERT: D 258 TYR cc_start: 0.9171 (t80) cc_final: 0.8906 (t80) REVERT: D 276 SER cc_start: 0.8955 (p) cc_final: 0.8710 (p) REVERT: D 285 ASN cc_start: 0.9352 (m-40) cc_final: 0.9100 (m-40) REVERT: D 332 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8734 (pp) REVERT: D 385 MET cc_start: 0.9050 (ttm) cc_final: 0.8597 (ttm) REVERT: D 395 GLU cc_start: 0.8973 (mp0) cc_final: 0.8298 (mp0) REVERT: D 399 GLU cc_start: 0.9174 (pm20) cc_final: 0.8921 (mp0) REVERT: D 404 ASP cc_start: 0.9210 (t0) cc_final: 0.8958 (t70) REVERT: E 21 GLN cc_start: 0.9108 (pt0) cc_final: 0.8691 (tm-30) REVERT: E 51 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8820 (pp) REVERT: E 258 TYR cc_start: 0.9163 (t80) cc_final: 0.8890 (t80) REVERT: E 274 ASP cc_start: 0.9144 (t0) cc_final: 0.8896 (t0) REVERT: E 276 SER cc_start: 0.9087 (p) cc_final: 0.8823 (p) REVERT: E 352 GLU cc_start: 0.9260 (tm-30) cc_final: 0.9018 (tm-30) REVERT: E 355 ARG cc_start: 0.9226 (ptm-80) cc_final: 0.8785 (ptm-80) REVERT: E 385 MET cc_start: 0.9025 (ttm) cc_final: 0.8466 (ttm) REVERT: E 395 GLU cc_start: 0.8927 (mp0) cc_final: 0.8340 (mp0) REVERT: E 510 GLU cc_start: 0.8306 (tp30) cc_final: 0.8052 (tp30) REVERT: F 21 GLN cc_start: 0.9071 (pt0) cc_final: 0.8677 (tm-30) REVERT: F 51 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8894 (pp) REVERT: F 105 ARG cc_start: 0.9142 (mtm110) cc_final: 0.8898 (mtm110) REVERT: F 109 LYS cc_start: 0.9453 (mptt) cc_final: 0.9054 (mttm) REVERT: F 274 ASP cc_start: 0.9118 (t0) cc_final: 0.8878 (t0) REVERT: F 276 SER cc_start: 0.8779 (p) cc_final: 0.8484 (p) REVERT: F 279 ASN cc_start: 0.8875 (t0) cc_final: 0.8281 (t0) REVERT: F 285 ASN cc_start: 0.9373 (m-40) cc_final: 0.9152 (m-40) REVERT: F 332 ILE cc_start: 0.8797 (OUTLIER) cc_final: 0.8551 (pp) REVERT: F 352 GLU cc_start: 0.9244 (tm-30) cc_final: 0.9000 (tm-30) REVERT: F 355 ARG cc_start: 0.9272 (ptm-80) cc_final: 0.8859 (ptm-80) REVERT: F 385 MET cc_start: 0.8859 (ttm) cc_final: 0.8469 (ttm) REVERT: F 395 GLU cc_start: 0.8908 (mp0) cc_final: 0.8264 (mp0) REVERT: F 404 ASP cc_start: 0.9298 (t0) cc_final: 0.9043 (t70) REVERT: F 407 ARG cc_start: 0.8910 (ttt90) cc_final: 0.8682 (ttt90) REVERT: F 438 LYS cc_start: 0.8257 (mmtt) cc_final: 0.8022 (mmtm) REVERT: G 21 GLN cc_start: 0.9188 (pt0) cc_final: 0.8761 (tm-30) REVERT: G 50 ASP cc_start: 0.9167 (t70) cc_final: 0.8952 (t0) REVERT: G 51 LEU cc_start: 0.9254 (OUTLIER) cc_final: 0.8929 (pp) REVERT: G 109 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.8997 (tmtt) REVERT: G 279 ASN cc_start: 0.8971 (t0) cc_final: 0.8424 (t0) REVERT: G 332 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8694 (pp) REVERT: G 352 GLU cc_start: 0.9247 (tm-30) cc_final: 0.8986 (tm-30) REVERT: G 355 ARG cc_start: 0.9164 (ptm-80) cc_final: 0.8689 (ptm-80) REVERT: G 385 MET cc_start: 0.8925 (ttm) cc_final: 0.8412 (ttm) REVERT: G 395 GLU cc_start: 0.8741 (mp0) cc_final: 0.8230 (mp0) REVERT: G 399 GLU cc_start: 0.9108 (pm20) cc_final: 0.8838 (pm20) REVERT: G 400 TYR cc_start: 0.8351 (m-80) cc_final: 0.7948 (m-10) REVERT: H 25 ASN cc_start: 0.9064 (m-40) cc_final: 0.8785 (p0) REVERT: H 51 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8929 (pp) REVERT: H 256 ASP cc_start: 0.9249 (m-30) cc_final: 0.8764 (p0) REVERT: H 276 SER cc_start: 0.9070 (p) cc_final: 0.8852 (p) REVERT: H 285 ASN cc_start: 0.9270 (m-40) cc_final: 0.9061 (m-40) REVERT: H 332 ILE cc_start: 0.9015 (OUTLIER) cc_final: 0.8781 (pp) REVERT: H 385 MET cc_start: 0.8979 (ttm) cc_final: 0.8363 (ttm) REVERT: H 395 GLU cc_start: 0.8889 (mp0) cc_final: 0.8333 (mp0) outliers start: 126 outliers final: 77 residues processed: 1027 average time/residue: 0.1552 time to fit residues: 253.1192 Evaluate side-chains 1026 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 933 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 332 ILE 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 280 SER 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 417 LEU Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 42 ILE 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 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 500 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 373 ILE 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 51 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 281 ILE 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 36 LEU 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 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 386 MET Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 36 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 78 MET Chi-restraints excluded: chain G residue 109 LYS Chi-restraints excluded: chain G residue 260 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 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 65 