Starting phenix.real_space_refine on Sun Sep 29 20:44:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8s_20691/09_2024/6u8s_20691.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8s_20691/09_2024/6u8s_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8s_20691/09_2024/6u8s_20691.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8s_20691/09_2024/6u8s_20691.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8s_20691/09_2024/6u8s_20691.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8s_20691/09_2024/6u8s_20691.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.054 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23080 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "B" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "C" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "D" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "E" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "F" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "G" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "H" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 13.59, per 1000 atoms: 0.59 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: 6.12 Conformation dependent library (CDL) restraints added in 2.9 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: 3.33 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: 7.57 Time building geometry restraints manager: 6.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.29: 3824 1.29 - 1.42: 5738 1.42 - 1.55: 13554 1.55 - 1.68: 124 1.68 - 1.80: 240 Bond restraints: 23480 Sorted by residual: bond pdb=" C3D NAD E 602 " pdb=" C4D NAD E 602 " ideal model delta sigma weight residual 1.531 1.301 0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C3D NAD G 602 " pdb=" C4D NAD G 602 " ideal model delta sigma weight residual 1.531 1.301 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3D NAD H 602 " pdb=" C4D NAD H 602 " ideal model delta sigma weight residual 1.531 1.301 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3D NAD C 602 " pdb=" C4D NAD C 602 " ideal model delta sigma weight residual 1.531 1.301 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3D NAD D 602 " pdb=" C4D NAD D 602 " ideal model delta sigma weight residual 1.531 1.301 0.230 2.00e-02 2.50e+03 1.32e+02 ... (remaining 23475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 30774 3.27 - 6.54: 847 6.54 - 9.82: 99 9.82 - 13.09: 48 13.09 - 16.36: 24 Bond angle restraints: 31792 Sorted by residual: angle pdb=" N1A NAD A 602 " pdb=" C6A NAD A 602 " pdb=" N6A NAD A 602 " ideal model delta sigma weight residual 119.35 102.99 16.36 3.00e+00 1.11e-01 2.97e+01 angle pdb=" N1A NAD E 602 " pdb=" C6A NAD E 602 " pdb=" N6A NAD E 602 " ideal model delta sigma weight residual 119.35 103.00 16.35 3.00e+00 1.11e-01 2.97e+01 angle pdb=" N1A NAD D 602 " pdb=" C6A NAD D 602 " pdb=" N6A NAD D 602 " ideal model delta sigma weight residual 119.35 103.00 16.35 3.00e+00 1.11e-01 2.97e+01 angle pdb=" N1A NAD C 602 " pdb=" C6A NAD C 602 " pdb=" N6A NAD C 602 " ideal model delta sigma weight residual 119.35 103.00 16.35 3.00e+00 1.11e-01 2.97e+01 angle pdb=" N1A NAD B 602 " pdb=" C6A NAD B 602 " pdb=" N6A NAD B 602 " ideal model delta sigma weight residual 119.35 103.00 16.35 3.00e+00 1.11e-01 2.97e+01 ... (remaining 31787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 12916 17.68 - 35.36: 812 35.36 - 53.04: 408 53.04 - 70.72: 88 70.72 - 88.41: 24 Dihedral angle restraints: 14248 sinusoidal: 5744 harmonic: 8504 Sorted by residual: dihedral pdb=" CA LEU B 235 " pdb=" C LEU B 235 " pdb=" N ALA B 236 " pdb=" CA ALA B 236 " ideal model delta harmonic sigma weight residual -180.00 -157.62 -22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU F 235 " pdb=" C LEU F 235 " pdb=" N ALA F 236 " pdb=" CA ALA F 236 " ideal model delta harmonic sigma weight residual -180.00 -157.65 -22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU H 235 " pdb=" C LEU H 235 " pdb=" N ALA H 236 " pdb=" CA ALA H 236 " ideal model delta harmonic sigma weight residual 180.00 -157.67 -22.33 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 14245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2755 0.071 - 0.142: 785 0.142 - 0.212: 92 0.212 - 0.283: 8 0.283 - 0.354: 16 Chirality restraints: 3656 Sorted by residual: chirality pdb=" C3B NAD H 602 " pdb=" C2B NAD H 602 " pdb=" C4B NAD H 602 " pdb=" O3B NAD H 602 " both_signs ideal model delta sigma weight residual False -2.71 -2.36 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" C3B NAD B 602 " pdb=" C2B NAD B 602 " pdb=" C4B NAD B 602 " pdb=" O3B NAD B 602 " both_signs ideal model delta sigma weight residual False -2.71 -2.36 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C3B NAD D 602 " pdb=" C2B NAD D 602 " pdb=" C4B NAD D 602 " pdb=" O3B NAD D 602 " both_signs ideal model delta sigma weight residual False -2.71 -2.36 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 3653 not shown) Planarity restraints: 4000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 63 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PRO H 64 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO H 64 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 64 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 63 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.10e+00 pdb=" N PRO D 64 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 64 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 64 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 63 " 0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO A 64 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " 0.031 5.00e-02 4.00e+02 ... (remaining 3997 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6152 2.79 - 3.31: 21250 3.31 - 3.84: 40598 3.84 - 4.37: 47493 4.37 - 4.90: 79132 Nonbonded interactions: 194625 Sorted by model distance: nonbonded pdb=" O SER F 327 " pdb=" OG SER F 327 " model vdw 2.257 3.040 nonbonded pdb=" O SER H 327 " pdb=" OG SER H 327 " model vdw 2.257 3.040 nonbonded pdb=" O SER G 327 " pdb=" OG SER G 327 " model vdw 2.257 3.040 nonbonded pdb=" O SER E 327 " pdb=" OG SER E 327 " model vdw 2.257 3.040 nonbonded pdb=" O SER D 327 " pdb=" OG SER D 327 " model vdw 2.258 3.040 ... (remaining 194620 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 2.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 51.670 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.230 23480 Z= 0.810 Angle : 1.355 16.360 31792 Z= 0.676 Chirality : 0.066 0.354 3656 Planarity : 0.007 0.056 4000 Dihedral : 15.528 88.405 8856 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 9.06 % Allowed : 8.05 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.007 0.001 HIS G 92 PHE 0.019 0.003 PHE B 401 TYR 0.019 0.003 TYR H 484 ARG 0.024 0.002 ARG C 407 *********************** 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 fitting. rotamer outliers: 216 poor density : 1262 time to evaluate : 2.676 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: 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: 0.8677 (mtm110) REVERT: A 109 LYS cc_start: 0.9327 (mttp) cc_final: 0.9037 (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: 0.8362 (p) REVERT: A 285 ASN cc_start: 0.9359 (m-40) cc_final: 0.9009 (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: 0.8343 (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: 0.9021 (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: C 404 ASP cc_start: 0.8926 (t0) cc_final: 0.8574 (t0) 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: 0.8301 (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: 0.8841 (mp0) cc_final: 0.8082 (mp0) REVERT: D 399 GLU cc_start: 0.8541 (pm20) cc_final: 0.8272 (pm20) REVERT: D 400 TYR cc_start: 0.8114 (m-80) cc_final: 0.7626 (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: 0.9004 (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 404 ASP cc_start: 0.8968 (t0) cc_final: 0.8624 (t0) REVERT: E 482 MET cc_start: 0.8964 (mtp) cc_final: 0.8705 (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: 0.9106 (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: 0.9296 (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: 0.8330 (pm20) 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: 0.9406 (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: 0.8486 (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: 0.8211 (pm20) REVERT: G 404 ASP cc_start: 0.8977 (t0) cc_final: 0.8606 (t0) REVERT: G 482 MET cc_start: 0.9001 (mtp) cc_final: 0.8758 (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: 0.8810 (mtm110) REVERT: H 106 LYS cc_start: 0.9586 (mtpt) cc_final: 0.9221 (mtpp) REVERT: H 109 LYS cc_start: 0.9339 (mttp) cc_final: 0.9109 (mttt) REVERT: H 274 ASP cc_start: 0.8788 (t0) cc_final: 0.8547 (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: 0.8277 (pm20) REVERT: H 400 TYR cc_start: 0.8104 (m-80) cc_final: 0.7875 (m-80) REVERT: H 404 ASP cc_start: 0.8928 (t0) cc_final: 0.8582 (t0) 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: 0.3295 time to fit residues: 686.9569 Evaluate side-chains 1053 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 941 time to evaluate : 2.429 ------------------------------------------------------------------------------- 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 249 optimal weight: 1.9990 chunk 224 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 232 optimal weight: 0.4980 chunk 89 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 172 optimal weight: 0.5980 chunk 268 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 25 ASN A 48 GLN A 93 HIS A 277 GLN A 309 GLN A 312 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN B 25 ASN B 48 GLN B 277 GLN B 309 GLN B 312 ASN B 343 GLN C 22 GLN C 25 ASN C 48 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN D 22 GLN D 25 ASN D 48 GLN D 93 HIS D 277 GLN ** D 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 309 GLN D 312 ASN D 343 GLN E 22 GLN E 25 ASN E 48 GLN E 93 HIS ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 ASN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 GLN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23480 Z= 0.238 Angle : 0.725 8.171 31792 Z= 0.364 Chirality : 0.047 0.162 3656 Planarity : 0.005 0.042 4000 Dihedral : 13.375 89.885 3925 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 6.92 % Allowed : 18.08 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.24 (0.13), residues: 2960 helix: -2.31 (0.12), residues: 1120 sheet: -2.66 (0.18), residues: 464 loop : -1.65 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 92 PHE 0.015 0.001 PHE A 401 TYR 0.018 0.002 TYR D 411 ARG 0.008 0.001 ARG G 407 *********************** 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 1217 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1052 time to evaluate : 2.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8643 (m-30) cc_final: 0.8248 (m-30) REVERT: A 50 ASP cc_start: 0.9026 (t0) cc_final: 0.8817 (t0) REVERT: A 105 ARG cc_start: 0.8990 (mtm110) cc_final: 0.8765 (mtm110) REVERT: A 109 LYS cc_start: 0.9302 (mttp) cc_final: 0.8652 (tptt) REVERT: A 255 ASP cc_start: 0.9236 (p0) cc_final: 0.9010 (p0) REVERT: A 275 SER cc_start: 0.9083 (t) cc_final: 0.8852 (t) REVERT: A 276 SER cc_start: 0.8444 (p) cc_final: 0.8151 (p) REVERT: A 285 ASN cc_start: 0.9398 (m-40) cc_final: 0.8994 (m-40) REVERT: A 352 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8730 (tm-30) REVERT: A 395 GLU cc_start: 0.8553 (mp0) cc_final: 0.7933 (mp0) REVERT: A 399 GLU cc_start: 0.8520 (pm20) cc_final: 0.8270 (mp0) REVERT: A 404 ASP cc_start: 0.8822 (t0) cc_final: 0.8479 (t0) REVERT: B 25 ASN cc_start: 0.8937 (m-40) cc_final: 0.8702 (p0) REVERT: B 28 ASP cc_start: 0.8651 (m-30) cc_final: 0.8300 (m-30) REVERT: B 47 ASP cc_start: 0.8914 (p0) cc_final: 0.8607 (p0) REVERT: B 50 ASP cc_start: 0.8895 (t70) cc_final: 0.8649 (t0) REVERT: B 58 LYS cc_start: 0.9372 (mmtp) cc_final: 0.9120 (mmmm) REVERT: B 105 ARG cc_start: 0.9047 (mtm110) cc_final: 0.8720 (mtm110) REVERT: B 109 LYS cc_start: 0.9306 (mttp) cc_final: 0.8896 (mttp) REVERT: B 255 ASP cc_start: 0.9260 (p0) cc_final: 0.9011 (p0) REVERT: B 276 SER cc_start: 0.8557 (p) cc_final: 0.8254 (p) REVERT: B 281 ILE cc_start: 0.8893 (tp) cc_final: 0.8519 (tt) REVERT: B 285 ASN cc_start: 0.9385 (m-40) cc_final: 0.9139 (m-40) REVERT: B 352 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8854 (tm-30) REVERT: B 395 GLU cc_start: 0.8661 (mp0) cc_final: 0.8245 (mp0) REVERT: B 399 GLU cc_start: 0.8548 (pm20) cc_final: 0.8326 (mp0) REVERT: B 400 TYR cc_start: 0.8068 (m-80) cc_final: 0.7056 (m-80) REVERT: B 404 ASP cc_start: 0.8874 (t0) cc_final: 0.8582 (t0) REVERT: B 407 ARG cc_start: 0.8798 (ttt-90) cc_final: 0.7646 (ttt-90) REVERT: B 449 ASP cc_start: 0.9122 (p0) cc_final: 0.8779 (p0) REVERT: B 461 ILE cc_start: 0.9160 (pp) cc_final: 0.8925 (pp) REVERT: B 482 MET cc_start: 0.9060 (mtp) cc_final: 0.8776 (mtp) REVERT: C 28 ASP cc_start: 0.8688 (m-30) cc_final: 0.8344 (m-30) REVERT: C 50 ASP cc_start: 0.8872 (t70) cc_final: 0.8632 (t0) REVERT: C 58 LYS cc_start: 0.9269 (mmtp) cc_final: 0.9013 (mmmm) REVERT: C 98 GLU cc_start: 0.9390 (mp0) cc_final: 0.9151 (mp0) REVERT: C 105 ARG cc_start: 0.8996 (mtm110) cc_final: 0.8726 (mtm110) REVERT: C 109 LYS cc_start: 0.9304 (mttp) cc_final: 0.8856 (mtmm) REVERT: C 255 ASP cc_start: 0.9250 (p0) cc_final: 0.9027 (p0) REVERT: C 275 SER cc_start: 0.9029 (t) cc_final: 0.8787 (t) REVERT: C 276 SER cc_start: 0.8348 (p) cc_final: 0.8041 (p) REVERT: C 281 ILE cc_start: 0.8863 (tp) cc_final: 0.8298 (tt) REVERT: C 285 ASN cc_start: 0.9422 (m-40) cc_final: 0.9096 (m-40) REVERT: C 352 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8743 (tm-30) REVERT: C 385 MET cc_start: 0.8733 (ttm) cc_final: 0.8371 (ttp) REVERT: C 395 GLU cc_start: 0.8616 (mp0) cc_final: 0.8109 (mp0) REVERT: C 399 GLU cc_start: 0.8525 (pm20) cc_final: 0.8276 (mp0) REVERT: C 404 ASP cc_start: 0.8900 (t0) cc_final: 0.8603 (t70) REVERT: D 28 ASP cc_start: 0.8662 (m-30) cc_final: 0.8248 (m-30) REVERT: D 47 ASP cc_start: 0.8870 (p0) cc_final: 0.8570 (p0) REVERT: D 50 ASP cc_start: 0.8878 (t70) cc_final: 0.8639 (t0) REVERT: D 58 LYS cc_start: 0.9350 (mmtp) cc_final: 0.9112 (mmmm) REVERT: D 105 ARG cc_start: 0.9097 (mtm110) cc_final: 0.8558 (mtm110) REVERT: D 108 LYS cc_start: 0.9550 (OUTLIER) cc_final: 0.9291 (tppt) REVERT: D 109 LYS cc_start: 0.9284 (mttp) cc_final: 0.9034 (mptt) REVERT: D 276 SER cc_start: 0.8361 (p) cc_final: 0.8122 (p) REVERT: D 285 ASN cc_start: 0.9399 (m-40) cc_final: 0.9014 (m-40) REVERT: D 352 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8707 (tm-30) REVERT: D 385 MET cc_start: 0.8808 (ttm) cc_final: 0.8477 (ttp) REVERT: D 395 GLU cc_start: 0.8655 (mp0) cc_final: 0.8094 (mp0) REVERT: D 399 GLU cc_start: 0.8565 (pm20) cc_final: 0.8285 (pm20) REVERT: D 400 TYR cc_start: 0.8178 (m-80) cc_final: 0.7931 (m-80) REVERT: D 404 ASP cc_start: 0.8784 (t0) cc_final: 0.8454 (t0) REVERT: D 414 MET cc_start: 0.9078 (mpt) cc_final: 0.8846 (mpt) REVERT: D 461 ILE cc_start: 0.9151 (pp) cc_final: 0.8924 (pp) REVERT: E 28 ASP cc_start: 0.8711 (m-30) cc_final: 0.8305 (m-30) REVERT: E 51 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.9078 (pp) REVERT: E 58 LYS cc_start: 0.9225 (mmtp) cc_final: 0.8939 (mmmm) REVERT: E 105 ARG cc_start: 0.8992 (mtm110) cc_final: 0.8755 (mtm110) REVERT: E 109 LYS cc_start: 0.9294 (mttp) cc_final: 0.8598 (tptt) REVERT: E 255 ASP cc_start: 0.9253 (p0) cc_final: 0.9044 (p0) REVERT: E 276 SER cc_start: 0.8434 (p) cc_final: 0.8100 (p) REVERT: E 281 ILE cc_start: 0.8794 (tp) cc_final: 0.7991 (tt) REVERT: E 285 ASN cc_start: 0.9357 (m-40) cc_final: 0.8956 (m-40) REVERT: E 299 VAL cc_start: 0.9446 (m) cc_final: 0.9234 (p) REVERT: E 352 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8766 (tm-30) REVERT: E 386 MET cc_start: 0.9003 (mtm) cc_final: 0.8617 (mtm) REVERT: E 395 GLU cc_start: 0.8550 (mp0) cc_final: 0.7952 (mp0) REVERT: E 399 GLU cc_start: 0.8539 (pm20) cc_final: 0.8270 (mp0) REVERT: E 400 TYR cc_start: 0.8304 (m-80) cc_final: 0.7224 (m-10) REVERT: E 404 ASP cc_start: 0.8938 (t0) cc_final: 0.8680 (t70) REVERT: E 407 ARG cc_start: 0.8961 (ttt-90) cc_final: 0.8151 (ttt-90) REVERT: E 512 ARG cc_start: 0.7909 (ttm-80) cc_final: 0.7600 (ttm-80) REVERT: F 28 ASP cc_start: 0.8656 (m-30) cc_final: 0.8269 (m-30) REVERT: F 47 ASP cc_start: 0.8936 (p0) cc_final: 0.8697 (p0) REVERT: F 105 ARG cc_start: 0.9079 (mtm110) cc_final: 0.8761 (mtm110) REVERT: F 108 LYS cc_start: 0.9567 (OUTLIER) cc_final: 0.9314 (tppt) REVERT: F 109 LYS cc_start: 0.9269 (mttp) cc_final: 0.9018 (mtmm) REVERT: F 255 ASP cc_start: 0.9256 (p0) cc_final: 0.9055 (p0) REVERT: F 276 SER cc_start: 0.8459 (p) cc_final: 0.8152 (p) REVERT: F 279 ASN cc_start: 0.8779 (t0) cc_final: 0.8514 (t0) REVERT: F 281 ILE cc_start: 0.8916 (tp) cc_final: 0.8529 (tt) REVERT: F 285 ASN cc_start: 0.9351 (m-40) cc_final: 0.9079 (m110) REVERT: F 322 ARG cc_start: 0.8023 (ppp80) cc_final: 0.7680 (ptm160) REVERT: F 352 GLU cc_start: 0.9027 (tm-30) cc_final: 0.8772 (tm-30) REVERT: F 385 MET cc_start: 0.8821 (ttm) cc_final: 0.8234 (ttp) REVERT: F 386 MET cc_start: 0.8973 (mtm) cc_final: 0.8758 (mtm) REVERT: F 395 GLU cc_start: 0.8682 (mp0) cc_final: 0.8062 (mp0) REVERT: F 399 GLU cc_start: 0.8646 (pm20) cc_final: 0.8322 (pm20) REVERT: F 400 TYR cc_start: 0.8172 (m-80) cc_final: 0.7832 (m-80) REVERT: F 404 ASP cc_start: 0.8917 (t0) cc_final: 0.8643 (t0) REVERT: F 407 ARG cc_start: 0.8995 (ttt90) cc_final: 0.8765 (ttt90) REVERT: F 461 ILE cc_start: 0.9135 (pp) cc_final: 0.8928 (pp) REVERT: F 482 MET cc_start: 0.8976 (mtp) cc_final: 0.8732 (mtp) REVERT: F 512 ARG cc_start: 0.7708 (ttm-80) cc_final: 0.7113 (ptm160) REVERT: G 28 ASP cc_start: 0.8738 (m-30) cc_final: 0.8429 (m-30) REVERT: G 50 ASP cc_start: 0.8840 (t70) cc_final: 0.8597 (t0) REVERT: G 51 LEU cc_start: 0.9431 (OUTLIER) cc_final: 0.9163 (pp) REVERT: G 70 MET cc_start: 0.8872 (mpp) cc_final: 0.8622 (mtt) REVERT: G 105 ARG cc_start: 0.8973 (mtm110) cc_final: 0.8327 (mtm110) REVERT: G 106 LYS cc_start: 0.9571 (mtpt) cc_final: 0.9349 (ttpt) REVERT: G 108 LYS cc_start: 0.9607 (OUTLIER) cc_final: 0.9372 (mttm) REVERT: G 255 ASP cc_start: 0.9189 (p0) cc_final: 0.8940 (p0) REVERT: G 275 SER cc_start: 0.9039 (t) cc_final: 0.8767 (t) REVERT: G 276 SER cc_start: 0.8364 (p) cc_final: 0.8149 (p) REVERT: G 281 ILE cc_start: 0.9087 (tp) cc_final: 0.8266 (tp) REVERT: G 285 ASN cc_start: 0.9301 (m-40) cc_final: 0.8815 (m-40) REVERT: G 352 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8793 (tm-30) REVERT: G 395 GLU cc_start: 0.8588 (mp0) cc_final: 0.8080 (mp0) REVERT: G 399 GLU cc_start: 0.8460 (pm20) cc_final: 0.8164 (pm20) REVERT: G 400 TYR cc_start: 0.8121 (m-80) cc_final: 0.7724 (m-80) REVERT: G 404 ASP cc_start: 0.8900 (t0) cc_final: 0.8575 (t70) REVERT: G 407 ARG cc_start: 0.8879 (ttt-90) cc_final: 0.8326 (ptm-80) REVERT: G 512 ARG cc_start: 0.7652 (ttm-80) cc_final: 0.7440 (ptm160) REVERT: H 25 ASN cc_start: 0.8940 (m-40) cc_final: 0.8704 (p0) REVERT: H 28 ASP cc_start: 0.8752 (m-30) cc_final: 0.8366 (m-30) REVERT: H 50 ASP cc_start: 0.8838 (t70) cc_final: 0.8605 (t0) REVERT: H 51 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9142 (pp) REVERT: H 58 LYS cc_start: 0.9372 (mmtp) cc_final: 0.9104 (mmmm) REVERT: H 105 ARG cc_start: 0.9114 (mtm110) cc_final: 0.8633 (mtm110) REVERT: H 109 LYS cc_start: 0.9301 (mttp) cc_final: 0.9084 (mttt) REVERT: H 255 ASP cc_start: 0.9146 (p0) cc_final: 0.8939 (p0) REVERT: H 276 SER cc_start: 0.8355 (p) cc_final: 0.8002 (p) REVERT: H 285 ASN cc_start: 0.9436 (m-40) cc_final: 0.9159 (m-40) REVERT: H 352 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8917 (tm-30) REVERT: H 355 ARG cc_start: 0.9510 (ptm-80) cc_final: 0.9116 (ptm-80) REVERT: H 395 GLU cc_start: 0.8585 (mp0) cc_final: 0.8150 (mp0) REVERT: H 399 GLU cc_start: 0.8478 (pm20) cc_final: 0.8238 (pm20) REVERT: H 404 ASP cc_start: 0.8846 (t0) cc_final: 0.8511 (t0) outliers start: 165 outliers final: 75 residues processed: 1117 average time/residue: 0.3341 time to fit residues: 576.8232 Evaluate side-chains 1015 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 934 time to evaluate : 2.421 ------------------------------------------------------------------------------- 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 245 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 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 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 269 ASP Chi-restraints excluded: chain G residue 282 PHE 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 51 LEU 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 149 optimal weight: 8.9990 chunk 83 optimal weight: 0.9990 chunk 223 optimal weight: 0.7980 chunk 183 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 269 optimal weight: 2.9990 chunk 290 optimal weight: 5.9990 chunk 239 optimal weight: 0.3980 chunk 267 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 216 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN B 93 HIS B 265 GLN C 22 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN E 22 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN F 498 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 265 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23480 Z= 0.240 Angle : 0.669 7.735 31792 Z= 0.341 Chirality : 0.047 0.158 3656 Planarity : 0.004 0.041 4000 Dihedral : 11.861 89.945 3801 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.70 % Allowed : 21.43 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.14), residues: 2960 helix: -1.78 (0.14), residues: 1120 sheet: -2.32 (0.21), residues: 432 loop : -1.37 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 92 PHE 0.012 0.001 PHE A 401 TYR 0.020 0.002 TYR H 400 ARG 0.007 0.001 ARG G 105 *********************** 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 1100 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 988 time to evaluate : 2.674 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8633 (m-30) cc_final: 0.8273 (m-30) REVERT: A 50 ASP cc_start: 0.9053 (t0) cc_final: 0.8846 (t0) REVERT: A 51 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.8970 (pp) REVERT: A 66 VAL cc_start: 0.7832 (OUTLIER) cc_final: 0.7600 (p) REVERT: A 70 MET cc_start: 0.9073 (mpp) cc_final: 0.8807 (mtt) REVERT: A 105 ARG cc_start: 0.8998 (mtm110) cc_final: 0.8780 (mtm110) REVERT: A 109 LYS cc_start: 0.9294 (mttp) cc_final: 0.8896 (tmtt) REVERT: A 258 TYR cc_start: 0.9002 (t80) cc_final: 0.8749 (t80) REVERT: A 276 SER cc_start: 0.8627 (p) cc_final: 0.8358 (p) REVERT: A 285 ASN cc_start: 0.9413 (m-40) cc_final: 0.9068 (m-40) REVERT: A 352 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8832 (tm-30) REVERT: A 355 ARG cc_start: 0.9415 (ptm-80) cc_final: 0.8982 (ptm-80) REVERT: A 395 GLU cc_start: 0.8597 (mp0) cc_final: 0.8015 (mp0) REVERT: A 399 GLU cc_start: 0.8556 (pm20) cc_final: 0.8343 (mp0) REVERT: A 400 TYR cc_start: 0.8373 (m-80) cc_final: 0.8075 (m-10) REVERT: A 404 ASP cc_start: 0.8893 (t0) cc_final: 0.8576 (t70) REVERT: A 438 LYS cc_start: 0.8903 (mttt) cc_final: 0.8509 (mmtt) REVERT: A 455 LYS cc_start: 0.9131 (mppt) cc_final: 0.8658 (mppt) REVERT: A 482 MET cc_start: 0.9149 (mtp) cc_final: 0.8935 (mtp) REVERT: B 25 ASN cc_start: 0.9066 (m-40) cc_final: 0.8836 (p0) REVERT: B 28 ASP cc_start: 0.8653 (m-30) cc_final: 0.8252 (m-30) REVERT: B 50 ASP cc_start: 0.8849 (t70) cc_final: 0.8618 (t0) REVERT: B 51 LEU cc_start: 0.9293 (OUTLIER) cc_final: 0.8950 (pp) REVERT: B 70 MET cc_start: 0.9095 (mpp) cc_final: 0.8742 (mtt) REVERT: B 105 ARG cc_start: 0.9038 (mtm110) cc_final: 0.8768 (mtm110) REVERT: B 109 LYS cc_start: 0.9315 (mttp) cc_final: 0.8990 (mttt) REVERT: B 258 TYR cc_start: 0.8975 (t80) cc_final: 0.8762 (t80) REVERT: B 276 SER cc_start: 0.8609 (p) cc_final: 0.8278 (p) REVERT: B 281 ILE cc_start: 0.8898 (tp) cc_final: 0.8539 (tp) REVERT: B 285 ASN cc_start: 0.9419 (m-40) cc_final: 0.9180 (m-40) REVERT: B 352 GLU cc_start: 0.9117 (tm-30) cc_final: 0.8848 (tm-30) REVERT: B 385 MET cc_start: 0.8783 (ttm) cc_final: 0.8521 (ttm) REVERT: B 395 GLU cc_start: 0.8673 (mp0) cc_final: 0.8228 (mp0) REVERT: B 399 GLU cc_start: 0.8634 (pm20) cc_final: 0.8421 (mp0) REVERT: B 404 ASP cc_start: 0.8932 (t0) cc_final: 0.8635 (t0) REVERT: B 407 ARG cc_start: 0.8796 (ttt-90) cc_final: 0.8554 (ttt90) REVERT: B 482 MET cc_start: 0.9061 (mtp) cc_final: 0.8759 (mtp) REVERT: C 28 ASP cc_start: 0.8676 (m-30) cc_final: 0.8314 (m-30) REVERT: C 51 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8919 (pp) REVERT: C 105 ARG cc_start: 0.8991 (mtm110) cc_final: 0.8750 (mtm110) REVERT: C 109 LYS cc_start: 0.9314 (mttp) cc_final: 0.8948 (mttt) REVERT: C 258 TYR cc_start: 0.8954 (t80) cc_final: 0.8684 (t80) REVERT: C 275 SER cc_start: 0.9037 (t) cc_final: 0.8811 (t) REVERT: C 276 SER cc_start: 0.8380 (p) cc_final: 0.8084 (p) REVERT: C 281 ILE cc_start: 0.8981 (tp) cc_final: 0.8757 (tt) REVERT: C 352 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8823 (tm-30) REVERT: C 395 GLU cc_start: 0.8599 (mp0) cc_final: 0.8079 (mp0) REVERT: C 399 GLU cc_start: 0.8528 (pm20) cc_final: 0.8308 (mp0) REVERT: C 404 ASP cc_start: 0.8905 (t0) cc_final: 0.8650 (t70) REVERT: C 438 LYS cc_start: 0.8907 (mtpp) cc_final: 0.8597 (mmtt) REVERT: D 25 ASN cc_start: 0.9050 (m-40) cc_final: 0.8840 (p0) REVERT: D 28 ASP cc_start: 0.8654 (m-30) cc_final: 0.8267 (m-30) REVERT: D 51 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.8989 (pp) REVERT: D 58 LYS cc_start: 0.9396 (mmtp) cc_final: 0.9053 (mmmm) REVERT: D 70 MET cc_start: 0.9038 (mpp) cc_final: 0.8806 (mtt) REVERT: D 105 ARG cc_start: 0.9087 (mtm110) cc_final: 0.8769 (mtm110) REVERT: D 108 LYS cc_start: 0.9474 (OUTLIER) cc_final: 0.9136 (tppt) REVERT: D 276 SER cc_start: 0.8439 (p) cc_final: 0.8070 (p) REVERT: D 285 ASN cc_start: 0.9440 (m-40) cc_final: 0.9093 (m-40) REVERT: D 332 ILE cc_start: 0.8979 (pp) cc_final: 0.8672 (pp) REVERT: D 352 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8693 (tm-30) REVERT: D 355 ARG cc_start: 0.9336 (ptm-80) cc_final: 0.8957 (ptm-80) REVERT: D 395 GLU cc_start: 0.8665 (mp0) cc_final: 0.8077 (mp0) REVERT: D 399 GLU cc_start: 0.8615 (pm20) cc_final: 0.8342 (pm20) REVERT: D 404 ASP cc_start: 0.8860 (t0) cc_final: 0.8555 (t0) REVERT: D 438 LYS cc_start: 0.8263 (mmtt) cc_final: 0.7885 (mmtm) REVERT: D 512 ARG cc_start: 0.8198 (ptm160) cc_final: 0.7927 (ptm160) REVERT: E 28 ASP cc_start: 0.8700 (m-30) cc_final: 0.8269 (m-30) REVERT: E 51 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9009 (pp) REVERT: E 105 ARG cc_start: 0.8997 (mtm110) cc_final: 0.8672 (mtm110) REVERT: E 109 LYS cc_start: 0.9292 (mttp) cc_final: 0.8940 (mttt) REVERT: E 258 TYR cc_start: 0.8982 (t80) cc_final: 0.8740 (t80) REVERT: E 276 SER cc_start: 0.8501 (p) cc_final: 0.8168 (p) REVERT: E 285 ASN cc_start: 0.9409 (m-40) cc_final: 0.9187 (m-40) REVERT: E 322 ARG cc_start: 0.8197 (ptm160) cc_final: 0.7793 (ptm160) REVERT: E 352 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8802 (tm-30) REVERT: E 355 ARG cc_start: 0.9395 (ptm-80) cc_final: 0.9011 (ptm-80) REVERT: E 385 MET cc_start: 0.8726 (ttm) cc_final: 0.8338 (ttm) REVERT: E 395 GLU cc_start: 0.8607 (mp0) cc_final: 0.8080 (mp0) REVERT: E 399 GLU cc_start: 0.8595 (pm20) cc_final: 0.8345 (pm20) REVERT: E 400 TYR cc_start: 0.8304 (m-80) cc_final: 0.7144 (m-10) REVERT: E 404 ASP cc_start: 0.8962 (t0) cc_final: 0.8700 (t70) REVERT: E 407 ARG cc_start: 0.8991 (ttt-90) cc_final: 0.8173 (ttt-90) REVERT: E 414 MET cc_start: 0.9194 (mpt) cc_final: 0.8855 (mpt) REVERT: E 476 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8837 (mt) REVERT: E 510 GLU cc_start: 0.7946 (tp30) cc_final: 0.7702 (tp30) REVERT: E 512 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7417 (ttm-80) REVERT: F 28 ASP cc_start: 0.8700 (m-30) cc_final: 0.8348 (m-30) REVERT: F 51 LEU cc_start: 0.9233 (OUTLIER) cc_final: 0.8929 (pp) REVERT: F 105 ARG cc_start: 0.9072 (mtm110) cc_final: 0.8671 (mtm110) REVERT: F 108 LYS cc_start: 0.9469 (OUTLIER) cc_final: 0.9195 (mttm) REVERT: F 258 TYR cc_start: 0.9127 (t80) cc_final: 0.8908 (t80) REVERT: F 276 SER cc_start: 0.8419 (p) cc_final: 0.8082 (p) REVERT: F 281 ILE cc_start: 0.8951 (tp) cc_final: 0.8632 (tt) REVERT: F 285 ASN cc_start: 0.9382 (m-40) cc_final: 0.9122 (m-40) REVERT: F 352 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8782 (tm-30) REVERT: F 355 ARG cc_start: 0.9432 (ptm-80) cc_final: 0.9143 (ptm-80) REVERT: F 385 MET cc_start: 0.8749 (ttm) cc_final: 0.8381 (ttm) REVERT: F 395 GLU cc_start: 0.8715 (mp0) cc_final: 0.8193 (mp0) REVERT: F 399 GLU cc_start: 0.8674 (pm20) cc_final: 0.8368 (pm20) REVERT: F 404 ASP cc_start: 0.8965 (t0) cc_final: 0.8703 (t0) REVERT: F 482 MET cc_start: 0.8962 (mtp) cc_final: 0.8639 (mtp) REVERT: G 28 ASP cc_start: 0.8756 (m-30) cc_final: 0.8485 (m-30) REVERT: G 50 ASP cc_start: 0.8889 (t70) cc_final: 0.8626 (t0) REVERT: G 51 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9054 (pp) REVERT: G 258 TYR cc_start: 0.9072 (t80) cc_final: 0.8817 (t80) REVERT: G 275 SER cc_start: 0.8988 (t) cc_final: 0.8744 (t) REVERT: G 276 SER cc_start: 0.8471 (p) cc_final: 0.8174 (p) REVERT: G 285 ASN cc_start: 0.9387 (m-40) cc_final: 0.9052 (m110) REVERT: G 352 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8864 (tm-30) REVERT: G 355 ARG cc_start: 0.9371 (ptm-80) cc_final: 0.8990 (ptm-80) REVERT: G 385 MET cc_start: 0.8638 (ttm) cc_final: 0.8162 (ttm) REVERT: G 395 GLU cc_start: 0.8634 (mp0) cc_final: 0.8114 (mp0) REVERT: G 399 GLU cc_start: 0.8453 (pm20) cc_final: 0.8191 (pm20) REVERT: G 400 TYR cc_start: 0.8149 (m-80) cc_final: 0.7753 (m-80) REVERT: G 404 ASP cc_start: 0.8928 (t0) cc_final: 0.8596 (t70) REVERT: G 407 ARG cc_start: 0.8945 (ttt-90) cc_final: 0.8315 (ptm-80) REVERT: G 449 ASP cc_start: 0.9151 (p0) cc_final: 0.8856 (p0) REVERT: G 510 GLU cc_start: 0.7687 (tp30) cc_final: 0.7329 (tp30) REVERT: H 25 ASN cc_start: 0.9046 (m-40) cc_final: 0.8812 (p0) REVERT: H 28 ASP cc_start: 0.8759 (m-30) cc_final: 0.8408 (m-30) REVERT: H 51 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.8930 (pp) REVERT: H 70 MET cc_start: 0.9072 (mpp) cc_final: 0.8742 (mtt) REVERT: H 256 ASP cc_start: 0.9124 (m-30) cc_final: 0.8892 (p0) REVERT: H 275 SER cc_start: 0.9074 (t) cc_final: 0.8839 (t) REVERT: H 276 SER cc_start: 0.8440 (p) cc_final: 0.8172 (p) REVERT: H 285 ASN cc_start: 0.9428 (m-40) cc_final: 0.9165 (m-40) REVERT: H 352 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8917 (tm-30) REVERT: H 385 MET cc_start: 0.8754 (ttm) cc_final: 0.8456 (ttm) REVERT: H 395 GLU cc_start: 0.8628 (mp0) cc_final: 0.8155 (mp0) REVERT: H 399 GLU cc_start: 0.8532 (pm20) cc_final: 0.8316 (pm20) REVERT: H 400 TYR cc_start: 0.8381 (m-80) cc_final: 0.7633 (m-10) REVERT: H 404 ASP cc_start: 0.8886 (t0) cc_final: 0.8579 (t0) REVERT: H 407 ARG cc_start: 0.8880 (ttt-90) cc_final: 0.8374 (ttt-90) REVERT: H 512 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7693 (ptm160) outliers start: 112 outliers final: 67 residues processed: 1029 average time/residue: 0.3264 time to fit residues: 522.8760 Evaluate side-chains 971 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 892 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 51 LEU 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 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 73 VAL Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 250 ILE 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 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 297 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 476 LEU Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 500 GLU 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 260 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 MET 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 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 73 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 0.0000 chunk 202 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 128 optimal weight: 0.7980 chunk 180 optimal weight: 2.9990 chunk 270 optimal weight: 5.9990 chunk 286 optimal weight: 0.0870 chunk 141 optimal weight: 4.9990 chunk 256 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 overall best weight: 0.9766 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** H 498 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23480 Z= 0.256 Angle : 0.660 8.486 31792 Z= 0.336 Chirality : 0.046 0.156 3656 Planarity : 0.004 0.038 4000 Dihedral : 11.455 89.938 3769 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.62 % Allowed : 22.99 % Favored : 71.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.14), residues: 2960 helix: -1.43 (0.14), residues: 1120 sheet: -2.08 (0.21), residues: 464 loop : -1.11 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 92 PHE 0.013 0.001 PHE F 401 TYR 0.021 0.001 TYR F 400 ARG 0.011 0.001 ARG D 105 *********************** 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 1088 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 954 time to evaluate : 2.365 Fit side-chains revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8612 (m-30) cc_final: 0.8295 (m-30) REVERT: A 88 ILE cc_start: 0.9041 (tp) cc_final: 0.8717 (tp) REVERT: A 105 ARG cc_start: 0.9020 (mtm110) cc_final: 0.8793 (mtm110) REVERT: A 258 TYR cc_start: 0.8990 (t80) cc_final: 0.8730 (t80) REVERT: A 276 SER cc_start: 0.8644 (p) cc_final: 0.8313 (p) REVERT: A 285 ASN cc_start: 0.9421 (m-40) cc_final: 0.9070 (m110) REVERT: A 352 GLU cc_start: 0.9132 (tm-30) cc_final: 0.8853 (tm-30) REVERT: A 385 MET cc_start: 0.8719 (ttm) cc_final: 0.8014 (ttm) REVERT: A 395 GLU cc_start: 0.8666 (mp0) cc_final: 0.8060 (mp0) REVERT: A 399 GLU cc_start: 0.8554 (pm20) cc_final: 0.8314 (mp0) REVERT: A 404 ASP cc_start: 0.8917 (t0) cc_final: 0.8647 (t70) REVERT: A 438 LYS cc_start: 0.8947 (mttt) cc_final: 0.8579 (mmtt) REVERT: A 455 LYS cc_start: 0.9157 (mppt) cc_final: 0.8702 (mppt) REVERT: B 25 ASN cc_start: 0.9076 (m-40) cc_final: 0.8839 (p0) REVERT: B 28 ASP cc_start: 0.8647 (m-30) cc_final: 0.8303 (m-30) REVERT: B 50 ASP cc_start: 0.8893 (t70) cc_final: 0.8620 (t0) REVERT: B 51 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.9008 (pp) REVERT: B 109 LYS cc_start: 0.9327 (mttp) cc_final: 0.9045 (mttm) REVERT: B 258 TYR cc_start: 0.8975 (t80) cc_final: 0.8730 (t80) REVERT: B 276 SER cc_start: 0.8684 (p) cc_final: 0.8345 (p) REVERT: B 285 ASN cc_start: 0.9410 (m-40) cc_final: 0.9057 (m-40) REVERT: B 352 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8887 (tm-30) REVERT: B 385 MET cc_start: 0.8794 (ttm) cc_final: 0.8386 (ttm) REVERT: B 395 GLU cc_start: 0.8651 (mp0) cc_final: 0.8146 (mp0) REVERT: B 399 GLU cc_start: 0.8665 (pm20) cc_final: 0.8428 (mp0) REVERT: B 404 ASP cc_start: 0.8923 (t0) cc_final: 0.8613 (t0) REVERT: B 407 ARG cc_start: 0.8987 (ttt-90) cc_final: 0.8513 (ttt-90) REVERT: B 482 MET cc_start: 0.9036 (mtp) cc_final: 0.8731 (mtp) REVERT: C 28 ASP cc_start: 0.8667 (m-30) cc_final: 0.8335 (m-30) REVERT: C 51 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8919 (pp) REVERT: C 105 ARG cc_start: 0.9012 (mtm110) cc_final: 0.8538 (mtm110) REVERT: C 109 LYS cc_start: 0.9323 (mttp) cc_final: 0.9031 (mptt) REVERT: C 242 LYS cc_start: 0.8053 (mttt) cc_final: 0.7849 (tttt) REVERT: C 258 TYR cc_start: 0.8950 (t80) cc_final: 0.8580 (t80) REVERT: C 276 SER cc_start: 0.8437 (p) cc_final: 0.8121 (p) REVERT: C 279 ASN cc_start: 0.8663 (t0) cc_final: 0.7818 (t0) REVERT: C 352 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8868 (tm-30) REVERT: C 355 ARG cc_start: 0.9326 (ptm-80) cc_final: 0.9119 (ptm-80) REVERT: C 395 GLU cc_start: 0.8627 (mp0) cc_final: 0.8213 (mp0) REVERT: C 404 ASP cc_start: 0.8934 (t0) cc_final: 0.8676 (t70) REVERT: C 409 LYS cc_start: 0.8779 (ttmp) cc_final: 0.8056 (tttt) REVERT: C 438 LYS cc_start: 0.8937 (mtpp) cc_final: 0.8632 (mmtt) REVERT: C 510 GLU cc_start: 0.7750 (tp30) cc_final: 0.7439 (tp30) REVERT: D 28 ASP cc_start: 0.8657 (m-30) cc_final: 0.8329 (m-30) REVERT: D 51 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9046 (pp) REVERT: D 108 LYS cc_start: 0.9514 (OUTLIER) cc_final: 0.9238 (tppt) REVERT: D 256 ASP cc_start: 0.9233 (m-30) cc_final: 0.8790 (p0) REVERT: D 276 SER cc_start: 0.8556 (p) cc_final: 0.8204 (p) REVERT: D 285 ASN cc_start: 0.9442 (m-40) cc_final: 0.9106 (m110) REVERT: D 332 ILE cc_start: 0.9022 (pp) cc_final: 0.8727 (pp) REVERT: D 352 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8782 (tm-30) REVERT: D 395 GLU cc_start: 0.8682 (mp0) cc_final: 0.8166 (mp0) REVERT: D 399 GLU cc_start: 0.8594 (pm20) cc_final: 0.8374 (pm20) REVERT: D 404 ASP cc_start: 0.8883 (t0) cc_final: 0.8619 (t70) REVERT: D 407 ARG cc_start: 0.9075 (ttt90) cc_final: 0.8809 (ttt90) REVERT: D 438 LYS cc_start: 0.8404 (mmtt) cc_final: 0.8033 (mmtm) REVERT: E 28 ASP cc_start: 0.8715 (m-30) cc_final: 0.8350 (m-30) REVERT: E 51 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9001 (pp) REVERT: E 70 MET cc_start: 0.9105 (mpp) cc_final: 0.8830 (mpp) REVERT: E 105 ARG cc_start: 0.8999 (mtm110) cc_final: 0.8742 (mtm110) REVERT: E 109 LYS cc_start: 0.9316 (mttp) cc_final: 0.8899 (tmtt) REVERT: E 258 TYR cc_start: 0.9001 (t80) cc_final: 0.8734 (t80) REVERT: E 276 SER cc_start: 0.8611 (p) cc_final: 0.8283 (p) REVERT: E 285 ASN cc_start: 0.9414 (m-40) cc_final: 0.9188 (m-40) REVERT: E 352 GLU cc_start: 0.9152 (tm-30) cc_final: 0.8867 (tm-30) REVERT: E 385 MET cc_start: 0.8814 (ttm) cc_final: 0.8323 (ttm) REVERT: E 395 GLU cc_start: 0.8636 (mp0) cc_final: 0.8146 (mp0) REVERT: E 399 GLU cc_start: 0.8604 (pm20) cc_final: 0.8367 (pm20) REVERT: E 404 ASP cc_start: 0.8986 (t0) cc_final: 0.8727 (t70) REVERT: E 407 ARG cc_start: 0.8986 (ttt-90) cc_final: 0.8777 (ttt90) REVERT: E 510 GLU cc_start: 0.7983 (tp30) cc_final: 0.7746 (tp30) REVERT: F 28 ASP cc_start: 0.8742 (m-30) cc_final: 0.8451 (m-30) REVERT: F 51 LEU cc_start: 0.9237 (OUTLIER) cc_final: 0.8823 (pp) REVERT: F 105 ARG cc_start: 0.9017 (mtm110) cc_final: 0.8757 (mtm110) REVERT: F 108 LYS cc_start: 0.9477 (OUTLIER) cc_final: 0.9268 (tppt) REVERT: F 109 LYS cc_start: 0.9395 (mptt) cc_final: 0.9115 (mttm) REVERT: F 258 TYR cc_start: 0.9136 (t80) cc_final: 0.8882 (t80) REVERT: F 276 SER cc_start: 0.8457 (p) cc_final: 0.8119 (p) REVERT: F 279 ASN cc_start: 0.8858 (t0) cc_final: 0.7972 (t0) REVERT: F 281 ILE cc_start: 0.9013 (tp) cc_final: 0.8700 (tt) REVERT: F 285 ASN cc_start: 0.9398 (m-40) cc_final: 0.9117 (m-40) REVERT: F 332 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8600 (pp) REVERT: F 352 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8855 (tm-30) REVERT: F 355 ARG cc_start: 0.9394 (ptm-80) cc_final: 0.9091 (ptm-80) REVERT: F 385 MET cc_start: 0.8760 (ttm) cc_final: 0.8334 (ttm) REVERT: F 395 GLU cc_start: 0.8693 (mp0) cc_final: 0.8155 (mp0) REVERT: F 399 GLU cc_start: 0.8694 (pm20) cc_final: 0.8434 (pm20) REVERT: F 400 TYR cc_start: 0.8187 (m-80) cc_final: 0.7922 (m-10) REVERT: F 404 ASP cc_start: 0.8973 (t0) cc_final: 0.8721 (t70) REVERT: F 407 ARG cc_start: 0.9152 (ttt90) cc_final: 0.8735 (ttt90) REVERT: G 28 ASP cc_start: 0.8730 (m-30) cc_final: 0.8489 (m-30) REVERT: G 50 ASP cc_start: 0.8930 (t70) cc_final: 0.8682 (t0) REVERT: G 51 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8915 (pp) REVERT: G 70 MET cc_start: 0.9128 (mpp) cc_final: 0.8820 (mpp) REVERT: G 275 SER cc_start: 0.8999 (t) cc_final: 0.8782 (t) REVERT: G 276 SER cc_start: 0.8561 (p) cc_final: 0.8252 (p) REVERT: G 285 ASN cc_start: 0.9381 (m-40) cc_final: 0.9072 (m110) REVERT: G 299 VAL cc_start: 0.9460 (m) cc_final: 0.9202 (p) REVERT: G 352 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8832 (tm-30) REVERT: G 385 MET cc_start: 0.8768 (ttm) cc_final: 0.8226 (ttm) REVERT: G 395 GLU cc_start: 0.8630 (mp0) cc_final: 0.8212 (mp0) REVERT: G 399 GLU cc_start: 0.8513 (pm20) cc_final: 0.8249 (pm20) REVERT: G 400 TYR cc_start: 0.8110 (m-80) cc_final: 0.7656 (m-80) REVERT: G 404 ASP cc_start: 0.8980 (t0) cc_final: 0.8685 (t70) REVERT: G 407 ARG cc_start: 0.8906 (ttt-90) cc_final: 0.8220 (ptm-80) REVERT: G 449 ASP cc_start: 0.9087 (p0) cc_final: 0.8864 (p0) REVERT: G 510 GLU cc_start: 0.7746 (tp30) cc_final: 0.7392 (tp30) REVERT: H 25 ASN cc_start: 0.9067 (m-40) cc_final: 0.8845 (p0) REVERT: H 28 ASP cc_start: 0.8695 (m-30) cc_final: 0.8398 (m-30) REVERT: H 51 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8914 (pp) REVERT: H 105 ARG cc_start: 0.9077 (mtm110) cc_final: 0.8639 (mtm110) REVERT: H 109 LYS cc_start: 0.9271 (mttp) cc_final: 0.8952 (mptt) REVERT: H 276 SER cc_start: 0.8584 (p) cc_final: 0.8271 (p) REVERT: H 285 ASN cc_start: 0.9441 (m-40) cc_final: 0.9121 (m110) REVERT: H 352 GLU cc_start: 0.9187 (tm-30) cc_final: 0.8921 (tm-30) REVERT: H 385 MET cc_start: 0.8799 (ttm) cc_final: 0.8269 (ttm) REVERT: H 395 GLU cc_start: 0.8688 (mp0) cc_final: 0.8153 (mp0) REVERT: H 399 GLU cc_start: 0.8606 (pm20) cc_final: 0.8401 (pm20) REVERT: H 400 TYR cc_start: 0.8245 (m-80) cc_final: 0.7552 (m-10) REVERT: H 404 ASP cc_start: 0.8900 (t0) cc_final: 0.8595 (t0) REVERT: H 407 ARG cc_start: 0.8976 (ttt-90) cc_final: 0.8324 (ttt-90) outliers start: 134 outliers final: 81 residues processed: 1012 average time/residue: 0.3519 time to fit residues: 557.5274 Evaluate side-chains 995 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 904 time to evaluate : 2.