Starting phenix.real_space_refine on Fri Jun 20 07:39:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u8s_20691/06_2025/6u8s_20691.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u8s_20691/06_2025/6u8s_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/cci-nas-00/data/ceres_data/6u8s_20691/06_2025/6u8s_20691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u8s_20691/06_2025/6u8s_20691.map" model { file = "/net/cci-nas-00/data/ceres_data/6u8s_20691/06_2025/6u8s_20691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u8s_20691/06_2025/6u8s_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-5710/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: 13.46, per 1000 atoms: 0.58 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: 6.10 Conformation dependent library (CDL) restraints added in 3.2 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: 3.05 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: 8.13 Time building geometry restraints manager: 7.22 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 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: 0.870 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 53.170 Find NCS groups from input model: 0.500 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.230 23488 Z= 0.593 Angle : 1.355 16.360 31792 Z= 0.676 Chirality : 0.066 0.354 3656 Planarity : 0.007 0.056 4000 Dihedral : 15.528 88.405 8856 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 9.06 % Allowed : 8.05 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 Details of bonding type rmsd hydrogen bonds : bond 0.20259 ( 841) hydrogen bonds : angle 8.62652 ( 2427) covalent geometry : bond 0.01240 (23480) covalent geometry : angle 1.35527 (31792) Misc. bond : bond 0.00121 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 1262 time to evaluate : 2.480 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: 0.3342 time to fit residues: 696.0491 Evaluate side-chains 1053 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 941 time to evaluate : 2.696 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.109233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.088578 restraints weight = 40856.260| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 4.04 r_work: 0.2866 rms_B_bonded: 4.49 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 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 23488 Z= 0.153 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 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 841) hydrogen bonds : angle 6.08695 ( 2427) covalent geometry : bond 0.00364 (23480) covalent geometry : angle 0.72526 (31792) Misc. bond : bond 0.00090 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 1052 time to evaluate : 2.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8822 (m-30) cc_final: 0.8450 (m-30) REVERT: A 50 ASP cc_start: 0.9030 (t0) cc_final: 0.8798 (t0) REVERT: A 105 ARG cc_start: 0.9159 (mtm110) cc_final: 0.8920 (mtm110) REVERT: A 109 LYS cc_start: 0.9408 (mttp) cc_final: 0.8772 (tptt) REVERT: A 276 SER cc_start: 0.8621 (p) cc_final: 0.8371 (p) REVERT: A 285 ASN cc_start: 0.9437 (m-40) cc_final: 0.9066 (m-40) REVERT: A 352 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8843 (tm-30) REVERT: A 395 GLU cc_start: 0.8747 (mp0) cc_final: 0.8038 (mp0) REVERT: A 399 GLU cc_start: 0.8971 (pm20) cc_final: 0.8703 (mp0) REVERT: A 404 ASP cc_start: 0.9133 (t0) cc_final: 0.8829 (t0) REVERT: A 512 ARG cc_start: 0.7772 (ttm-80) cc_final: 