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 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: 0.6980 chunk 227 optimal weight: 3.9990 chunk 225 optimal weight: 0.8980 chunk 287 optimal weight: 0.7980 chunk 16 optimal weight: 2.9990 chunk 261 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 247 optimal weight: 0.5980 chunk 292 optimal weight: 0.9980 chunk 185 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 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** ** D 279 ASN ** 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.106951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.086075 restraints weight = 40901.509| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.98 r_work: 0.2829 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4079 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= 0.146 Angle : 0.723 9.624 31792 Z= 0.359 Chirality : 0.048 0.209 3656 Planarity : 0.004 0.050 4000 Dihedral : 8.602 82.510 3337 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 5.29 % Allowed : 27.10 % Favored : 67.62 % 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: -1.20 (0.15), residues: 1136 sheet: -1.89 (0.27), residues: 320 loop : -1.11 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 105 TYR 0.015 0.001 TYR H 258 PHE 0.012 0.001 PHE D 401 HIS 0.005 0.000 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (23480) covalent geometry : angle 0.72302 / 0.36 (31792) hydrogen bonds : bond 0.03412 / 2.19 ( 841) hydrogen bonds : angle 5.22286 / 3.56 ( 2427) Misc. bond : bond 0.00069 / 0.03 ( 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 1106 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 980 time to evaluate : 0.926 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4410 (ptp) cc_final: 0.3885 (ptm) REVERT: A 21 GLN cc_start: 0.9106 (pt0) cc_final: 0.8678 (tm-30) REVERT: A 25 ASN cc_start: 0.9164 (m-40) cc_final: 0.8798 (m-40) REVERT: A 51 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8726 (pp) REVERT: A 105 ARG cc_start: 0.9163 (mtm110) cc_final: 0.8867 (mtm110) REVERT: A 109 LYS cc_start: 0.9433 (mttp) cc_final: 0.9088 (mptt) REVERT: A 258 TYR cc_start: 0.9142 (t80) cc_final: 0.8913 (t80) REVERT: A 276 SER cc_start: 0.9069 (p) cc_final: 0.8811 (p) REVERT: A 332 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8836 (pp) REVERT: A 352 GLU cc_start: 0.9197 (tm-30) cc_final: 0.8952 (tm-30) REVERT: A 355 ARG cc_start: 0.9211 (ptm-80) cc_final: 0.8911 (ptm-80) REVERT: A 385 MET cc_start: 0.8964 (ttm) cc_final: 0.8363 (ttm) REVERT: A 395 GLU cc_start: 0.8984 (mp0) cc_final: 0.8372 (mp0) REVERT: A 404 ASP cc_start: 0.9188 (t70) cc_final: 0.8984 (t70) REVERT: A 406 ILE cc_start: 0.9187 (mm) cc_final: 0.8918 (mp) REVERT: A 438 LYS cc_start: 0.9145 (mttt) cc_final: 0.8550 (mmtm) REVERT: B 21 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8730 (tm-30) REVERT: B 25 ASN cc_start: 0.9122 (m-40) cc_final: 0.8501 (p0) REVERT: B 50 ASP cc_start: 0.9044 (t70) cc_final: 0.8795 (t0) REVERT: B 51 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8891 (pp) REVERT: B 276 SER cc_start: 0.8983 (p) cc_final: 0.8710 (p) REVERT: B 332 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8690 (pp) REVERT: B 352 GLU cc_start: 0.9193 (tm-30) cc_final: 0.8960 (tm-30) REVERT: B 355 ARG cc_start: 0.9158 (ptm-80) cc_final: 0.8877 (ptm-80) REVERT: B 385 MET cc_start: 0.8964 (ttm) cc_final: 0.8320 (ttm) REVERT: B 395 GLU cc_start: 0.8911 (mp0) cc_final: 0.8298 (mp0) REVERT: B 404 ASP cc_start: 0.9250 (t0) cc_final: 0.8989 (t70) REVERT: B 407 ARG cc_start: 0.8989 (ttt-90) cc_final: 0.8725 (ttt-90) REVERT: B 438 LYS cc_start: 0.9088 (mttt) cc_final: 0.8594 (mmtm) REVERT: C 21 GLN cc_start: 0.9109 (pt0) cc_final: 0.8624 (tm-30) REVERT: C 51 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8813 (pp) REVERT: C 66 VAL cc_start: 0.7880 (OUTLIER) cc_final: 0.6934 (t) REVERT: C 109 LYS cc_start: 0.9613 (mmmt) cc_final: 0.9030 (tptt) REVERT: C 276 SER cc_start: 0.8645 (p) cc_final: 0.8338 (p) REVERT: C 279 ASN cc_start: 0.8974 (t0) cc_final: 0.8234 (t0) REVERT: C 325 MET cc_start: 0.8604 (ptm) cc_final: 0.8320 (ptt) REVERT: C 332 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8440 (pp) REVERT: C 335 GLU cc_start: 0.8482 (tm-30) cc_final: 0.7734 (tm-30) REVERT: C 385 MET cc_start: 0.8986 (ttm) cc_final: 0.8548 (ttm) REVERT: C 395 GLU cc_start: 0.8923 (mp0) cc_final: 0.8385 (mp0) REVERT: C 400 TYR cc_start: 0.8111 (m-10) cc_final: 0.7054 (m-10) REVERT: C 407 ARG cc_start: 0.9078 (ttt-90) cc_final: 0.8566 (ttt-90) REVERT: C 438 LYS cc_start: 0.9100 (mttt) cc_final: 0.8568 (mmtm) REVERT: C 510 GLU cc_start: 0.8175 (tp30) cc_final: 0.7894 (tp30) REVERT: D 21 GLN cc_start: 0.9074 (pt0) cc_final: 0.8714 (tm-30) REVERT: D 25 ASN cc_start: 0.9187 (m-40) cc_final: 0.8831 (p0) REVERT: D 50 ASP