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 51 LEU 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 297 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU 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 377 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 499 VAL 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 66 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 MET 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 313 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 377 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 238 optimal weight: 0.8980 chunk 162 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 213 optimal weight: 0.9980 chunk 118 optimal weight: 0.8980 chunk 244 optimal weight: 0.5980 chunk 197 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 146 optimal weight: 0.7980 chunk 256 optimal weight: 0.6980 chunk 72 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 303 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN C 334 GLN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23480 Z= 0.229 Angle : 0.652 8.257 31792 Z= 0.329 Chirality : 0.046 0.151 3656 Planarity : 0.004 0.037 4000 Dihedral : 10.931 88.777 3762 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.70 % Allowed : 24.75 % Favored : 69.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.15), residues: 2960 helix: -1.20 (0.15), residues: 1120 sheet: -2.01 (0.22), residues: 376 loop : -1.03 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS D 92 PHE 0.012 0.001 PHE H 401 TYR 0.017 0.001 TYR E 400 ARG 0.010 0.001 ARG G 105 *********************** 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 1113 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 977 time to evaluate : 2.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8541 (m-30) cc_final: 0.8265 (m-30) REVERT: A 51 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.8977 (pp) REVERT: A 109 LYS cc_start: 0.9589 (mmmt) cc_final: 0.9022 (tptt) REVERT: A 258 TYR cc_start: 0.9003 (t80) cc_final: 0.8777 (t80) REVERT: A 276 SER cc_start: 0.8720 (p) cc_final: 0.8423 (p) REVERT: A 285 ASN cc_start: 0.9432 (m-40) cc_final: 0.9064 (m110) REVERT: A 352 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8842 (tm-30) REVERT: A 385 MET cc_start: 0.8781 (ttm) cc_final: 0.8184 (ttm) REVERT: A 395 GLU cc_start: 0.8639 (mp0) cc_final: 0.8108 (mp0) REVERT: A 399 GLU cc_start: 0.8635 (pm20) cc_final: 0.8419 (mp0) REVERT: A 404 ASP cc_start: 0.8913 (t0) cc_final: 0.8626 (t70) REVERT: A 406 ILE cc_start: 0.9109 (mp) cc_final: 0.8750 (mp) REVERT: A 409 LYS cc_start: 0.8822 (ttmm) cc_final: 0.8535 (ttmm) REVERT: A 438 LYS cc_start: 0.8975 (mttt) cc_final: 0.8583 (mmtt) REVERT: A 510 GLU cc_start: 0.7743 (tp30) cc_final: 0.7457 (tp30) REVERT: B 25 ASN cc_start: 0.9109 (m-40) cc_final: 0.8905 (p0) REVERT: B 28 ASP cc_start: 0.8574 (m-30) cc_final: 0.8311 (m-30) REVERT: B 50 ASP cc_start: 0.8917 (t70) cc_final: 0.8670 (t0) REVERT: B 51 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8973 (pp) REVERT: B 258 TYR cc_start: 0.8977 (t80) cc_final: 0.8692 (t80) REVERT: B 276 SER cc_start: 0.8636 (p) cc_final: 0.8305 (p) REVERT: B 285 ASN cc_start: 0.9420 (m-40) cc_final: 0.9061 (m110) REVERT: B 332 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8795 (pp) REVERT: B 352 GLU cc_start: 0.9154 (tm-30) cc_final: 0.8896 (tm-30) REVERT: B 385 MET cc_start: 0.8819 (ttm) cc_final: 0.8327 (ttm) REVERT: B 395 GLU cc_start: 0.8658 (mp0) cc_final: 0.8153 (mp0) REVERT: B 399 GLU cc_start: 0.8610 (pm20) cc_final: 0.8392 (pm20) REVERT: B 404 ASP cc_start: 0.8919 (t0) cc_final: 0.8652 (t0) REVERT: B 407 ARG cc_start: 0.9029 (ttt-90) cc_final: 0.8461 (ttt-90) REVERT: B 510 GLU cc_start: 0.8029 (tp30) cc_final: 0.7777 (tp30) REVERT: C 28 ASP cc_start: 0.8592 (m-30) cc_final: 0.8331 (m-30) REVERT: C 51 LEU cc_start: 0.9282 (OUTLIER) cc_final: 0.8979 (pp) REVERT: C 78 MET cc_start: 0.8497 (OUTLIER) cc_final: 0.8249 (ptm) REVERT: C 105 ARG cc_start: 0.9009 (mtm110) cc_final: 0.8522 (mtm110) REVERT: C 109 LYS cc_start: 0.9316 (mttp) cc_final: 0.9037 (mptt) REVERT: C 258 TYR cc_start: 0.9001 (t80) cc_final: 0.8660 (t80) REVERT: C 276 SER cc_start: 0.8352 (p) cc_final: 0.8007 (p) REVERT: C 279 ASN cc_start: 0.8825 (t0) cc_final: 0.7951 (t0) REVERT: C 332 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8797 (pp) REVERT: C 352 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8892 (tm-30) REVERT: C 385 MET cc_start: 0.8831 (ttm) cc_final: 0.8560 (ttm) REVERT: C 395 GLU cc_start: 0.8690 (mp0) cc_final: 0.8229 (mp0) REVERT: C 404 ASP cc_start: 0.8938 (t0) cc_final: 0.8707 (t70) REVERT: C 407 ARG cc_start: 0.8916 (ttt90) cc_final: 0.8672 (ttt90) REVERT: C 409 LYS cc_start: 0.8835 (ttmp) cc_final: 0.8307 (tttt) REVERT: C 438 LYS cc_start: 0.8929 (mtpp) cc_final: 0.8658 (mptt) REVERT: C 510 GLU cc_start: 0.7769 (tp30) cc_final: 0.7447 (tp30) REVERT: D 28 ASP cc_start: 0.8609 (m-30) cc_final: 0.8341 (m-30) REVERT: D 51 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9004 (pp) REVERT: D 276 SER cc_start: 0.8508 (p) cc_final: 0.8160 (p) REVERT: D 285 ASN cc_start: 0.9450 (m-40) cc_final: 0.9125 (m110) REVERT: D 332 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8790 (pp) REVERT: D 352 GLU cc_start: 0.9082 (tm-30) cc_final: 0.8736 (tm-30) REVERT: D 395 GLU cc_start: 0.8722 (mp0) cc_final: 0.8006 (mp0) REVERT: D 399 GLU cc_start: 0.8596 (pm20) cc_final: 0.8383 (pm20) REVERT: D 404 ASP cc_start: 0.8844 (t0) cc_final: 0.8584 (t70) REVERT: D 407 ARG cc_start: 0.8892 (ttt90) cc_final: 0.8685 (ttt90) REVERT: D 438 LYS cc_start: 0.8417 (mmtt) cc_final: 0.8087 (mmtm) REVERT: E 28 ASP cc_start: 0.8651 (m-30) cc_final: 0.8366 (m-30) REVERT: E 51 LEU cc_start: 0.9306 (OUTLIER) cc_final: 0.9030 (pp) REVERT: E 78 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8291 (ptm) REVERT: E 105 ARG cc_start: 0.8995 (mtm110) cc_final: 0.8732 (mtm110) REVERT: E 109 LYS cc_start: 0.9311 (mttp) cc_final: 0.8919 (tmtt) REVERT: E 258 TYR cc_start: 0.9002 (t80) cc_final: 0.8762 (t80) REVERT: E 276 SER cc_start: 0.8720 (p) cc_final: 0.8412 (p) REVERT: E 285 ASN cc_start: 0.9428 (m-40) cc_final: 0.9094 (m-40) REVERT: E 332 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8747 (pp) REVERT: E 352 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8854 (tm-30) REVERT: E 385 MET cc_start: 0.8822 (ttm) cc_final: 0.8268 (ttm) REVERT: E 395 GLU cc_start: 0.8604 (mp0) cc_final: 0.8190 (mp0) REVERT: E 404 ASP cc_start: 0.8960 (t0) cc_final: 0.8692 (t70) REVERT: F 28 ASP cc_start: 0.8680 (m-30) cc_final: 0.8442 (m-30) REVERT: F 51 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9023 (pp) REVERT: F 105 ARG cc_start: 0.9052 (mtm110) cc_final: 0.8623 (mtm110) REVERT: F 109 LYS cc_start: 0.9377 (mptt) cc_final: 0.9116 (mttt) REVERT: F 258 TYR cc_start: 0.9106 (t80) cc_final: 0.8798 (t80) REVERT: F 276 SER cc_start: 0.8207 (p) cc_final: 0.7838 (p) REVERT: F 279 ASN cc_start: 0.8916 (t0) cc_final: 0.8039 (t0) REVERT: F 285 ASN cc_start: 0.9442 (m-40) cc_final: 0.9141 (m110) REVERT: F 332 ILE cc_start: 0.8838 (OUTLIER) cc_final: 0.8588 (pp) REVERT: F 352 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8856 (tm-30) REVERT: F 355 ARG cc_start: 0.9373 (ptm-80) cc_final: 0.9073 (ptm-80) REVERT: F 385 MET cc_start: 0.8679 (ttm) cc_final: 0.8174 (ttm) REVERT: F 395 GLU cc_start: 0.8740 (mp0) cc_final: 0.8204 (mp0) REVERT: F 399 GLU cc_start: 0.8708 (pm20) cc_final: 0.8471 (pm20) REVERT: F 400 TYR cc_start: 0.8083 (m-80) cc_final: 0.7451 (m-10) REVERT: F 404 ASP cc_start: 0.8936 (t0) cc_final: 0.8698 (t0) REVERT: F 407 ARG cc_start: 0.9115 (ttt90) cc_final: 0.8626 (ttt-90) REVERT: G 28 ASP cc_start: 0.8697 (m-30) cc_final: 0.8497 (m-30) REVERT: G 50 ASP cc_start: 0.8937 (t70) cc_final: 0.8683 (t0) REVERT: G 51 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8858 (pp) REVERT: G 105 ARG cc_start: 0.9007 (ttp80) cc_final: 0.8794 (ttp80) REVERT: G 256 ASP cc_start: 0.9227 (m-30) cc_final: 0.8748 (p0) REVERT: G 275 SER cc_start: 0.8950 (t) cc_final: 0.8712 (t) REVERT: G 276 SER cc_start: 0.8680 (p) cc_final: 0.8407 (p) REVERT: G 285 ASN cc_start: 0.9393 (m-40) cc_final: 0.9059 (m110) REVERT: G 299 VAL cc_start: 0.9447 (m) cc_final: 0.9160 (p) REVERT: G 352 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8793 (tm-30) REVERT: G 385 MET cc_start: 0.8769 (ttm) cc_final: 0.8259 (ttm) REVERT: G 395 GLU cc_start: 0.8584 (mp0) cc_final: 0.8187 (mp0) REVERT: G 399 GLU cc_start: 0.8518 (pm20) cc_final: 0.8264 (pm20) REVERT: G 400 TYR cc_start: 0.8110 (m-80) cc_final: 0.7094 (m-80) REVERT: G 404 ASP cc_start: 0.8967 (t0) cc_final: 0.8662 (t70) REVERT: G 407 ARG cc_start: 0.8880 (ttt-90) cc_final: 0.8641 (ttt-90) REVERT: H 25 ASN cc_start: 0.9087 (m-40) cc_final: 0.8872 (p0) REVERT: H 28 ASP cc_start: 0.8666 (m-30) cc_final: 0.8419 (m-30) REVERT: H 51 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8970 (pp) REVERT: H 105 ARG cc_start: 0.9084 (mtm110) cc_final: 0.8692 (mtm110) REVERT: H 276 SER cc_start: 0.8710 (p) cc_final: 0.8305 (p) REVERT: H 285 ASN cc_start: 0.9426 (m-40) cc_final: 0.9108 (m110) REVERT: H 332 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8641 (pp) REVERT: H 335 GLU cc_start: 0.8541 (tm-30) cc_final: 0.7917 (tm-30) REVERT: H 352 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8929 (tm-30) REVERT: H 355 ARG cc_start: 0.9254 (ptm-80) cc_final: 0.9049 (ptm-80) REVERT: H 385 MET cc_start: 0.8784 (ttm) cc_final: 0.8248 (ttm) REVERT: H 395 GLU cc_start: 0.8697 (mp0) cc_final: 0.8170 (mp0) REVERT: H 399 GLU cc_start: 0.8591 (pm20) cc_final: 0.8384 (pm20) REVERT: H 400 TYR cc_start: 0.8213 (m-80) cc_final: 0.7512 (m-10) REVERT: H 404 ASP cc_start: 0.8918 (t0) cc_final: 0.8615 (t0) REVERT: H 407 ARG cc_start: 0.8981 (ttt-90) cc_final: 0.8339 (ttt-90) REVERT: H 410 LYS cc_start: 0.8646 (ptmt) cc_final: 0.8383 (ptmt) REVERT: H 512 ARG cc_start: 0.8015 (ttm-80) cc_final: 0.7558 (ptm160) outliers start: 136 outliers final: 81 residues processed: 1033 average time/residue: 0.3274 time to fit residues: 528.6829 Evaluate side-chains 999 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 902 time to evaluate : 2.687 ------------------------------------------------------------------------------- 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 73 VAL Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 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 45 THR Chi-restraints excluded: chain B residue 51 LEU 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 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 500 GLU Chi-restraints excluded: chain C residue 51 LEU 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 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 297 LEU Chi-restraints excluded: chain D residue 332 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 E residue 51 LEU 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 280 SER Chi-restraints excluded: chain E residue 282 PHE 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 499 VAL 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 250 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 282 PHE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 382 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 260 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 1.9990 chunk 257 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 167 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 286 optimal weight: 5.9990 chunk 237 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** 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 F 498 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** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23480 Z= 0.237 Angle : 0.664 8.274 31792 Z= 0.336 Chirality : 0.046 0.193 3656 Planarity : 0.004 0.038 4000 Dihedral : 10.570 89.717 3748 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 6.04 % Allowed : 25.50 % Favored : 68.