cc_start: 0.9148 (t70) cc_final: 0.8894 (t0) REVERT: D 105 ARG cc_start: 0.9295 (mtm110) cc_final: 0.8884 (mtm110) REVERT: D 109 LYS cc_start: 0.9495 (mttt) cc_final: 0.9202 (mttt) REVERT: D 258 TYR cc_start: 0.9180 (t80) cc_final: 0.8918 (t80) REVERT: D 276 SER cc_start: 0.8926 (p) cc_final: 0.8694 (p) REVERT: D 332 ILE cc_start: 0.8956 (OUTLIER) cc_final: 0.8720 (pp) REVERT: D 385 MET cc_start: 0.8985 (ttm) cc_final: 0.8517 (ttm) REVERT: D 393 THR cc_start: 0.9242 (p) cc_final: 0.8475 (p) REVERT: D 395 GLU cc_start: 0.8991 (mp0) cc_final: 0.8339 (mp0) REVERT: D 399 GLU cc_start: 0.9187 (pm20) cc_final: 0.8968 (mp0) REVERT: D 400 TYR cc_start: 0.8320 (m-10) cc_final: 0.8107 (m-10) REVERT: D 404 ASP cc_start: 0.9257 (t0) cc_final: 0.9019 (t70) REVERT: E 21 GLN cc_start: 0.9122 (pt0) cc_final: 0.8708 (tm-30) REVERT: E 25 ASN cc_start: 0.9230 (m-40) cc_final: 0.8876 (m-40) REVERT: E 51 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8829 (pp) REVERT: E 78 MET cc_start: 0.8338 (OUTLIER) cc_final: 0.8061 (ptm) REVERT: E 105 ARG cc_start: 0.9118 (mtm110) cc_final: 0.8783 (mtm110) REVERT: E 109 LYS cc_start: 0.9378 (mttt) cc_final: 0.9113 (mttt) REVERT: E 258 TYR cc_start: 0.9171 (t80) cc_final: 0.8915 (t80) REVERT: E 259 ARG cc_start: 0.9306 (ttm-80) cc_final: 0.8848 (ttm170) REVERT: E 274 ASP cc_start: 0.9145 (t0) cc_final: 0.8888 (t0) REVERT: E 276 SER cc_start: 0.9071 (p) cc_final: 0.8870 (p) REVERT: E 352 GLU cc_start: 0.9248 (tm-30) cc_final: 0.9006 (tm-30) REVERT: E 355 ARG cc_start: 0.9229 (ptm-80) cc_final: 0.8786 (ptm-80) REVERT: E 385 MET cc_start: 0.8949 (ttm) cc_final: 0.8562 (ttm) REVERT: E 395 GLU cc_start: 0.8937 (mp0) cc_final: 0.8308 (mp0) REVERT: E 400 TYR cc_start: 0.8371 (m-10) cc_final: 0.7279 (m-10) REVERT: E 510 GLU cc_start: 0.8344 (tp30) cc_final: 0.8103 (tp30) REVERT: F 21 GLN cc_start: 0.9090 (pt0) cc_final: 0.8712 (tm-30) REVERT: F 51 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8808 (pp) REVERT: F 105 ARG cc_start: 0.9181 (mtm110) cc_final: 0.8793 (mtm110) REVERT: F 109 LYS cc_start: 0.9424 (mptt) cc_final: 0.9186 (mttt) REVERT: F 274 ASP cc_start: 0.9120 (t0) cc_final: 0.8851 (t0) REVERT: F 276 SER cc_start: 0.8735 (p) cc_final: 0.8454 (p) REVERT: F 279 ASN cc_start: 0.8839 (t0) cc_final: 0.8261 (t0) REVERT: F 285 ASN cc_start: 0.9386 (m-40) cc_final: 0.9147 (m-40) REVERT: F 332 ILE cc_start: 0.8772 (OUTLIER) cc_final: 0.8547 (pp) REVERT: F 352 GLU cc_start: 0.9236 (tm-30) cc_final: 0.8991 (tm-30) REVERT: F 355 ARG cc_start: 0.9259 (ptm-80) cc_final: 0.8876 (ptm-80) REVERT: F 385 MET cc_start: 0.8903 (ttm) cc_final: 0.8517 (ttm) REVERT: F 395 GLU cc_start: 0.8947 (mp0) cc_final: 0.8362 (mp0) REVERT: F 404 ASP cc_start: 0.9306 (t0) cc_final: 0.9065 (t70) REVERT: F 438 LYS cc_start: 0.8260 (mmtt) cc_final: 0.8015 (mmtm) REVERT: G 21 GLN cc_start: 0.9203 (pt0) cc_final: 0.8800 (tm-30) REVERT: G 50 ASP cc_start: 0.9178 (t70) cc_final: 0.8978 (t0) REVERT: G 51 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8782 (pp) REVERT: G 78 MET cc_start: 0.8292 (OUTLIER) cc_final: 0.7973 (ptm) REVERT: G 105 ARG cc_start: 0.8991 (mtm110) cc_final: 0.8581 (mtm110) REVERT: G 109 LYS cc_start: 0.9366 (OUTLIER) cc_final: 0.9156 (mttt) REVERT: G 279 ASN cc_start: 0.8946 (t0) cc_final: 0.8445 (t0) REVERT: G 332 ILE cc_start: 0.8944 (OUTLIER) cc_final: 0.8702 (pp) REVERT: G 352 GLU cc_start: 0.9240 (tm-30) cc_final: 0.9010 (tm-30) REVERT: G 385 MET cc_start: 0.8892 (ttm) cc_final: 0.8411 (ttm) REVERT: G 395 GLU cc_start: 0.8757 (mp0) cc_final: 0.8271 (mp0) REVERT: G 399 GLU cc_start: 0.9170 (pm20) cc_final: 0.8940 (pm20) REVERT: G 400 TYR cc_start: 0.8309 (m-80) cc_final: 0.7932 (m-10) REVERT: H 25 ASN cc_start: 0.9082 (m-40) cc_final: 0.8768 (p0) REVERT: H 51 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8800 (pp) REVERT: H 105 ARG cc_start: 0.9165 (mtm110) cc_final: 0.8906 (mtm110) REVERT: H 109 LYS cc_start: 0.9458 (mttt) cc_final: 0.9131 (mtmm) REVERT: H 256 ASP cc_start: 0.9240 (m-30) cc_final: 0.8754 (p0) REVERT: H 276 SER cc_start: 0.9025 (p) cc_final: 0.8754 (p) REVERT: H 285 ASN cc_start: 0.9256 (m-40) cc_final: 0.9027 (m-40) REVERT: H 332 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8791 (pp) REVERT: H 385 MET cc_start: 0.8911 (ttm) cc_final: 0.8336 (ttm) REVERT: H 395 GLU cc_start: 0.8887 (mp0) cc_final: 0.8360 (mp0) outliers start: 126 outliers final: 76 residues processed: 1044 average time/residue: 0.1505 time to fit residues: 251.5506 Evaluate side-chains 1035 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 940 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 21 GLN 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 417 LEU Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 42 ILE Chi-restraints excluded: chain C residue 45 THR 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 73 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 388 SER 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 65 LEU Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain D residue 309 GLN 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 373 ILE 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 78 MET Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 280 SER 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 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 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 78 MET Chi-restraints excluded: chain G residue 109 LYS Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 332 ILE 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 65 LEU Chi-restraints excluded: chain H residue 73 VAL 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 333 THR Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 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: 2.9990 chunk 239 optimal weight: 0.9980 chunk 262 optimal weight: 0.5980 chunk 148 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 253 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 126 optimal weight: 1.9990 chunk 225 optimal weight: 0.5980 chunk 200 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 GLN ** 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 279 ASN ** 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** ** F 368 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 G 498 GLN ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.105965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.086079 restraints weight = 41115.046| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 3.83 r_work: 0.2828 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4165 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= 0.159 Angle : 0.747 9.273 31792 Z= 0.368 Chirality : 0.048 0.183 3656 Planarity : 0.004 0.047 4000 Dihedral : 8.511 82.172 3336 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 5.03 % Allowed : 27.98 % Favored : 66.99 % 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: -1.86 (0.15), residues: 2960 helix: -1.11 (0.15), residues: 1136 sheet: -1.83 (0.28), residues: 320 loop : -1.08 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 105 TYR 0.022 0.001 TYR F 258 PHE 0.011 0.001 PHE H 401 HIS 0.004 0.000 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (23480) covalent geometry : angle 0.74702 / 0.37 (31792) hydrogen bonds : bond 0.03409 / 2.20 ( 841) hydrogen bonds : angle 5.19637 / 3.55 ( 2427) Misc. bond : bond 0.00082 / 0.04 ( 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 1088 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 968 time to evaluate : 0.674 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4504 (ptp) cc_final: 0.3928 (ptm) REVERT: A 21 GLN cc_start: 0.9130 (pt0) cc_final: 0.8747 (tm-30) REVERT: A 25 ASN cc_start: 0.9171 (m-40) cc_final: 0.8830 (m-40) REVERT: A 51 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.8988 (pp) REVERT: A 105 ARG cc_start: 0.9147 (mtm110) cc_final: 0.8881 (mtm110) REVERT: A 258 TYR cc_start: 0.9238 (t80) cc_final: 0.9006 (t80) REVERT: A 276 SER cc_start: 0.9095 (p) cc_final: 0.8845 (p) REVERT: A 332 ILE cc_start: 0.9122 (OUTLIER) cc_final: 0.8899 (pp) REVERT: A 352 GLU cc_start: 0.9242 (tm-30) cc_final: 0.9006 (tm-30) REVERT: A 355 ARG cc_start: 0.9235 (ptm-80) cc_final: 0.8939 (ptm-80) REVERT: A 385 MET cc_start: 0.8976 (ttm) cc_final: 0.8360 (ttm) REVERT: A 395 GLU cc_start: 0.8968 (mp0) cc_final: 0.8414 (mp0) REVERT: A 406 ILE cc_start: 0.9182 (mm) cc_final: 0.8963 (mp) REVERT: A 438 LYS cc_start: 0.9123 (mttt) cc_final: 0.8630 (mmtt) REVERT: B 21 GLN cc_start: 0.9091 (OUTLIER) cc_final: 0.8770 (tm-30) REVERT: B 25 ASN cc_start: 0.9146 (m-40) cc_final: 0.8502 (p0) REVERT: B 50 ASP cc_start: 0.9077 (t70) cc_final: 0.8856 (t0) REVERT: B 51 LEU cc_start: 0.9234 (OUTLIER) cc_final: 0.8914 (pp) REVERT: B 105 ARG cc_start: 0.9136 (mtm110) cc_final: 0.8775 (mtm110) REVERT: B 276 SER cc_start: 0.8991 (p) cc_final: 0.8720 (p) REVERT: B 332 ILE cc_start: 0.8948 (OUTLIER) cc_final: 0.8388 (pp) REVERT: B 335 GLU cc_start: 0.8658 (tm-30) cc_final: 0.7953 (tm-30) REVERT: B 352 GLU cc_start: 0.9233 (tm-30) cc_final: 0.8827 (tm-30) REVERT: B 355 ARG cc_start: 0.9199 (ptm-80) cc_final: 0.8932 (ptm-80) REVERT: B 385 MET cc_start: 0.8953 (ttm) cc_final: 0.8327 (ttm) REVERT: B 395 GLU cc_start: 0.8893 (mp0) cc_final: 0.8312 (mp0) REVERT: B 404 ASP cc_start: 0.9265 (t0) cc_final: 0.9006 (t70) REVERT: B 407 ARG cc_start: 0.8986 (ttt-90) cc_final: 0.8683 (ttt-90) REVERT: B 438 LYS cc_start: 0.9049 (mttt) cc_final: 0.8843 (tptm) REVERT: C 21 GLN cc_start: 0.9149 (pt0) cc_final: 0.8664 (tm-30) REVERT: C 51 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8802 (pp) REVERT: C 66 VAL cc_start: 