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.15), residues: 2960 helix: -1.18 (0.15), residues: 1120 sheet: -1.87 (0.23), residues: 368 loop : -0.99 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS D 92 PHE 0.011 0.001 PHE F 401 TYR 0.014 0.001 TYR C 353 ARG 0.008 0.001 ARG D 105 *********************** 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 1098 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 954 time to evaluate : 2.625 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8541 (m-30) cc_final: 0.8309 (m-30) REVERT: A 51 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9041 (pp) REVERT: A 98 GLU cc_start: 0.9384 (mp0) cc_final: 0.9166 (mp0) REVERT: A 109 LYS cc_start: 0.9589 (mmmt) cc_final: 0.9022 (tptt) REVERT: A 275 SER cc_start: 0.8948 (t) cc_final: 0.8722 (t) REVERT: A 276 SER cc_start: 0.8727 (p) cc_final: 0.8422 (p) REVERT: A 285 ASN cc_start: 0.9452 (m-40) cc_final: 0.9081 (m-40) REVERT: A 352 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8865 (tm-30) REVERT: A 385 MET cc_start: 0.8833 (ttm) cc_final: 0.8273 (ttm) REVERT: A 395 GLU cc_start: 0.8688 (mp0) cc_final: 0.8154 (mp0) REVERT: A 404 ASP cc_start: 0.8936 (t0) cc_final: 0.8660 (t0) REVERT: A 406 ILE cc_start: 0.9101 (mp) cc_final: 0.8880 (mp) REVERT: A 407 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8546 (ttt90) REVERT: A 438 LYS cc_start: 0.8984 (mttt) cc_final: 0.8599 (mmtt) REVERT: A 510 GLU cc_start: 0.7759 (tp30) cc_final: 0.7472 (tp30) REVERT: B 28 ASP cc_start: 0.8557 (m-30) cc_final: 0.8319 (m-30) REVERT: B 50 ASP cc_start: 0.8928 (t70) cc_final: 0.8652 (t0) REVERT: B 51 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8996 (pp) REVERT: B 258 TYR cc_start: 0.8992 (t80) cc_final: 0.8685 (t80) REVERT: B 276 SER cc_start: 0.8629 (p) cc_final: 0.8294 (p) REVERT: B 285 ASN cc_start: 0.9439 (m-40) cc_final: 0.9089 (m110) REVERT: B 332 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8811 (pp) REVERT: B 352 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8889 (tm-30) REVERT: B 385 MET cc_start: 0.8745 (ttm) cc_final: 0.8297 (ttm) REVERT: B 395 GLU cc_start: 0.8687 (mp0) cc_final: 0.8148 (mp0) REVERT: B 399 GLU cc_start: 0.8629 (pm20) cc_final: 0.8429 (mp0) REVERT: B 404 ASP cc_start: 0.8943 (t0) cc_final: 0.8699 (t70) REVERT: B 410 LYS cc_start: 0.8690 (ptmt) cc_final: 0.8427 (ptmt) REVERT: C 21 GLN cc_start: 0.8780 (pt0) cc_final: 0.8494 (tt0) REVERT: C 28 ASP cc_start: 0.8588 (m-30) cc_final: 0.8378 (m-30) REVERT: C 51 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8878 (pp) REVERT: C 105 ARG cc_start: 0.8948 (mtm110) cc_final: 0.8728 (mtm110) REVERT: C 258 TYR cc_start: 0.8977 (t80) cc_final: 0.8638 (t80) REVERT: C 276 SER cc_start: 0.8331 (p) cc_final: 0.7988 (p) REVERT: C 279 ASN cc_start: 0.8893 (t0) cc_final: 0.8057 (t0) REVERT: C 332 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8439 (pp) REVERT: C 335 GLU cc_start: 0.8436 (tm-30) cc_final: 0.7715 (tm-30) REVERT: C 352 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8888 (tm-30) REVERT: C 385 MET cc_start: 0.8695 (ttm) cc_final: 0.8363 (ttm) REVERT: C 395 GLU cc_start: 0.8703 (mp0) cc_final: 0.8098 (mp0) REVERT: C 404 ASP cc_start: 0.8944 (t0) cc_final: 0.8707 (t70) REVERT: C 409 LYS cc_start: 0.8829 (ttmp) cc_final: 0.8262 (tttt) REVERT: C 438 LYS cc_start: 0.9003 (mtpp) cc_final: 0.8708 (mptt) REVERT: C 510 GLU cc_start: 0.7799 (tp30) cc_final: 0.7481 (tp30) REVERT: D 28 ASP cc_start: 0.8589 (m-30) cc_final: 0.8356 (m-30) REVERT: D 51 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8813 (pp) REVERT: D 105 ARG cc_start: 0.9042 (mtm110) cc_final: 0.8694 (mtm110) REVERT: D 276 SER cc_start: 0.8508 (p) cc_final: 0.8152 (p) REVERT: D 285 ASN cc_start: 0.9465 (m-40) cc_final: 0.9132 (m110) REVERT: D 332 ILE cc_start: 0.9072 (OUTLIER) cc_final: 0.8812 (pp) REVERT: D 352 GLU cc_start: 0.9100 (tm-30) cc_final: 0.8757 (tm-30) REVERT: D 395 GLU cc_start: 0.8678 (mp0) cc_final: 0.8086 (mp0) REVERT: D 399 GLU cc_start: 0.8623 (pm20) cc_final: 0.8379 (pm20) REVERT: D 404 ASP cc_start: 0.8872 (t0) cc_final: 0.8605 (t70) REVERT: D 407 ARG cc_start: 0.8874 (ttt90) cc_final: 0.8616 (ttt90) REVERT: D 409 LYS cc_start: 0.8794 (ttmp) cc_final: 0.8078 (tttt) REVERT: D 438 LYS cc_start: 0.8449 (mmtt) cc_final: 0.8131 (mmtm) REVERT: E 21 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8467 (tm-30) REVERT: E 25 ASN cc_start: 0.9121 (m-40) cc_final: 0.8713 (m-40) REVERT: E 28 ASP cc_start: 0.8655 (m-30) cc_final: 0.8400 (m-30) REVERT: E 51 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9018 (pp) REVERT: E 105 ARG cc_start: 0.9004 (mtm110) cc_final: 0.8781 (mtm110) REVERT: E 276 SER cc_start: 0.8728 (p) cc_final: 0.8401 (p) REVERT: E 285 ASN cc_start: 0.9439 (m-40) cc_final: 0.9089 (m-40) REVERT: E 332 ILE cc_start: 0.9026 (OUTLIER) cc_final: 0.8775 (pp) REVERT: E 352 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8858 (tm-30) REVERT: E 355 ARG cc_start: 0.9235 (ptm-80) cc_final: 0.8914 (ptm-80) REVERT: E 385 MET cc_start: 0.8836 (ttm) cc_final: 0.8323 (ttm) REVERT: E 395 GLU cc_start: 0.8630 (mp0) cc_final: 0.8227 (mp0) REVERT: E 404 ASP cc_start: 0.8993 (t0) cc_final: 0.8746 (t70) REVERT: E 406 ILE cc_start: 0.9143 (mp) cc_final: 0.8937 (mp) REVERT: E 409 LYS cc_start: 0.8716 (ttmp) cc_final: 0.8236 (ttmt) REVERT: F 21 GLN cc_start: 0.8712 (pt0) cc_final: 0.8456 (tm-30) REVERT: F 28 ASP cc_start: 0.8654 (m-30) cc_final: 0.8437 (m-30) REVERT: F 51 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8800 (pp) REVERT: F 105 ARG cc_start: 0.9050 (mtm110) cc_final: 0.8841 (mtm110) REVERT: F 108 LYS cc_start: 0.9215 (tppt) cc_final: 0.8972 (mmtp) REVERT: F 109 LYS cc_start: 0.9387 (mptt) cc_final: 0.8988 (mtmm) REVERT: F 258 TYR cc_start: 0.9096 (t80) cc_final: 0.8789 (t80) REVERT: F 276 SER cc_start: 0.8198 (p) cc_final: 0.7830 (p) REVERT: F 279 ASN cc_start: 0.8940 (t0) cc_final: 0.8066 (t0) REVERT: F 285 ASN cc_start: 0.9460 (m-40) cc_final: 0.9179 (m-40) REVERT: F 332 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8569 (pp) REVERT: F 352 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8875 (tm-30) REVERT: F 385 MET cc_start: 0.8607 (ttm) cc_final: 0.8226 (ttm) REVERT: F 395 GLU cc_start: 0.8785 (mp0) cc_final: 0.8248 (mp0) REVERT: F 399 GLU cc_start: 0.8734 (pm20) cc_final: 0.8486 (pm20) REVERT: F 400 TYR cc_start: 0.8069 (m-80) cc_final: 0.7302 (m-10) REVERT: F 404 ASP cc_start: 0.8951 (t0) cc_final: 0.8716 (t70) REVERT: F 407 ARG cc_start: 0.9179 (ttt90) cc_final: 0.8675 (ttt-90) REVERT: G 50 ASP cc_start: 0.8954 (t70) cc_final: 0.8699 (t0) REVERT: G 51 LEU cc_start: 0.9297 (OUTLIER) cc_final: 0.8932 (pp) REVERT: G 105 ARG cc_start: 0.9019 (ttp80) cc_final: 0.8810 (ttp80) REVERT: G 275 SER cc_start: 0.8950 (t) cc_final: 0.8719 (t) REVERT: G 276 SER cc_start: 0.8695 (p) cc_final: 0.8425 (p) REVERT: G 285 ASN cc_start: 0.9369 (m-40) cc_final: 0.9041 (m110) REVERT: G 332 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8558 (pp) REVERT: G 335 GLU cc_start: 0.8511 (tm-30) cc_final: 0.7759 (tm-30) REVERT: G 352 GLU cc_start: 0.9110 (tm-30) cc_final: 0.8786 (tm-30) REVERT: G 385 MET cc_start: 0.8715 (ttm) cc_final: 0.8158 (ttm) REVERT: G 395 GLU cc_start: 0.8580 (mp0) cc_final: 0.8192 (mp0) REVERT: G 399 GLU cc_start: 0.8568 (pm20) cc_final: 0.8356 (pm20) REVERT: G 404 ASP cc_start: 0.8986 (t0) cc_final: 0.8680 (t70) REVERT: H 25 ASN cc_start: 0.9098 (m-40) cc_final: 0.8895 (p0) REVERT: H 28 ASP cc_start: 0.8680 (m-30) cc_final: 0.8466 (m-30) REVERT: H 51 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8885 (pp) REVERT: H 105 ARG cc_start: 0.9061 (mtm110) cc_final: 0.8648 (mtm110) REVERT: H 276 SER cc_start: 0.8700 (p) cc_final: 0.8349 (p) REVERT: H 285 ASN cc_start: 0.9411 (m-40) cc_final: 0.9077 (m110) REVERT: H 332 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8627 (pp) REVERT: H 335 GLU cc_start: 0.8529 (tm-30) cc_final: 0.7898 (tm-30) REVERT: H 352 GLU cc_start: 0.9190 (tm-30) cc_final: 0.8933 (tm-30) REVERT: H 355 ARG cc_start: 0.9224 (ptm-80) cc_final: 0.8884 (ptm-80) REVERT: H 385 MET cc_start: 0.8716 (ttm) cc_final: 0.8194 (ttm) REVERT: H 395 GLU cc_start: 0.8757 (mp0) cc_final: 0.8216 (mp0) REVERT: H 404 ASP cc_start: 0.8929 (t0) cc_final: 0.8615 (t0) REVERT: H 410 LYS cc_start: 0.8694 (ptmt) cc_final: 0.8455 (ptmt) REVERT: H 512 ARG cc_start: 0.7979 (ttm-80) cc_final: 0.7581 (ptm160) outliers start: 144 outliers final: 96 residues processed: 1021 average time/residue: 0.3327 time to fit residues: 532.5049 Evaluate side-chains 1027 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 914 time to evaluate : 2.494 ------------------------------------------------------------------------------- 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 73 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU 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 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 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 73 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 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 66 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 282 PHE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 499 VAL 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 250 ILE Chi-restraints excluded: chain F residue 282 PHE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 485 SER 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 73 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 282 PHE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 382 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 73 VAL Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 163 optimal weight: 0.4980 chunk 209 optimal weight: 2.9990 chunk 162 optimal weight: 0.9990 chunk 241 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 285 optimal weight: 3.9990 chunk 178 optimal weight: 0.9980 chunk 173 optimal weight: 1.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 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** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23480 Z= 0.237 Angle : 0.682 7.988 31792 Z= 0.345 Chirality : 0.046 0.190 3656 Planarity : 0.004 0.040 4000 Dihedral : 10.399 89.116 3743 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 5.87 % Allowed : 26.55 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.15), residues: 2960 helix: -1.25 (0.15), residues: 1128 sheet: -1.82 (0.24), residues: 368 loop : -1.04 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS D 92 PHE 0.011 0.001 PHE E 401 TYR 0.019 0.001 TYR G 400 ARG 0.009 0.001 ARG B 105 *********************** 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 1104 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 964 time to evaluate : 2.686 Fit side-chains REVERT: A 1 MET cc_start: 0.4229 (ptp) cc_final: 0.3509 (ptm) REVERT: A 21 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8426 (tm-30) REVERT: A 28 ASP cc_start: 0.8533 (m-30) cc_final: 0.8319 (m-30) REVERT: A 51 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8834 (pp) REVERT: A 109 LYS cc_start: 0.9592 (mmmt) cc_final: 0.9052 (tptt) REVERT: A 276 SER cc_start: 0.8756 (p) cc_final: 0.8425 (p) REVERT: A 285 ASN cc_start: 0.9459 (m-40) cc_final: 0.9136 (m-40) REVERT: A 332 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8930 (pp) REVERT: A 352 GLU cc_start: 0.9112 (tm-30) cc_final: 0.8835 (tm-30) REVERT: A 355 ARG cc_start: 0.9214 (ptm-80) cc_final: 0.8863 (ptm-80) REVERT: A 385 MET cc_start: 0.8796 (ttm) cc_final: 0.8266 (ttm) REVERT: A 395 GLU cc_start: 0.8748 (mp0) cc_final: 0.8187 (mp0) REVERT: A 404 ASP cc_start: 0.8984 (t0) cc_final: 0.8719 (t0) REVERT: A 406 ILE cc_start: 0.9087 (mp) cc_final: 0.8871 (mp) REVERT: A 407 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8300 (ttt-90) REVERT: A 438 LYS cc_start: 0.9003 (mttt) cc_final: 0.8558 (mmtm) REVERT: A 510 GLU cc_start: 0.7757 (tp30) cc_final: 0.7455 (tp30) REVERT: B 21 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.8500 (tm-30) REVERT: B 28 ASP cc_start: 0.8565 (m-30) cc_final: 0.8355 (m-30) REVERT: B 50 ASP cc_start: 0.8939 (t70) cc_final: 0.8681 (t0) REVERT: B 51 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8793 (pp) REVERT: B 258 TYR cc_start: 0.9003 (t80) cc_final: 0.8689 (t80) REVERT: B 276 SER cc_start: 0.8692 (p) cc_final: 0.8397 (p) REVERT: B 285 ASN cc_start: 0.9444 (m-40) cc_final: 0.9134 (m110) REVERT: B 332 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8521 (pp) REVERT: B 335 GLU cc_start: 0.8498 (tm-30) cc_final: 0.7765 (tm-30) REVERT: B 352 GLU cc_start: 0.9145 (tm-30) cc_final: 0.8846 (tm-30) REVERT: B 385 MET cc_start: 0.8796 (ttm) cc_final: 0.8332 (ttm) REVERT: B 395 GLU cc_start: 0.8753 (mp0) cc_final: 0.8238 (mp0) REVERT: B 404 ASP cc_start: 0.8965 (t0) cc_final: 0.8728 (t70) REVERT: B 410 LYS cc_start: 0.8715 (ptmt) cc_final: 0.8459 (ptmt) REVERT: B 438 LYS cc_start: 0.8275 (mmtt) cc_final: 0.8048 (mtpt) REVERT: B 510 GLU cc_start: 0.7811 (tp30) cc_final: 0.7469 (tp30) REVERT: C 21 GLN cc_start: 0.8790 (pt0) cc_final: 0.8375 (tm-30) REVERT: C 51 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8810 (pp) REVERT: C 109 LYS cc_start: 0.9637 (mmmt) cc_final: 0.8942 (tptt) REVERT: C 258 TYR cc_start: 0.8993 (t80) cc_final: 0.8696 (t80) REVERT: C 276 SER cc_start: 0.8433 (p) cc_final: 0.8095 (p) REVERT: C 279 ASN cc_start: 0.8905 (t0) cc_final: 0.8062 (t0) REVERT: C 332 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8495 (pp) REVERT: C 335 GLU cc_start: 0.8418 (tm-30) cc_final: 0.7687 (tm-30) REVERT: C 352 GLU cc_start: 0.9141 (tm-30) cc_final: 0.8871 (tm-30) REVERT: C 395 GLU cc_start: 0.8628 (mp0) cc_final: 0.8282 (mp0) REVERT: C 404 ASP cc_start: 0.8954 (t0) cc_final: 0.8713 (t70) REVERT: C 409 LYS cc_start: 0.8779 (tttp) cc_final: 0.8541 (ttmt) REVERT: C 438 LYS cc_start: 0.9006 (mtpp) cc_final: 0.8607 (mmtm) REVERT: C 510 GLU cc_start: 0.7799 (tp30) cc_final: 0.7471 (tp30) REVERT: D 21 GLN cc_start: 0.8733 (pt0) cc_final: 0.8442 (tm-30) REVERT: D 28 ASP cc_start: 0.8573 (m-30) cc_final: 0.8373 (m-30) REVERT: D 51 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8792 (pp) REVERT: D 105 ARG cc_start: 0.9038 (mtm110) cc_final: 0.8663 (mtm110) REVERT: D 276 SER cc_start: 0.8613 (p) cc_final: 0.8301 (p) REVERT: D 285 ASN cc_start: 0.9476 (m-40) cc_final: 0.9132 (m110) REVERT: D 332 ILE cc_start: 0.9066 (OUTLIER) cc_final: 0.8810 (pp) REVERT: D 352 GLU cc_start: 0.9117 (tm-30) cc_final: 0.8773 (tm-30) REVERT: D 355 ARG cc_start: 0.9165 (ptm-80) cc_final: 0.8858 (ptm-80) REVERT: D 395 GLU cc_start: 0.8733 (mp0) cc_final: 0.8277 (mp0) REVERT: D 399 GLU cc_start: 0.8624 (pm20) cc_final: 0.8355 (mp0) REVERT: D 404 ASP cc_start: 0.8890 (t0) cc_final: 0.8653 (t70) REVERT: D 407 ARG cc_start: 0.8849 (ttt90) cc_final: 0.8538 (ttt90) REVERT: D 409 LYS cc_start: 0.8763 (ttmp) cc_final: 0.8238 (tttt) REVERT: D 438 LYS cc_start: 0.8486 (mmtt) cc_final: 0.8171 (mmtm) REVERT: E 