0.7777 (OUTLIER) cc_final: 0.7535 (p) REVERT: C 109 LYS cc_start: 0.9609 (mmmt) cc_final: 0.9046 (tptt) REVERT: C 276 SER cc_start: 0.8630 (p) cc_final: 0.8326 (p) REVERT: C 279 ASN cc_start: 0.8978 (t0) cc_final: 0.8146 (t0) REVERT: C 322 ARG cc_start: 0.8799 (ptm-80) cc_final: 0.8395 (ptm160) REVERT: C 325 MET cc_start: 0.8636 (ptm) cc_final: 0.8361 (ptt) REVERT: C 332 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8497 (pp) REVERT: C 335 GLU cc_start: 0.8531 (tm-30) cc_final: 0.7807 (tm-30) REVERT: C 395 GLU cc_start: 0.8905 (mp0) cc_final: 0.8400 (mp0) REVERT: C 438 LYS cc_start: 0.9106 (mttt) cc_final: 0.8654 (mptt) REVERT: C 510 GLU cc_start: 0.8207 (tp30) cc_final: 0.7935 (tp30) REVERT: D 21 GLN cc_start: 0.9130 (pt0) cc_final: 0.8801 (tm-30) REVERT: D 25 ASN cc_start: 0.9151 (m-40) cc_final: 0.8728 (p0) REVERT: D 105 ARG cc_start: 0.9275 (mtm110) cc_final: 0.8664 (mtm110) REVERT: D 109 LYS cc_start: 0.9504 (mttt) cc_final: 0.9037 (tmtt) REVERT: D 258 TYR cc_start: 0.9173 (t80) cc_final: 0.8911 (t80) REVERT: D 276 SER cc_start: 0.8957 (p) cc_final: 0.8717 (p) REVERT: D 332 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8777 (pp) REVERT: D 385 MET cc_start: 0.9014 (ttm) cc_final: 0.8543 (ttm) REVERT: D 395 GLU cc_start: 0.9014 (mp0) cc_final: 0.8359 (mp0) REVERT: D 399 GLU cc_start: 0.9190 (pm20) cc_final: 0.8987 (mp0) REVERT: D 404 ASP cc_start: 0.9252 (t0) cc_final: 0.8983 (t70) REVERT: D 406 ILE cc_start: 0.8977 (mp) cc_final: 0.8643 (mp) REVERT: E 21 GLN cc_start: 0.9170 (OUTLIER) cc_final: 0.8780 (tm-30) REVERT: E 25 ASN cc_start: 0.9239 (m-40) cc_final: 0.8895 (m-40) REVERT: E 51 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8874 (pp) REVERT: E 78 MET cc_start: 0.8224 (OUTLIER) cc_final: 0.7934 (ptm) REVERT: E 105 ARG cc_start: 0.9103 (mtm110) cc_final: 0.8874 (mtm110) REVERT: E 109 LYS cc_start: 0.9367 (mttt) cc_final: 0.8928 (tmtt) REVERT: E 258 TYR cc_start: 0.9185 (t80) cc_final: 0.8970 (t80) REVERT: E 274 ASP cc_start: 0.9135 (t0) cc_final: 0.8869 (t0) REVERT: E 275 SER cc_start: 0.9000 (t) cc_final: 0.8697 (t) REVERT: E 276 SER cc_start: 0.9099 (p) cc_final: 0.8878 (p) REVERT: E 352 GLU cc_start: 0.9278 (tm-30) cc_final: 0.9040 (tm-30) REVERT: E 355 ARG cc_start: 0.9271 (ptm-80) cc_final: 0.8835 (ptm-80) REVERT: E 385 MET cc_start: 0.8933 (ttm) cc_final: 0.8360 (ttm) REVERT: E 395 GLU cc_start: 0.8865 (mp0) cc_final: 0.8383 (mp0) REVERT: E 400 TYR cc_start: 0.8327 (m-10) cc_final: 0.8033 (m-10) REVERT: E 407 ARG cc_start: 0.8943 (ttt-90) cc_final: 0.8361 (tmt170) REVERT: E 510 GLU cc_start: 0.8351 (tp30) cc_final: 0.8125 (tp30) REVERT: F 21 GLN cc_start: 0.9077 (OUTLIER) cc_final: 0.8732 (tm-30) REVERT: F 51 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8849 (pp) REVERT: F 105 ARG cc_start: 0.9161 (mtm110) cc_final: 0.8943 (mtm110) REVERT: F 109 LYS cc_start: 0.9475 (mptt) cc_final: 0.9264 (mttp) REVERT: F 259 ARG cc_start: 0.9474 (ttm-80) cc_final: 0.8955 (ttm170) REVERT: F 274 ASP cc_start: 0.9110 (t0) cc_final: 0.8846 (t0) REVERT: F 276 SER cc_start: 0.8749 (p) cc_final: 0.8470 (p) REVERT: F 279 ASN cc_start: 0.8881 (t0) cc_final: 0.8286 (t0) REVERT: F 332 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8594 (pp) REVERT: F 352 GLU cc_start: 0.9248 (tm-30) cc_final: 0.9005 (tm-30) REVERT: F 355 ARG cc_start: 0.9298 (ptm-80) cc_final: 0.8933 (ptm-80) REVERT: F 385 MET cc_start: 0.8950 (ttm) cc_final: 0.8548 (ttm) REVERT: F 386 MET cc_start: 0.9227 (ptp) cc_final: 0.9026 (ptp) REVERT: F 395 GLU cc_start: 0.8899 (mp0) cc_final: 0.8376 (mp0) REVERT: F 404 ASP cc_start: 0.9302 (t0) cc_final: 0.9069 (t70) REVERT: F 407 ARG cc_start: 0.8943 (ttt90) cc_final: 0.8605 (tmt90) REVERT: F 438 LYS cc_start: 0.8377 (mmtt) cc_final: 0.8131 (mmtm) REVERT: G 21 GLN cc_start: 0.9185 (pt0) cc_final: 0.8808 (tm-30) REVERT: G 50 ASP cc_start: 0.9153 (t70) cc_final: 0.8946 (t0) REVERT: G 51 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8923 (pp) REVERT: G 78 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7911 (ptm) REVERT: G 105 ARG cc_start: 0.8996 (mtm110) cc_final: 0.8548 (mtm110) REVERT: G 258 TYR cc_start: 0.9170 (t80) cc_final: 0.8867 (t80) REVERT: G 279 ASN cc_start: 0.8947 (t0) cc_final: 0.8419 (t0) REVERT: G 332 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8445 (pp) REVERT: G 335 GLU cc_start: 0.8654 (tm-30) cc_final: 0.7928 (tm-30) REVERT: G 352 GLU cc_start: 0.9289 (tm-30) cc_final: 0.9061 (tm-30) REVERT: G 355 ARG cc_start: 0.9272 (ptm-80) cc_final: 0.8996 (ptm-80) REVERT: G 385 MET cc_start: 0.8906 (ttm) cc_final: 0.8434 (ttm) REVERT: G 395 GLU cc_start: 0.8781 (mp0) cc_final: 0.8311 (mp0) REVERT: G 399 GLU cc_start: 0.9191 (pm20) cc_final: 0.8980 (pm20) REVERT: G 400 TYR cc_start: 0.8347 (m-80) cc_final: 0.7953 (m-10) REVERT: H 21 GLN cc_start: 0.9140 (pt0) cc_final: 0.8785 (tm-30) REVERT: H 25 ASN cc_start: 0.9112 (m-40) cc_final: 0.8531 (p0) REVERT: H 51 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8831 (pp) REVERT: H 259 ARG cc_start: 0.9412 (ttm-80) cc_final: 0.8896 (ttm170) REVERT: H 285 ASN cc_start: 0.9285 (m-40) cc_final: 0.9015 (m-40) REVERT: H 332 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8851 (pp) REVERT: H 385 MET cc_start: 0.9019 (ttm) cc_final: 0.8809 (ttp) REVERT: H 395 GLU cc_start: 0.8912 (mp0) cc_final: 0.8442 (mp0) outliers start: 120 outliers final: 85 residues processed: 1029 average time/residue: 0.1573 time to fit residues: 258.1808 Evaluate side-chains 1059 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 954 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 333 THR 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 21 GLN 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 66 VAL Chi-restraints excluded: chain B residue 73 VAL 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 417 LEU Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 42 ILE 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 65 LEU 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 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 417 LEU Chi-restraints excluded: chain C residue 499 VAL 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 65 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain D residue 309 GLN 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 373 ILE 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 21 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 THR 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 327 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR 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 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 78 MET Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 282 PHE 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 5 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 235 LEU 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 333 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 168 optimal weight: 0.7980 chunk 218 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 283 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 141 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 chunk 145 optimal weight: 0.7980 chunk 178 optimal weight: 0.9980 chunk 77 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN ** 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** C 454 HIS ** D 279 ASN ** 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** ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 HIS ** 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 ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 309 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.106308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.086277 restraints weight = 41046.669| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.85 r_work: 0.2831 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23488 Z= 0.164 Angle : 0.767 8.997 31792 Z= 0.377 Chirality : 0.048 0.185 3656 Planarity : 0.004 0.043 4000 Dihedral : 8.389 81.489 3336 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.70 % Allowed : 28.94 % Favored : 66.36 % 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: -1.86 (0.15), residues: 2960 helix: -1.11 (0.15), residues: 1144 sheet: -1.81 (0.28), residues: 320 loop : -1.08 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 105 TYR 0.021 0.001 TYR E 400 PHE 0.012 0.001 PHE E 282 HIS 0.003 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 (23480) covalent geometry : angle 0.76706 / 0.38 (31792) hydrogen bonds : bond 0.03464 / 2.21 ( 841) hydrogen bonds : angle 5.22271 / 3.57 ( 2427) Misc. bond : bond 0.00087 / 0.04 ( 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 1091 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 979 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4531 (ptp) cc_final: 0.3963 (ptm) REVERT: A 21 GLN cc_start: 0.9156 (pt0) cc_final: 0.8737 (tm-30) REVERT: A 25 ASN cc_start: 0.9181 (m-40) cc_final: 0.8843 (m-40) REVERT: A 51 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9014 (pp) REVERT: A 109 LYS cc_start: 0.9583 (mmmt) cc_final: 0.9019 (tptt) REVERT: A 258 TYR cc_start: 0.9231 (t80) cc_final: 0.8978 (t80) REVERT: A 276 SER cc_start: 0.9103 (p) cc_final: 0.8757 (p) REVERT: A 332 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8928 (pp) REVERT: A 352 GLU cc_start: 0.9234 (tm-30) cc_final: 0.8995 (tm-30) REVERT: A 355 ARG cc_start: 0.9234 (ptm-80) cc_final: 0.8781 (ptm-80) REVERT: A 385 MET cc_start: 0.8944 (ttm) cc_final: 0.8383 (ttm) REVERT: A 395 GLU cc_start: 0.8919 (mp0) cc_final: 0.8390 (mp0) REVERT: A 406 ILE cc_start: 0.9184 (mm) cc_final: 0.8960 (mp) REVERT: A 