21 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8453 (tm-30) REVERT: E 28 ASP cc_start: 0.8656 (m-30) cc_final: 0.8454 (m-30) REVERT: E 51 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.9007 (pp) REVERT: E 98 GLU cc_start: 0.9333 (mp0) cc_final: 0.9121 (mp0) REVERT: E 109 LYS cc_start: 0.9571 (mmmt) cc_final: 0.8977 (tptt) REVERT: E 242 LYS cc_start: 0.7856 (mttt) cc_final: 0.7637 (mttt) REVERT: E 276 SER cc_start: 0.8760 (p) cc_final: 0.8422 (p) REVERT: E 285 ASN cc_start: 0.9450 (m-40) cc_final: 0.9076 (m-40) REVERT: E 332 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8458 (pp) REVERT: E 335 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7738 (tm-30) REVERT: E 352 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8868 (tm-30) REVERT: E 355 ARG cc_start: 0.9252 (ptm-80) cc_final: 0.8937 (ptm-80) REVERT: E 385 MET cc_start: 0.8841 (ttm) cc_final: 0.8329 (ttm) REVERT: E 395 GLU cc_start: 0.8659 (mp0) cc_final: 0.8255 (mp0) REVERT: E 404 ASP cc_start: 0.8993 (t0) cc_final: 0.8750 (t70) REVERT: E 409 LYS cc_start: 0.8733 (ttmp) cc_final: 0.8324 (ttmt) REVERT: F 21 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8396 (tm-30) REVERT: F 51 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8782 (pp) REVERT: F 105 ARG cc_start: 0.9049 (mtm110) cc_final: 0.8603 (mtm110) REVERT: F 109 LYS cc_start: 0.9404 (mptt) cc_final: 0.9172 (mttt) REVERT: F 258 TYR cc_start: 0.9110 (t80) cc_final: 0.8799 (t80) REVERT: F 276 SER cc_start: 0.8300 (p) cc_final: 0.7915 (p) REVERT: F 279 ASN cc_start: 0.8954 (t0) cc_final: 0.8073 (t0) REVERT: F 285 ASN cc_start: 0.9439 (m-40) cc_final: 0.9207 (m-40) REVERT: F 332 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8578 (pp) REVERT: F 352 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8894 (tm-30) REVERT: F 385 MET cc_start: 0.8698 (ttm) cc_final: 0.8216 (ttm) REVERT: F 386 MET cc_start: 0.9349 (ptp) cc_final: 0.8957 (ptp) REVERT: F 395 GLU cc_start: 0.8760 (mp0) cc_final: 0.8245 (mp0) REVERT: F 399 GLU cc_start: 0.8729 (pm20) cc_final: 0.8467 (mp0) REVERT: F 404 ASP cc_start: 0.8948 (t0) cc_final: 0.8719 (t70) REVERT: F 407 ARG cc_start: 0.9165 (ttt90) cc_final: 0.8825 (ttt90) REVERT: F 438 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7933 (mmtm) REVERT: G 21 GLN cc_start: 0.8439 (tm130) cc_final: 0.8213 (tm-30) REVERT: G 51 LEU cc_start: 0.9307 (OUTLIER) cc_final: 0.8945 (pp) REVERT: G 105 ARG cc_start: 0.9003 (ttp80) cc_final: 0.8778 (ttp80) REVERT: G 275 SER cc_start: 0.8960 (t) cc_final: 0.8736 (t) REVERT: G 276 SER cc_start: 0.8722 (p) cc_final: 0.8457 (p) REVERT: G 332 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8858 (pp) REVERT: G 352 GLU cc_start: 0.9125 (tm-30) cc_final: 0.8833 (tm-30) REVERT: G 355 ARG cc_start: 0.9212 (ptm-80) cc_final: 0.8897 (ptm-80) REVERT: G 385 MET cc_start: 0.8716 (ttm) cc_final: 0.8153 (ttm) REVERT: G 395 GLU cc_start: 0.8592 (mp0) cc_final: 0.8204 (mp0) REVERT: G 400 TYR cc_start: 0.8100 (m-80) cc_final: 0.7501 (m-10) REVERT: G 404 ASP cc_start: 0.9003 (t0) cc_final: 0.8683 (t70) REVERT: G 407 ARG cc_start: 0.9105 (ttt-90) cc_final: 0.8548 (ttt-90) REVERT: G 510 GLU cc_start: 0.7921 (tp30) cc_final: 0.7453 (tp30) REVERT: H 21 GLN cc_start: 0.8862 (pt0) cc_final: 0.8559 (tm-30) REVERT: H 25 ASN cc_start: 0.9091 (m-40) cc_final: 0.8763 (p0) REVERT: H 51 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8863 (pp) REVERT: H 105 ARG cc_start: 0.9066 (mtm110) cc_final: 0.8566 (mtm110) REVERT: H 109 LYS cc_start: 0.9325 (mttp) cc_final: 0.9015 (mptt) REVERT: H 276 SER cc_start: 0.8741 (p) cc_final: 0.8473 (p) REVERT: H 285 ASN cc_start: 0.9408 (m-40) cc_final: 0.9070 (m110) REVERT: H 332 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8620 (pp) REVERT: H 335 GLU cc_start: 0.8520 (tm-30) cc_final: 0.7852 (tm-30) REVERT: H 352 GLU cc_start: 0.9194 (tm-30) cc_final: 0.8935 (tm-30) REVERT: H 355 ARG cc_start: 0.9206 (ptm-80) cc_final: 0.8911 (ptm-80) REVERT: H 385 MET cc_start: 0.8781 (ttm) cc_final: 0.8249 (ttm) REVERT: H 395 GLU cc_start: 0.8761 (mp0) cc_final: 0.8251 (mp0) REVERT: H 400 TYR cc_start: 0.8174 (m-10) cc_final: 0.7971 (m-10) REVERT: H 404 ASP cc_start: 0.8953 (t0) cc_final: 0.8677 (t70) REVERT: H 512 ARG cc_start: 0.7931 (ttm-80) cc_final: 0.7704 (ptm160) outliers start: 140 outliers final: 93 residues processed: 1021 average time/residue: 0.3492 time to fit residues: 562.1074 Evaluate side-chains 1031 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 917 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 65 LEU 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 282 PHE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU 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 313 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 51 LEU 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 282 PHE Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 388 SER 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 66 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 282 PHE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 499 VAL 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 66 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 282 PHE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 417 LEU 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 260 LEU Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 282 PHE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 382 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 5 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 282 PHE 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 333 THR Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 4.9990 chunk 113 optimal weight: 0.8980 chunk 170 optimal weight: 0.5980 chunk 85 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 181 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 141 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 chunk 224 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN ** 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 312 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 23480 Z= 0.238 Angle : 0.695 9.096 31792 Z= 0.349 Chirality : 0.046 0.172 3656 Planarity : 0.004 0.047 4000 Dihedral : 10.234 89.349 3739 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 6.42 % Allowed : 27.01 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.91 (0.15), residues: 2960 helix: -1.21 (0.15), residues: 1136 sheet: -1.78 (0.24), residues: 368 loop : -1.02 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 92 PHE 0.011 0.001 PHE A 401 TYR 0.020 0.001 TYR G 258 ARG 0.014 0.001 ARG B 105 *********************** 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 1114 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 961 time to evaluate : 2.580 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4085 (ptp) cc_final: 0.3610 (ptm) REVERT: A 21 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8508 (tm-30) REVERT: A 28 ASP cc_start: 0.8541 (m-30) cc_final: 0.8339 (m-30) REVERT: A 51 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8792 (pp) REVERT: A 70 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8590 (mtp) REVERT: A 109 LYS cc_start: 0.9562 (mmmt) cc_final: 0.9012 (tptt) REVERT: A 256 ASP cc_start: 0.9208 (m-30) cc_final: 0.8762 (p0) REVERT: A 285 ASN cc_start: 0.9505 (m-40) cc_final: 0.9117 (m-40) REVERT: A 332 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8625 (pp) REVERT: A 335 GLU cc_start: 0.8380 (tm-30) cc_final: 0.7611 (tm-30) REVERT: A 352 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8853 (tm-30) REVERT: A 355 ARG cc_start: 0.9210 (ptm-80) cc_final: 0.8879 (ptm-80) REVERT: A 385 MET cc_start: 0.8792 (ttm) cc_final: 0.8269 (ttm) REVERT: A 395 GLU cc_start: 0.8669 (mp0) cc_final: 0.8203 (mp0) REVERT: A 404 ASP cc_start: 0.8986 (t0) cc_final: 0.8730 (t0) REVERT: A 406 ILE cc_start: 0.9071 (mp) cc_final: 0.8863 (mp) REVERT: A 407 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8294 (ttt-90) REVERT: A 438 LYS cc_start: 0.9012 (mttt) cc_final: 0.8566 (mmtm) REVERT: A 510 GLU cc_start: 0.7729 (tp30) cc_final: 0.7436 (tp30) REVERT: B 51 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8776 (pp) REVERT: B 256 ASP cc_start: 0.9222 (m-30) cc_final: 0.8656 (p0) REVERT: B 258 TYR cc_start: 0.8998 (t80) cc_final: 0.8744 (t80) REVERT: B 276 SER cc_start: 0.8724 (p) cc_final: 0.8409 (p) REVERT: B 281 ILE cc_start: 0.9017 (tp) cc_final: 0.8739 (tp) REVERT: B 332 ILE cc_start: 0.9037 (OUTLIER) cc_final: 0.8476 (pp) REVERT: B 335 GLU cc_start: 0.8468 (tm-30) cc_final: 0.7772 (tm-30) REVERT: B 352 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8862 (tm-30) REVERT: B 385 MET cc_start: 0.8802 (ttm) cc_final: 0.8345 (ttm) REVERT: B 395 GLU cc_start: 0.8769 (mp0) cc_final: 0.8313 (mp0) REVERT: B 400 TYR cc_start: 0.8189 (m-10) cc_final: 0.7835 (m-10) REVERT: B 404 ASP cc_start: 0.8982 (t0) cc_final: 0.8742 (t70) REVERT: B 407 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8503 (ttt90) REVERT: B 409 LYS cc_start: 0.8665 (ttmp) cc_final: 0.8009 (tttt) REVERT: C 21 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8421 (tm-30) REVERT: C 51 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8843 (pp) REVERT: C 109 LYS cc_start: 0.9640 (mmmt) cc_final: 0.8975 (tptt) REVERT: C 258 TYR cc_start: 0.9003 (t80) cc_final: 0.8729 (t80) REVERT: C 276 SER cc_start: 0.8454 (p) cc_final: 0.8116 (p) REVERT: C 279 ASN cc_start: 0.8913 (t0) cc_final: 0.8062 (t0) REVERT: C 332 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8797 (pp) REVERT: C 352 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8886 (tm-30) REVERT: C 395 GLU cc_start: 0.8671 (mp0) cc_final: 0.8317 (mp0) REVERT: C 404 ASP cc_start: 0.8928 (t0) cc_final: 0.8709 (t70) REVERT: C 409 LYS cc_start: 0.8819 (tttp) cc_final: 0.8602 (ttmt) REVERT: C 438 LYS cc_start: 0.9016 (mtpp) cc_final: 0.8615 (mmtm) REVERT: C 510 GLU cc_start: 0.7788 (tp30) cc_final: 0.7482 (tp30) REVERT: D 51 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8750 (pp) REVERT: D 84 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8205 (mm) REVERT: D 105 ARG cc_start: 0.8981 (mtm110) cc_final: 0.8597 (mtm110) REVERT: D 276 SER cc_start: 0.8651 (p) cc_final: 0.8338 (p) REVERT: D 285 ASN cc_start: 0.9484 (m-40) cc_final: 0.9168 (m110) REVERT: D 332 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8808 (pp) REVERT: D 352 GLU cc_start: 0.9130 (tm-30) cc_final: 0.8792 (tm-30) REVERT: D 355 ARG cc_start: 0.9133 (ptm-80) cc_final: 0.8830 (ptm-80) REVERT: D 369 ASN cc_start: 0.8371 (p0) cc_final: 0.8030 (p0) REVERT: D 395 GLU cc_start: 0.8772 (mp0) cc_final: 0.8323 (mp0) REVERT: D 399 GLU cc_start: 0.8640 (pm20) cc_final: 0.8436 (mp0) REVERT: D 404 ASP cc_start: 0.8932 (t0) cc_final: 0.8693 (t70) REVERT: D 407 ARG cc_start: 0.8858 (ttt90) cc_final: 0.8563 (ttt90) REVERT: D 409 LYS cc_start: 0.8784 (ttmp) cc_final: 0.8217 (tttt) REVERT: D 438 LYS cc_start: 0.8545 (mmtt) cc_final: 0.8212 (mmtm) REVERT: E 21 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8522 (tm-30) REVERT: E 25 ASN cc_start: 0.9123 (m-40) cc_final: 0.8744 (m-40) REVERT: E 51 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8968 (pp) REVERT: E 78 MET cc_start: 0.8305 (OUTLIER) cc_final: 0.8005 (ptm) REVERT: E 109 LYS cc_start: 0.9633 (mmmt) cc_final: 0.8948 (tptt) REVERT: E 256 ASP cc_start: 0.9219 (m-30) cc_final: 0.8649 (p0) REVERT: E 259 ARG cc_start: 0.9316 (ttm-80) cc_final: 0.9083 (ttm-80) REVERT: E 285 ASN cc_start: 0.9459 (m-40) cc_final: 0.9116 (m-40) REVERT: E 332 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8446 (pp) REVERT: E 335 GLU cc_start: 0.8419 (tm-30) cc_final: 0.7708 (tm-30) REVERT: E 352 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8858 (tm-30) REVERT: E 355 ARG cc_start: 0.9229 (ptm-80) cc_final: 0.8921 (ptm-80) REVERT: E 385 MET cc_start: 0.8810 (ttm) cc_final: 0.8242 (ttm) REVERT: E 395 GLU cc_start: 0.8695 (mp0) cc_final: 0.8176 (mp0) REVERT: E 404 ASP cc_start: 0.9014 (t0) cc_final: 0.8792 (t70) REVERT: F 21 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8505 (tm-30) REVERT: F 51 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8761 (pp) REVERT: F 84 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8103 (mm) REVERT: F 109 LYS cc_start: 0.9418 (mptt) cc_final: 0.9119 (mttm) REVERT: F 258 TYR cc_start: 0.9115 (t80) cc_final: 0.8816 (t80) REVERT: F 276 SER cc_start: 0.8181 (p) cc_final: 0.7773 (p) REVERT: F 279 ASN cc_start: 0.8955 (t0) cc_final: 0.8080 (t0) REVERT: F 285 ASN cc_start: 0.9443 (m-40) cc_final: 0.9165 (m-40) REVERT: F 332 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8583 (pp) REVERT: F 352 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8848 (tm-30) REVERT: F 385 MET cc_start: 0.8716 (ttm) cc_final: 0.8223 (ttm) REVERT: F 386 MET cc_start: 0.9368 (ptp) cc_final: 0.9074 (ptp) REVERT: F 395 GLU cc_start: 0.8749 (mp0) cc_final: 0.8175 (mp0) REVERT: F 399 GLU cc_start: 0.8708 (pm20) cc_final: 0.8422 (mp0) REVERT: F 404 ASP cc_start: 0.8969 (t0) cc_final: 0.8743 (t70) REVERT: F 409 LYS cc_start: 0.8863 (ttmp) cc_final: 0.8362 (ttmt) REVERT: F 438 LYS cc_start: 0.8243 (mmtt) cc_final: 0.7987 (mmtm) REVERT: G 51 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8921 (pp) REVERT: G 275 SER cc_start: 0.8940 (t) cc_final: 0.8713 (t) REVERT: G 276 SER cc_start: 0.8765 (p) cc_final: 0.8439 (p) REVERT: G 285 ASN cc_start: 0.9229 (m-40) cc_final: 0.8963 (m110) REVERT: G 332 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8525 (pp) REVERT: G 335 GLU cc_start: 0.8509 (tm-30) cc_final: 0.7763 (tm-30) REVERT: G 352 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8866 (tm-30) REVERT: G 355 ARG cc_start: 0.9198 (ptm-80) cc_final: 0.8880 (ptm-80) REVERT: G 385 MET cc_start: 0.8651 (ttm) cc_final: 0.8160 (ttm) REVERT: G 395 GLU cc_start: 0.8615 (mp0) cc_final: 0.8208 (mp0) REVERT: G 400 TYR cc_start: 0.8055 (m-80) cc_final: 0.7111 (m-10) REVERT: G 404 ASP cc_start: 0.9019 (t0) cc_final: 0.8704 (t70) REVERT: G 407 ARG cc_start: 0.9103 (ttt-90) cc_final: 0.8567 (ttt-90) REVERT: H 21 GLN cc_start: 0.8870 (pt0) cc_final: 0.8579 (tm-30) REVERT: H 25 ASN cc_start: 0.9080 (m-40) cc_final: 0.8762 (p0) REVERT: H 36 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8090 (pp) REVERT: H 51 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8810 (pp) REVERT: H 276 SER cc_start: 0.8744 (p) cc_final: 0.8387 (p) REVERT: H 285 ASN cc_start: 0.9415 (m-40) cc_final: 0.9092 (m110) REVERT: H 332 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8651 (pp) REVERT: H 335 GLU cc_start: 0.8529 (tm-30) cc_final: 0.7914 (tm-30) REVERT: H 352 GLU cc_start: 0.9196 (tm-30) cc_final: 0.8941 (tm-30) REVERT: H 355 ARG cc_start: 0.9201 (ptm-80) cc_final: 0.8924 (ptm-80) REVERT: H 385 MET cc_start: 0.8766 (ttm) cc_final: 0.8239 (ttm) REVERT: H 395 GLU cc_start: 0.8739 (mp0) cc_final: 0.8323 (mp0) REVERT: H 404 ASP cc_start: 0.8963 (t0) cc_final: 0.8695 (t70) REVERT: H 512 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7727 (ptm160) outliers start: 153 outliers final: 104 residues processed: 1024 average time/residue: 0.3273 time to fit residues: 522.6516 Evaluate side-chains 1058 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 927 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 MET 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 280 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 THR 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 260 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 407 ARG 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 21 GLN 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 78 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 282 PHE Chi-restraints excluded: chain C residue 313 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 388 SER 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 51 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 388 SER 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 66 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 282 PHE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 499 VAL 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 66 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 282 PHE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 384 VAL 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 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 260 LEU Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 282 PHE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 386 MET 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 36 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 5.9990 chunk 273 optimal weight: 5.9990 chunk 249 optimal weight: 5.9990 chunk 265 optimal weight: 0.7980 chunk 160 optimal weight: 0.7980 chunk 115 optimal weight: 0.9980 chunk 208 optimal weight: 0.3980 chunk 81 optimal weight: 2.9990 chunk 240 optimal weight: 0.8980 chunk 251 optimal weight: 6.9990 chunk 264 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN ** 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 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23480 Z= 0.242 Angle : 0.712 9.748 31792 Z= 0.357 Chirality : 0.046 0.187 3656 Planarity : 0.004 0.043 4000 Dihedral : 10.108 88.394 3739 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 6.25 % Allowed : 26.89 % Favored : 66.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.15), residues: 2960 helix: -1.19 (0.15), residues: 1144 sheet: -2.05 (0.26), residues: 320 loop : -0.99 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS D 92 PHE 0.011 0.001 PHE A 401 TYR 0.018 0.001 TYR F 400 ARG 0.016 0.001 ARG H 105 *********************** 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 1109 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 960 time to evaluate : 2.624 Fit side-chains REVERT: A 1 MET cc_start: 0.4092 (ptp) cc_final: 0.3662 (ptm) REVERT: A 21 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.8499 (tm-30) REVERT: A 51 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.8965 (pp) REVERT: A 70 MET cc_start: 0.8910 (OUTLIER) cc_final: 0.8115 (mtp) REVERT: A 105 ARG cc_start: 0.9018 (ttp80) cc_final: 0.8670 (ttp-110) REVERT: A 109 LYS cc_start: 0.9550 (mmmt) cc_final: 0.9139 (tmtt) REVERT: A 256 ASP cc_start: 0.9182 (m-30) cc_final: 0.8736 (p0) REVERT: A 275 SER cc_start: 0.8962 (t) cc_final: 0.8740 (t) REVERT: A 285 ASN cc_start: 0.9518 (m-40) cc_final: 0.9106 (m-40) REVERT: A 332 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8638 (pp) REVERT: A 335 GLU cc_start: 0.8384 (tm-30) cc_final: 0.7617 (tm-30) REVERT: A 352 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8851 (tm-30) REVERT: A 355 ARG cc_start: 0.9169 (ptm-80) cc_final: 0.8843 (ptm-80) REVERT: A 385 MET cc_start: 0.8786 (ttm) cc_final: 0.8267 (ttm) REVERT: A 395 GLU cc_start: 0.8674 (mp0) cc_final: 0.8208 (mp0) REVERT: A 404 ASP cc_start: 0.9000 (t0) cc_final: 0.8759 (t0) REVERT: A 406 ILE cc_start: 0.9096 (mp) cc_final: 0.8896 (mp) REVERT: A 407 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8234 (ttt-90) REVERT: A 438 LYS cc_start: 0.9077 (mttt) cc_final: 0.8662 (mmtt) REVERT: A 510 GLU cc_start: 0.7725 (tp30) cc_final: 0.7434 (tp30) REVERT: B 51 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8677 (pp) REVERT: B 258 TYR cc_start: 0.9009 (t80) cc_final: 0.8779 (t80) REVERT: B 276 SER cc_start: 0.8795 (p) cc_final: 0.8481 (p) REVERT: B 281 ILE cc_start: 0.8911 (tp) cc_final: 0.8580 (tp) REVERT: B 332 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8425 (pp) REVERT: B 335 GLU cc_start: 0.8430 (tm-30) cc_final: 0.7759 (tm-30) REVERT: B 352 GLU cc_start: 0.9160 (tm-30) cc_final: 0.8876 (tm-30) REVERT: B 385 MET cc_start: 0.8805 (ttm) cc_final: 0.8344 (ttm) REVERT: B 395 GLU cc_start: 0.8797 (mp0) cc_final: 0.8351 (mp0) REVERT: B 400 TYR cc_start: 0.8203 (m-10) cc_final: 0.7793 (m-10) REVERT: B 404 ASP cc_start: 0.9015 (t0) cc_final: 0.8786 (t70) REVERT: B 407 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8495 (ttt90) REVERT: C 21 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8419 (tm-30) REVERT: C 51 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8885 (pp) REVERT: C 70 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8029 (mtp) REVERT: C 109 LYS cc_start: 0.9632 (mmmt) cc_final: 0.8991 (tptt) REVERT: C 258 TYR cc_start: 0.9003 (t80) cc_final: 0.8772 (t80) REVERT: C 276 SER cc_start: 0.8478 (p) cc_final: 0.8137 (p) REVERT: C 279 ASN cc_start: 0.8910 (t0) cc_final: 0.8067 (t0) REVERT: C 332 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8477 (pp) REVERT: C 335 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7694 (tm-30) REVERT: C 352 GLU cc_start: 0.9171 (tm-30) cc_final: 0.8913 (tm-30) REVERT: C 395 GLU cc_start: 0.8682 (mp0) cc_final: 0.8319 (mp0) REVERT: C 404 ASP cc_start: 0.8981 (t0) cc_final: 0.8780 (t70) REVERT: C 409 LYS cc_start: 0.8797 (tttp) cc_final: 0.8326 (tttt) REVERT: C 438 LYS cc_start: 0.9017 (mtpp) cc_final: 0.8718 (mptt) REVERT: C 510 GLU cc_start: 0.7789 (tp30) cc_final: 0.7481 (tp30) REVERT: D 51 LEU cc_start: 0.9189 (OUTLIER) cc_final: 0.8854 (pp) REVERT: D 70 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8522 (mtp) REVERT: D 84 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8200 (mm) REVERT: D 105 ARG cc_start: 0.9067 (mtm110) cc_final: 0.8677 (mtm110) REVERT: D 276 SER cc_start: 0.8755 (p) cc_final: 0.8468 (p) REVERT: D 285 ASN cc_start: 0.9529 (m-40) cc_final: 0.9156 (m-40) REVERT: D 332 ILE cc_start: 0.9047 (OUTLIER) cc_final: 0.8462 (pp) REVERT: D 335 GLU cc_start: 0.8403 (tm-30) cc_final: 0.7690 (tm-30) REVERT: D 352 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8658 (tm-30) REVERT: D 355 ARG cc_start: 0.9129 (ptm-80) cc_final: 0.8905 (ptm-80) REVERT: D 369 ASN cc_start: 0.8329 (p0) cc_final: 0.8011 (p0) REVERT: D 395 GLU cc_start: 0.8808 (mp0) cc_final: 0.8360 (mp0) REVERT: D 400 TYR cc_start: 0.7960 (m-10) cc_final: 0.7663 (m-10) REVERT: D 404 ASP cc_start: 0.8948 (t0) cc_final: 0.8702 (t70) REVERT: D 407 ARG cc_start: 0.8883 (ttt90) cc_final: 0.8554 (ttt90) REVERT: D 409 LYS cc_start: 0.8783 (ttmp) cc_final: 0.8225 (tttt) REVERT: D 438 LYS cc_start: 0.8553 (mmtt) cc_final: 0.8269 (mmtm) REVERT: E 21 GLN cc_start: 0.8817 (OUTLIER) cc_final: 0.8566 (tm-30) REVERT: E 25 ASN cc_start: 0.9132 (m-40) cc_final: 0.8753 (m-40) REVERT: E 51 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8968 (pp) REVERT: E 78 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8009 (ptm) REVERT: E 109 LYS cc_start: 0.9620 (mmmt) cc_final: 0.8986 (tptt) REVERT: E 259 ARG cc_start: 0.9314 (ttm-80) cc_final: 0.9109 (ttm-80) REVERT: E 285 ASN cc_start: 0.9498 (m-40) cc_final: 0.9096 (m-40) REVERT: E 332 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8449 (pp) REVERT: E 335 GLU cc_start: 0.8400 (tm-30) cc_final: 0.7691 (tm-30) REVERT: E 352 GLU cc_start: 0.9127 (tm-30) cc_final: 0.8872 (tm-30) REVERT: E 355 ARG cc_start: 0.9206 (ptm-80) cc_final: 0.8922 (ptm-80) REVERT: E 385 MET cc_start: 0.8805 (ttm) cc_final: 0.8282 (ttm) REVERT: E 395 GLU cc_start: 0.8657 (mp0) cc_final: 0.8258 (mp0) REVERT: E 404 ASP cc_start: 0.9030 (t0) cc_final: 0.8824 (t70) REVERT: E 410 LYS cc_start: 0.8570 (ptmt) cc_final: 0.8281 (ptmt) REVERT: F 51 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8948 (pp) REVERT: F 84 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8090 (mm) REVERT: F 105 ARG cc_start: 0.9092 (mtm110) cc_final: 0.8789 (mtm110) REVERT: F 109 LYS cc_start: 0.9402 (mptt) cc_final: 0.9160 (mttt) REVERT: F 258 TYR cc_start: 0.9107 (t80) cc_final: 0.8805 (t80) REVERT: F 276 SER cc_start: 0.8215 (p) cc_final: 0.7810 (p) REVERT: F 279 ASN cc_start: 0.8962 (t0) cc_final: 0.8078 (t0) REVERT: F 285 ASN cc_start: 0.9443 (m-40) cc_final: 0.9214 (m-40) REVERT: F 332 ILE cc_start: 0.8828 (OUTLIER) cc_final: 0.8593 (pp) REVERT: F 352 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8871 (tm-30) REVERT: F 385 MET cc_start: 0.8765 (ttm) cc_final: 0.8274 (ttm) REVERT: F 386 MET cc_start: 0.9343 (ptp) cc_final: 0.9101 (ptp) REVERT: F 395 GLU cc_start: 0.8684 (mp0) cc_final: 0.8314 (mp0) REVERT: F 399 GLU cc_start: 0.8711 (pm20) cc_final: 0.8454 (mp0) REVERT: F 400 TYR cc_start: 0.8066 (m-10) cc_final: 0.7144 (m-10) REVERT: F 404 ASP cc_start: 0.8981 (t0) cc_final: 0.8757 (t0) REVERT: F 407 ARG cc_start: 0.9026 (ttt90) cc_final: 0.8514 (ttt-90) REVERT: F 409 LYS cc_start: 0.8816 (ttmp) cc_final: 0.8269 (ttmt) REVERT: F 438 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7985 (mmtm) REVERT: F 449 ASP cc_start: 0.9155 (p0) cc_final: 0.8616 (p0) REVERT: G 51 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8763 (pp) REVERT: G 110 TYR cc_start: 0.7967 (t80) cc_final: 0.7747 (t80) REVERT: G 276 SER cc_start: 0.8793 (p) cc_final: 0.8445 (p) REVERT: G 285 ASN cc_start: 0.9262 (m-40) cc_final: 0.9029 (m110) REVERT: G 332 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8565 (pp) REVERT: G 335 GLU cc_start: 0.8487 (tm-30) cc_final: 0.7798 (tm-30) REVERT: G 352 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8888 (tm-30) REVERT: G 355 ARG cc_start: 0.9178 (ptm-80) cc_final: 0.8874 (ptm-80) REVERT: G 385 MET cc_start: 0.8617 (ttm) cc_final: 0.8104 (ttm) REVERT: G 395 GLU cc_start: 0.8641 (mp0) cc_final: 0.8263 (mp0) REVERT: G 400 TYR cc_start: 0.8097 (m-80) cc_final: 0.7302 (m-10) REVERT: G 404 ASP cc_start: 0.9033 (t0) cc_final: 0.8746 (t70) REVERT: G 407 ARG cc_start: 0.9126 (ttt-90) cc_final: 0.8575 (ttt-90) REVERT: H 21 GLN cc_start: 0.8885 (pt0) cc_final: 0.8611 (tm-30) REVERT: H 25 ASN cc_start: 0.9090 (m-40) cc_final: 0.8790 (p0) REVERT: H 51 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8739 (pp) REVERT: H 70 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.7982 (mtp) REVERT: H 84 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8120 (mm) REVERT: H 285 ASN cc_start: 0.9453 (m-40) cc_final: 0.9093 (m-40) REVERT: H 332 ILE cc_start: 0.9152 (OUTLIER) cc_final: 0.8645 (pp) REVERT: H 335 GLU cc_start: 0.8496 (tm-30) cc_final: 0.7896 (tm-30) REVERT: H 352 GLU cc_start: 0.9196 (tm-30) cc_final: 0.8945 (tm-30) REVERT: H 355 ARG cc_start: 0.9172 (ptm-80) cc_final: 0.8917 (ptm-80) REVERT: H 385 MET cc_start: 0.8761 (ttm) cc_final: 0.8221 (ttm) REVERT: H 395 GLU cc_start: 0.8749 (mp0) cc_final: 0.8243 (mp0) REVERT: H 404 ASP cc_start: 0.8969 (t0) cc_final: 0.8728 (t70) outliers start: 149 outliers final: 106 residues processed: 1024 average time/residue: 0.3254 time to fit residues: 520.6236 Evaluate side-chains 1072 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 937 time to evaluate : 2.