438 LYS cc_start: 0.9146 (mttt) cc_final: 0.8871 (tptm) REVERT: B 21 GLN cc_start: 0.9089 (OUTLIER) cc_final: 0.8584 (tm-30) REVERT: B 51 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8920 (pp) REVERT: B 105 ARG cc_start: 0.9125 (mtm110) cc_final: 0.8835 (mtm110) REVERT: B 276 SER cc_start: 0.8973 (p) cc_final: 0.8699 (p) REVERT: B 332 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8360 (pp) REVERT: B 335 GLU cc_start: 0.8639 (tm-30) cc_final: 0.7934 (tm-30) REVERT: B 352 GLU cc_start: 0.9236 (tm-30) cc_final: 0.8997 (tm-30) REVERT: B 355 ARG cc_start: 0.9194 (ptm-80) cc_final: 0.8940 (ptm-80) REVERT: B 385 MET cc_start: 0.8944 (ttm) cc_final: 0.8318 (ttm) REVERT: B 395 GLU cc_start: 0.8870 (mp0) cc_final: 0.8290 (mp0) REVERT: B 400 TYR cc_start: 0.8565 (m-10) cc_final: 0.7394 (m-10) REVERT: B 404 ASP cc_start: 0.9271 (t0) cc_final: 0.9019 (t70) REVERT: B 407 ARG cc_start: 0.8998 (ttt-90) cc_final: 0.8690 (ttt-90) REVERT: C 21 GLN cc_start: 0.9129 (pt0) cc_final: 0.8621 (tm-30) REVERT: C 51 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8752 (pp) REVERT: C 66 VAL cc_start: 0.7745 (OUTLIER) cc_final: 0.6739 (t) REVERT: C 109 LYS cc_start: 0.9608 (mmmt) cc_final: 0.9060 (tptt) REVERT: C 256 ASP cc_start: 0.9313 (m-30) cc_final: 0.8693 (p0) REVERT: C 276 SER cc_start: 0.8594 (p) cc_final: 0.8285 (p) REVERT: C 279 ASN cc_start: 0.8969 (t0) cc_final: 0.8116 (t0) REVERT: C 325 MET cc_start: 0.8658 (ptm) cc_final: 0.8382 (ptt) REVERT: C 332 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8502 (pp) REVERT: C 335 GLU cc_start: 0.8500 (tm-30) cc_final: 0.7785 (tm-30) REVERT: C 395 GLU cc_start: 0.8949 (mp0) cc_final: 0.8460 (mp0) REVERT: C 438 LYS cc_start: 0.9146 (mttt) cc_final: 0.8700 (mptt) REVERT: C 510 GLU cc_start: 0.8223 (tp30) cc_final: 0.7954 (tp30) REVERT: D 21 GLN cc_start: 0.9142 (pt0) cc_final: 0.8778 (tm-30) REVERT: D 25 ASN cc_start: 0.9180 (m-40) cc_final: 0.8757 (p0) REVERT: D 105 ARG cc_start: 0.9276 (mtm110) cc_final: 0.8686 (mtm110) REVERT: D 109 LYS cc_start: 0.9508 (mttt) cc_final: 0.9098 (mttt) REVERT: D 244 LEU cc_start: 0.8813 (mt) cc_final: 0.8528 (mt) REVERT: D 258 TYR cc_start: 0.9167 (t80) cc_final: 0.8934 (t80) REVERT: D 276 SER cc_start: 0.8951 (p) cc_final: 0.8710 (p) REVERT: D 332 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8798 (pp) REVERT: D 369 ASN cc_start: 0.8460 (p0) cc_final: 0.8166 (p0) REVERT: D 385 MET cc_start: 0.9011 (ttm) cc_final: 0.8536 (ttm) REVERT: D 395 GLU cc_start: 0.8956 (mp0) cc_final: 0.8477 (mp0) REVERT: D 404 ASP cc_start: 0.9264 (t0) cc_final: 0.8989 (t70) REVERT: D 406 ILE cc_start: 0.8969 (mp) cc_final: 0.8637 (mp) REVERT: D 407 ARG cc_start: 0.8898 (ttt90) cc_final: 0.8047 (tpt-90) REVERT: D 510 GLU cc_start: 0.8339 (tp30) cc_final: 0.8029 (tp30) REVERT: E 21 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.8697 (tm-30) REVERT: E 51 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8877 (pp) REVERT: E 78 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7946 (ptm) REVERT: E 256 ASP cc_start: 0.9294 (m-30) cc_final: 0.8777 (p0) REVERT: E 258 TYR cc_start: 0.9235 (t80) cc_final: 0.8978 (t80) REVERT: E 274 ASP cc_start: 0.9122 (t0) cc_final: 0.8856 (t0) REVERT: E 276 SER cc_start: 0.9142 (p) cc_final: 0.8867 (p) REVERT: E 352 GLU cc_start: 0.9272 (tm-30) cc_final: 0.9034 (tm-30) REVERT: E 355 ARG cc_start: 0.9283 (ptm-80) cc_final: 0.8861 (ptm-80) REVERT: E 385 MET cc_start: 0.8931 (ttm) cc_final: 0.8384 (ttm) REVERT: E 395 GLU cc_start: 0.8873 (mp0) cc_final: 0.8409 (mp0) REVERT: E 400 TYR cc_start: 0.8333 (m-10) cc_final: 0.7669 (m-10) REVERT: E 449 ASP cc_start: 0.9332 (p0) cc_final: 0.8787 (t0) REVERT: E 510 GLU cc_start: 0.8364 (tp30) cc_final: 0.8146 (tp30) REVERT: F 21 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8721 (tm-30) REVERT: F 51 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8838 (pp) REVERT: F 105 ARG cc_start: 0.9175 (mtm110) cc_final: 0.8787 (mtm110) REVERT: F 109 LYS cc_start: 0.9498 (mptt) cc_final: 0.9278 (mttt) REVERT: F 244 LEU cc_start: 0.8817 (mt) cc_final: 0.8541 (mt) REVERT: F 257 LYS cc_start: 0.9404 (mttt) cc_final: 0.9045 (mttm) REVERT: F 259 ARG cc_start: 0.9470 (ttm-80) cc_final: 0.8947 (ttm170) REVERT: F 274 ASP cc_start: 0.9159 (t0) cc_final: 0.8940 (t0) REVERT: F 276 SER cc_start: 0.8729 (p) cc_final: 0.8451 (p) REVERT: F 279 ASN cc_start: 0.8903 (t0) cc_final: 0.8309 (t0) REVERT: F 332 ILE cc_start: 0.8818 (OUTLIER) cc_final: 0.8586 (pp) REVERT: F 352 GLU cc_start: 0.9250 (tm-30) cc_final: 0.9008 (tm-30) REVERT: F 355 ARG cc_start: 0.9321 (ptm-80) cc_final: 0.8997 (ptm-80) REVERT: F 385 MET cc_start: 0.8934 (ttm) cc_final: 0.8534 (ttm) REVERT: F 395 GLU cc_start: 0.8889 (mp0) cc_final: 0.8386 (mp0) REVERT: F 438 LYS cc_start: 0.8447 (mmtt) cc_final: 0.8153 (mmtm) REVERT: G 21 GLN cc_start: 0.9188 (pt0) cc_final: 0.8829 (tm-30) REVERT: G 50 ASP cc_start: 0.9118 (t70) cc_final: 0.8895 (t0) REVERT: G 51 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8908 (pp) REVERT: G 78 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7916 (ptm) REVERT: G 105 ARG cc_start: 0.8805 (mtm110) cc_final: 0.8581 (mtm110) REVERT: G 256 ASP cc_start: 0.9251 (m-30) cc_final: 0.8721 (p0) REVERT: G 258 TYR cc_start: 0.9171 (t80) cc_final: 0.8884 (t80) REVERT: G 279 ASN cc_start: 0.8879 (t0) cc_final: 0.8313 (t0) REVERT: G 332 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8521 (pp) REVERT: G 335 GLU cc_start: 0.8644 (tm-30) cc_final: 0.7911 (tm-30) REVERT: G 352 GLU cc_start: 0.9289 (tm-30) cc_final: 0.9064 (tm-30) REVERT: G 355 ARG cc_start: 0.9254 (ptm-80) cc_final: 0.9005 (ptm-80) REVERT: G 385 MET cc_start: 0.8885 (ttm) cc_final: 0.8423 (ttm) REVERT: G 395 GLU cc_start: 0.8798 (mp0) cc_final: 0.8373 (mp0) REVERT: G 399 GLU cc_start: 0.9191 (pm20) cc_final: 0.8985 (pm20) REVERT: G 400 TYR cc_start: 0.8349 (m-80) cc_final: 0.7941 (m-10) REVERT: G 438 LYS cc_start: 0.7983 (mmtt) cc_final: 0.7640 (mmtt) REVERT: H 21 GLN cc_start: 0.9142 (pt0) cc_final: 0.8796 (tm-30) REVERT: H 25 ASN cc_start: 0.9111 (m-40) cc_final: 0.8527 (p0) REVERT: H 51 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8830 (pp) REVERT: H 105 ARG cc_start: 0.9068 (mtm110) cc_final: 0.8746 (mtm110) REVERT: H 109 LYS cc_start: 0.9627 (mmmt) cc_final: 0.9367 (mttt) REVERT: H 259 ARG cc_start: 0.9401 (ttm-80) cc_final: 0.8884 (ttm170) REVERT: H 285 ASN cc_start: 0.9344 (m-40) cc_final: 0.9088 (m110) REVERT: H 332 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8548 (pp) REVERT: H 335 GLU cc_start: 0.8573 (tm-30) cc_final: 0.7872 (tm-30) REVERT: H 385 MET cc_start: 0.8998 (ttm) cc_final: 0.8788 (ttp) REVERT: H 395 GLU cc_start: 0.8930 (mp0) cc_final: 0.8490 (mp0) outliers start: 112 outliers final: 77 residues processed: 1033 average time/residue: 0.1545 time to fit residues: 254.5808 Evaluate side-chains 1055 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 958 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 333 THR 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 21 GLN 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 66 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 280 SER 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 500 GLU Chi-restraints excluded: chain C residue 42 ILE 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 65 LEU 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 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 499 VAL Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 309 GLN 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 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 21 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 THR 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 327 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 21 GLN Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR 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 G residue 45 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 260 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 5 LEU Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 235 LEU 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 333 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 99 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 256 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** C 454 HIS ** D 279 ASN ** 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** ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 454 HIS ** 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.106167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.086153 restraints weight = 40833.133| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 3.84 r_work: 0.2828 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23488 Z= 0.170 Angle : 0.781 10.157 31792 Z= 0.383 Chirality : 0.049 0.199 3656 Planarity : 0.004 0.052 4000 Dihedral : 8.338 80.601 3336 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.66 % Allowed : 29.61 % Favored : 65.73 % 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: -1.81 (0.15), residues: 2960 helix: -1.05 (0.15), residues: 1144 sheet: -1.78 (0.28), residues: 320 loop : -1.08 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 105 TYR 0.024 0.001 TYR B 258 PHE 0.011 0.001 PHE A 282 HIS 0.004 0.001 HIS C 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (23480) covalent geometry : angle 0.78114 / 0.38 (31792) hydrogen bonds : bond 0.03435 / 2.20 ( 841) hydrogen bonds : angle 5.19842 / 3.55 ( 2427) Misc. bond : bond 0.00095 / 0.05 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6300.69 seconds wall clock time: 108 minutes 55.53 seconds (6535.53 seconds total)