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 MET 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 280 SER Chi-restraints excluded: chain A residue 282 PHE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 THR 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 107 VAL Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 282 PHE Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 407 ARG 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 21 GLN 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 70 MET 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 282 PHE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 VAL 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 36 LEU 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 70 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 388 SER 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 37 ILE Chi-restraints excluded: chain E residue 51 LEU 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 280 SER Chi-restraints excluded: chain E residue 282 PHE Chi-restraints excluded: chain E residue 313 LEU Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 499 VAL 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 73 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 282 PHE Chi-restraints excluded: chain F residue 286 MET 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 384 VAL 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 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 260 LEU Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 282 PHE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 386 MET 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 70 MET Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 510 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 3.9990 chunk 281 optimal weight: 0.9980 chunk 171 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 chunk 195 optimal weight: 0.7980 chunk 294 optimal weight: 0.6980 chunk 271 optimal weight: 6.9990 chunk 234 optimal weight: 6.9990 chunk 24 optimal weight: 0.3980 chunk 181 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 21 GLN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23480 Z= 0.238 Angle : 0.726 9.778 31792 Z= 0.363 Chirality : 0.046 0.196 3656 Planarity : 0.004 0.067 4000 Dihedral : 9.955 88.432 3738 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 5.75 % Allowed : 27.89 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.15), residues: 2960 helix: -1.19 (0.15), residues: 1136 sheet: -2.03 (0.26), residues: 320 loop : -0.99 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 92 PHE 0.011 0.001 PHE A 401 TYR 0.029 0.001 TYR A 258 ARG 0.015 0.001 ARG B 105 ********************** 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 1105 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 968 time to evaluate : 2.520 Fit side-chains REVERT: A 21 GLN cc_start: 0.8826 (OUTLIER) cc_final: 0.8481 (tm-30) REVERT: A 51 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8751 (pp) REVERT: A 70 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8210 (mtp) REVERT: A 109 LYS cc_start: 0.9546 (mmmt) cc_final: 0.9168 (tmtt) REVERT: A 256 ASP cc_start: 0.9157 (m-30) cc_final: 0.8724 (p0) REVERT: A 285 ASN cc_start: 0.9517 (m-40) cc_final: 0.9117 (m-40) REVERT: A 332 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8631 (pp) REVERT: A 335 GLU cc_start: 0.8349 (tm-30) cc_final: 0.7618 (tm-30) REVERT: A 352 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8864 (tm-30) REVERT: A 353 TYR cc_start: 0.9090 (t80) cc_final: 0.8761 (t80) REVERT: A 355 ARG cc_start: 0.9165 (ptm-80) cc_final: 0.8822 (ptm-80) REVERT: A 385 MET cc_start: 0.8813 (ttm) cc_final: 0.8283 (ttm) REVERT: A 395 GLU cc_start: 0.8699 (mp0) cc_final: 0.8273 (mp0) REVERT: A 404 ASP cc_start: 0.9013 (t0) cc_final: 0.8777 (t0) REVERT: A 407 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8347 (ttt-90) REVERT: A 438 LYS cc_start: 0.9079 (mttt) cc_final: 0.8683 (mmtt) REVERT: A 510 GLU cc_start: 0.7718 (tp30) cc_final: 0.7372 (tp30) REVERT: B 51 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8664 (pp) REVERT: B 258 TYR cc_start: 0.9031 (t80) cc_final: 0.8821 (t80) REVERT: B 276 SER cc_start: 0.8828 (p) cc_final: 0.8523 (p) REVERT: B 332 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8390 (pp) REVERT: B 335 GLU cc_start: 0.8414 (tm-30) cc_final: 0.7757 (tm-30) REVERT: B 352 GLU cc_start: 0.9149 (tm-30) cc_final: 0.8687 (tm-30) REVERT: B 355 ARG cc_start: 0.9150 (ptm-80) cc_final: 0.8618 (ptm-80) REVERT: B 385 MET cc_start: 0.8802 (ttm) cc_final: 0.8579 (ttp) REVERT: B 395 GLU cc_start: 0.8813 (mp0) cc_final: 0.8278 (mp0) REVERT: B 400 TYR cc_start: 0.8371 (m-10) cc_final: 0.7627 (m-10) REVERT: B 407 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8146 (ttt-90) REVERT: C 21 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8385 (tm-30) REVERT: C 51 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8735 (pp) REVERT: C 105 ARG cc_start: 0.9013 (ttp80) cc_final: 0.8729 (ttp-110) REVERT: C 109 LYS cc_start: 0.9556 (mmmt) cc_final: 0.8992 (tptt) REVERT: C 258 TYR cc_start: 0.9015 (t80) cc_final: 0.8795 (t80) REVERT: C 276 SER cc_start: 0.8457 (p) cc_final: 0.8109 (p) REVERT: C 279 ASN cc_start: 0.8908 (t0) cc_final: 0.8077 (t0) REVERT: C 332 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8475 (pp) REVERT: C 335 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7710 (tm-30) REVERT: C 352 GLU cc_start: 0.9169 (tm-30) cc_final: 0.8915 (tm-30) REVERT: C 395 GLU cc_start: 0.8721 (mp0) cc_final: 0.8358 (mp0) REVERT: C 404 ASP cc_start: 0.8962 (t0) cc_final: 0.8757 (t70) REVERT: C 407 ARG cc_start: 0.9065 (ttt90) cc_final: 0.8841 (ttt90) REVERT: C 409 LYS cc_start: 0.8839 (tttp) cc_final: 0.8381 (tttt) REVERT: C 438 LYS cc_start: 0.9042 (mtpp) cc_final: 0.8754 (mptt) REVERT: C 510 GLU cc_start: 0.7789 (tp30) cc_final: 0.7481 (tp30) REVERT: D 51 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8685 (pp) REVERT: D 70 MET cc_start: 0.9052 (OUTLIER) cc_final: 0.8562 (mtp) REVERT: D 84 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8235 (tp) REVERT: D 108 LYS cc_start: 0.9366 (tppt) cc_final: 0.9116 (mmtp) REVERT: D 276 SER cc_start: 0.8709 (p) cc_final: 0.8468 (p) REVERT: D 285 ASN cc_start: 0.9534 (m-40) cc_final: 0.9111 (m-40) REVERT: D 332 ILE cc_start: 0.9035 (OUTLIER) cc_final: 0.8458 (pp) REVERT: D 335 GLU cc_start: 0.8374 (tm-30) cc_final: 0.7684 (tm-30) REVERT: D 352 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8638 (tm-30) REVERT: D 355 ARG cc_start: 0.9129 (ptm-80) cc_final: 0.8910 (ptm-80) REVERT: D 369 ASN cc_start: 0.8335 (p0) cc_final: 0.8040 (p0) REVERT: D 395 GLU cc_start: 0.8840 (mp0) cc_final: 0.8386 (mp0) REVERT: D 404 ASP cc_start: 0.8929 (t0) cc_final: 0.8702 (t70) REVERT: D 407 ARG cc_start: 0.8898 (ttt90) cc_final: 0.8593 (ttt90) REVERT: D 409 LYS cc_start: 0.8783 (ttmp) cc_final: 0.8261 (tttt) REVERT: D 438 LYS cc_start: 0.8550 (mmtt) cc_final: 0.8269 (mmtm) REVERT: E 21 GLN cc_start: 0.8815 (pt0) cc_final: 0.8593 (tm-30) REVERT: E 25 ASN cc_start: 0.9143 (m-40) cc_final: 0.8778 (m-40) REVERT: E 51 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8959 (pp) REVERT: E 78 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.8004 (ptm) REVERT: E 105 ARG cc_start: 0.9063 (ttp80) cc_final: 0.8731 (ttp-110) REVERT: E 109 LYS cc_start: 0.9622 (mmmt) cc_final: 0.8976 (tptt) REVERT: E 285 ASN cc_start: 0.9513 (m-40) cc_final: 0.9213 (m-40) REVERT: E 332 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8421 (pp) REVERT: E 335 GLU cc_start: 0.8389 (tm-30) cc_final: 0.7680 (tm-30) REVERT: E 352 GLU cc_start: 0.9126 (tm-30) cc_final: 0.8876 (tm-30) REVERT: E 355 ARG cc_start: 0.9202 (ptm-80) cc_final: 0.8940 (ptm-80) REVERT: E 385 MET cc_start: 0.8768 (ttm) cc_final: 0.8262 (ttm) REVERT: E 395 GLU cc_start: 0.8664 (mp0) cc_final: 0.8240 (mp0) REVERT: E 404 ASP cc_start: 0.9038 (t0) cc_final: 0.8818 (t70) REVERT: F 51 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8753 (pp) REVERT: F 84 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8052 (mm) REVERT: F 105 ARG cc_start: 0.8995 (mtm110) cc_final: 0.8782 (mtm110) REVERT: F 109 LYS cc_start: 0.9431 (mptt) cc_final: 0.9165 (mttt) REVERT: F 258 TYR cc_start: 0.9104 (t80) cc_final: 0.8871 (t80) REVERT: F 276 SER cc_start: 0.8218 (p) cc_final: 0.7818 (p) REVERT: F 279 ASN cc_start: 0.8959 (t0) cc_final: 0.8082 (t0) REVERT: F 285 ASN cc_start: 0.9444 (m-40) cc_final: 0.9162 (m-40) REVERT: F 332 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8594 (pp) REVERT: F 352 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8884 (tm-30) REVERT: F 385 MET cc_start: 0.8723 (ttm) cc_final: 0.8244 (ttm) REVERT: F 395 GLU cc_start: 0.8732 (mp0) cc_final: 0.8369 (mp0) REVERT: F 400 TYR cc_start: 0.8047 (m-10) cc_final: 0.6723 (m-10) REVERT: F 404 ASP cc_start: 0.8997 (t0) cc_final: 0.8790 (t70) REVERT: F 407 ARG cc_start: 0.9010 (ttt90) cc_final: 0.8538 (ttt-90) REVERT: F 438 LYS cc_start: 0.8302 (mmtt) cc_final: 0.8023 (mmtm) REVERT: F 512 ARG cc_start: 0.7867 (ttm-80) cc_final: 0.7495 (ttm-80) REVERT: G 51 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8835 (pp) REVERT: G 276 SER cc_start: 0.8828 (p) cc_final: 0.8522 (p) REVERT: G 285 ASN cc_start: 0.9259 (m-40) cc_final: 0.9002 (m110) REVERT: G 332 ILE cc_start: 0.9094 (OUTLIER) cc_final: 0.8560 (pp) REVERT: G 335 GLU cc_start: 0.8456 (tm-30) cc_final: 0.7783 (tm-30) REVERT: G 352 GLU cc_start: 0.9139 (tm-30) cc_final: 0.8882 (tm-30) REVERT: G 355 ARG cc_start: 0.9176 (ptm-80) cc_final: 0.8888 (ptm-80) REVERT: G 385 MET cc_start: 0.8630 (ttm) cc_final: 0.8150 (ttm) REVERT: G 395 GLU cc_start: 0.8661 (mp0) cc_final: 0.8278 (mp0) REVERT: G 400 TYR cc_start: 0.8101 (m-80) cc_final: 0.7389 (m-10) REVERT: G 404 ASP cc_start: 0.9036 (t0) cc_final: 0.8750 (t70) REVERT: G 407 ARG cc_start: 0.9094 (ttt-90) cc_final: 0.8515 (ttt-90) REVERT: H 21 GLN cc_start: 0.8876 (pt0) cc_final: 0.8619 (tm-30) REVERT: H 25 ASN cc_start: 0.9088 (m-40) cc_final: 0.8807 (p0) REVERT: H 51 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8729 (pp) REVERT: H 70 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.7988 (mtp) REVERT: H 84 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8065 (mm) REVERT: H 109 LYS cc_start: 0.9611 (mmmt) cc_final: 0.9018 (tptt) REVERT: H 285 ASN cc_start: 0.9463 (m-40) cc_final: 0.9072 (m-40) REVERT: H 332 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8627 (pp) REVERT: H 335 GLU cc_start: 0.8479 (tm-30) cc_final: 0.7910 (tm-30) REVERT: H 352 GLU cc_start: 0.9175 (tm-30) cc_final: 0.8941 (tm-30) REVERT: H 385 MET cc_start: 0.8776 (ttm) cc_final: 0.8243 (ttm) REVERT: H 388 SER cc_start: 0.9388 (p) cc_final: 0.8506 (m) REVERT: H 395 GLU cc_start: 0.8604 (mp0) cc_final: 0.8244 (mp0) REVERT: H 404 ASP cc_start: 0.8992 (t0) cc_final: 0.8744 (t70) outliers start: 137 outliers final: 97 residues processed: 1026 average time/residue: 0.3152 time to fit residues: 508.3672 Evaluate side-chains 1079 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 955 time to evaluate : 2.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 70 MET 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 282 PHE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 373 ILE Chi-restraints excluded: chain A residue 407 ARG Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 45 THR 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 73 VAL Chi-restraints excluded: chain B residue 260 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 333 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 407 ARG 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 21 GLN 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 78 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 282 PHE 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 384 VAL 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 70 MET Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 388 SER 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 37 ILE Chi-restraints excluded: chain E residue 51 LEU 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 282 PHE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 499 VAL 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 73 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 282 PHE Chi-restraints excluded: chain F residue 286 MET 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 384 VAL 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 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 260 LEU Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 282 PHE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 386 MET 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 70 MET Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 286 MET Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 510 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 0.0770 chunk 250 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 235 optimal weight: 2.9990 chunk 98 optimal weight: 0.4980 chunk 241 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 overall best weight: 1.0340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 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** ** 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 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 HIS ** H 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.107142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.086160 restraints weight = 40759.615| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 3.90 r_work: 0.2831 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.4286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 23480 Z= 0.282 Angle : 0.750 9.456 31792 Z= 0.375 Chirality : 0.047 0.198 3656 Planarity : 0.004 0.041 4000 Dihedral : 9.953 88.658 3738 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 5.83 % Allowed : 28.48 % Favored : 65.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.15), residues: 2960 helix: -1.10 (0.15), residues: 1136 sheet: -1.66 (0.24), residues: 368 loop : -1.04 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 92 PHE 0.010 0.001 PHE A 401 TYR 0.028 0.002 TYR A 258 ARG 0.017 0.001 ARG D 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8405.99 seconds wall clock time: 148 minutes 4.30 seconds (8884.30 seconds total)