0.7555 (ptm160) REVERT: B 25 ASN cc_start: 0.9106 (m-40) cc_final: 0.8844 (p0) REVERT: B 28 ASP cc_start: 0.8857 (m-30) cc_final: 0.8524 (m-30) REVERT: B 47 ASP cc_start: 0.9166 (p0) cc_final: 0.8894 (p0) REVERT: B 50 ASP cc_start: 0.9050 (t70) cc_final: 0.8755 (t0) REVERT: B 58 LYS cc_start: 0.9441 (mmtp) cc_final: 0.9195 (mmmm) REVERT: B 105 ARG cc_start: 0.9198 (mtm110) cc_final: 0.8864 (mtm110) REVERT: B 109 LYS cc_start: 0.9399 (mttp) cc_final: 0.9005 (mttp) REVERT: B 276 SER cc_start: 0.8674 (p) cc_final: 0.8398 (p) REVERT: B 281 ILE cc_start: 0.8907 (tp) cc_final: 0.8567 (tt) REVERT: B 285 ASN cc_start: 0.9419 (m-40) cc_final: 0.9188 (m-40) REVERT: B 352 GLU cc_start: 0.9208 (tm-30) cc_final: 0.8952 (tm-30) REVERT: B 395 GLU cc_start: 0.8829 (mp0) cc_final: 0.8337 (mp0) REVERT: B 399 GLU cc_start: 0.9037 (pm20) cc_final: 0.8804 (mp0) REVERT: B 400 TYR cc_start: 0.8405 (m-80) cc_final: 0.7513 (m-80) REVERT: B 404 ASP cc_start: 0.9146 (t0) cc_final: 0.8874 (t0) REVERT: B 407 ARG cc_start: 0.8774 (ttt-90) cc_final: 0.7753 (ttt-90) REVERT: B 438 LYS cc_start: 0.8312 (mmtt) cc_final: 0.8096 (mtpp) REVERT: B 449 ASP cc_start: 0.9267 (p0) cc_final: 0.9008 (p0) REVERT: B 461 ILE cc_start: 0.9143 (pp) cc_final: 0.8928 (pp) REVERT: B 512 ARG cc_start: 0.7779 (ttm-80) cc_final: 0.7573 (ptm160) REVERT: C 28 ASP cc_start: 0.8884 (m-30) cc_final: 0.8560 (m-30) REVERT: C 50 ASP cc_start: 0.9017 (t70) cc_final: 0.8704 (t0) REVERT: C 58 LYS cc_start: 0.9345 (mmtp) cc_final: 0.9088 (mmmm) REVERT: C 66 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8190 (p) REVERT: C 98 GLU cc_start: 0.9458 (mp0) cc_final: 0.9226 (mp0) REVERT: C 105 ARG cc_start: 0.9167 (mtm110) cc_final: 0.8880 (mtm110) REVERT: C 109 LYS cc_start: 0.9404 (mttp) cc_final: 0.8982 (mtmm) REVERT: C 275 SER cc_start: 0.8935 (t) cc_final: 0.8726 (t) REVERT: C 276 SER cc_start: 0.8538 (p) cc_final: 0.8275 (p) REVERT: C 281 ILE cc_start: 0.8862 (tp) cc_final: 0.8351 (tt) REVERT: C 285 ASN cc_start: 0.9459 (m-40) cc_final: 0.9154 (m-40) REVERT: C 299 VAL cc_start: 0.9341 (m) cc_final: 0.9138 (p) REVERT: C 352 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8819 (tm-30) REVERT: C 385 MET cc_start: 0.8814 (ttm) cc_final: 0.8466 (ttp) REVERT: C 395 GLU cc_start: 0.8817 (mp0) cc_final: 0.8236 (mp0) REVERT: C 399 GLU cc_start: 0.8994 (pm20) cc_final: 0.8725 (mp0) REVERT: C 404 ASP cc_start: 0.9202 (t0) cc_final: 0.8901 (t70) REVERT: C 438 LYS cc_start: 0.8310 (mmtt) cc_final: 0.8069 (mtpp) REVERT: D 1 MET cc_start: 0.5915 (ptp) cc_final: 0.5665 (ptp) REVERT: D 28 ASP cc_start: 0.8869 (m-30) cc_final: 0.8478 (m-30) REVERT: D 47 ASP cc_start: 0.9130 (p0) cc_final: 0.8865 (p0) REVERT: D 50 ASP cc_start: 0.9025 (t70) cc_final: 0.8732 (t0) REVERT: D 58 LYS cc_start: 0.9425 (mmtp) cc_final: 0.9174 (mmmm) REVERT: D 105 ARG cc_start: 0.9238 (mtm110) cc_final: 0.8717 (mtm110) REVERT: D 108 LYS cc_start: 0.9577 (OUTLIER) cc_final: 0.9321 (tppt) REVERT: D 109 LYS cc_start: 0.9396 (mttp) cc_final: 0.9146 (mptt) REVERT: D 276 SER cc_start: 0.8560 (p) cc_final: 0.8356 (p) REVERT: D 285 ASN cc_start: 0.9434 (m-40) cc_final: 0.9069 (m-40) REVERT: D 312 ASN cc_start: 0.9041 (OUTLIER) cc_final: 0.8813 (t0) REVERT: D 352 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8818 (tm-30) REVERT: D 385 MET cc_start: 0.8875 (ttm) cc_final: 0.8543 (ttp) REVERT: D 395 GLU cc_start: 0.8818 (mp0) cc_final: 0.8199 (mp0) REVERT: D 399 GLU cc_start: 0.9047 (pm20) cc_final: 0.8767 (pm20) REVERT: D 404 ASP cc_start: 0.9115 (t0) cc_final: 0.8821 (t0) REVERT: D 414 MET cc_start: 0.9166 (mpt) cc_final: 0.8936 (mpt) REVERT: D 461 ILE cc_start: 0.9137 (pp) cc_final: 0.8924 (pp) REVERT: E 28 ASP cc_start: 0.8887 (m-30) cc_final: 0.8508 (m-30) REVERT: E 58 LYS cc_start: 0.9304 (mmtp) cc_final: 0.9015 (mmmm) REVERT: E 105 ARG cc_start: 0.9154 (mtm110) cc_final: 0.8902 (mtm110) REVERT: E 109 LYS cc_start: 0.9391 (mttp) cc_final: 0.8701 (tptt) REVERT: E 276 SER cc_start: 0.8575 (p) cc_final: 0.8281 (p) REVERT: E 281 ILE cc_start: 0.8777 (tp) cc_final: 0.8060 (tt) REVERT: E 285 ASN cc_start: 0.9393 (m-40) cc_final: 0.9020 (m-40) REVERT: E 299 VAL cc_start: 0.9382 (m) cc_final: 0.9169 (p) REVERT: E 322 ARG cc_start: 0.8119 (ppp80) cc_final: 0.7805 (ptm160) REVERT: E 352 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8865 (tm-30) REVERT: E 386 MET cc_start: 0.9288 (mtm) cc_final: 0.8988 (mtm) REVERT: E 395 GLU cc_start: 0.8722 (mp0) cc_final: 0.8070 (mp0) REVERT: E 399 GLU cc_start: 0.8950 (pm20) cc_final: 0.8672 (mp0) REVERT: E 400 TYR cc_start: 0.8633 (m-80) cc_final: 0.7718 (m-10) REVERT: E 404 ASP cc_start: 0.9213 (t0) cc_final: 0.8946 (t70) REVERT: E 407 ARG cc_start: 0.8984 (ttt-90) cc_final: 0.8279 (ttt-90) REVERT: E 512 ARG cc_start: 0.7781 (ttm-80) cc_final: 0.7498 (ttm-80) REVERT: F 28 ASP cc_start: 0.8847 (m-30) cc_final: 0.8478 (m-30) REVERT: F 47 ASP cc_start: 0.9149 (p0) cc_final: 0.8920 (p0) REVERT: F 105 ARG cc_start: 0.9227 (mtm110) cc_final: 0.8926 (mtm110) REVERT: F 108 LYS cc_start: 0.9583 (OUTLIER) cc_final: 0.9337 (tppt) REVERT: F 109 LYS cc_start: 0.9382 (mttp) cc_final: 0.9112 (mtmm) REVERT: F 244 LEU cc_start: 0.9564 (mt) cc_final: 0.9319 (mt) REVERT: F 276 SER cc_start: 0.8618 (p) cc_final: 0.8344 (p) REVERT: F 279 ASN cc_start: 0.8896 (t0) cc_final: 0.8627 (t0) REVERT: F 281 ILE cc_start: 0.8902 (tp) cc_final: 0.8557 (tt) REVERT: F 285 ASN cc_start: 0.9380 (m-40) cc_final: 0.9128 (m110) REVERT: F 312 ASN cc_start: 0.9005 (t160) cc_final: 0.8795 (t0) REVERT: F 322 ARG cc_start: 0.8048 (ppp80) cc_final: 0.7499 (ptm160) REVERT: F 352 GLU cc_start: 0.9091 (tm-30) cc_final: 0.8852 (tm-30) REVERT: F 385 MET cc_start: 0.8861 (ttm) cc_final: 0.8274 (ttp) REVERT: F 395 GLU cc_start: 0.8845 (mp0) cc_final: 0.8171 (mp0) REVERT: F 399 GLU cc_start: 0.9079 (pm20) cc_final: 0.8767 (pm20) REVERT: F 400 TYR cc_start: 0.8440 (m-80) cc_final: 0.8186 (m-80) REVERT: F 404 ASP cc_start: 0.9190 (t0) cc_final: 0.8934 (t0) REVERT: F 512 ARG cc_start: 0.7620 (ttm-80) cc_final: 0.7076 (ptm160) REVERT: G 28 ASP cc_start: 0.8941 (m-30) cc_final: 0.8652 (m-30) REVERT: G 50 ASP cc_start: 0.9014 (t70) cc_final: 0.8722 (t0) REVERT: G 51 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9112 (pp) REVERT: G 105 ARG cc_start: 0.9114 (mtm110) cc_final: 0.8499 (mtm110) REVERT: G 108 LYS cc_start: 0.9629 (OUTLIER) cc_final: 0.9367 (mttm) REVERT: G 109 LYS cc_start: 0.9351 (mttp) cc_final: 0.9125 (mttt) REVERT: G 275 SER cc_start: 0.8928 (t) cc_final: 0.8694 (t) REVERT: G 281 ILE cc_start: 0.9045 (tp) cc_final: 0.8331 (tp) REVERT: G 285 ASN cc_start: 0.9329 (m-40) cc_final: 0.8890 (m-40) REVERT: G 352 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8874 (tm-30) REVERT: G 395 GLU cc_start: 0.8754 (mp0) cc_final: 0.8173 (mp0) REVERT: G 399 GLU cc_start: 0.9020 (pm20) cc_final: 0.8710 (pm20) REVERT: G 400 TYR cc_start: 0.8476 (m-80) cc_final: 0.8083 (m-80) REVERT: G 404 ASP cc_start: 0.9201 (t0) cc_final: 0.8876 (t70) REVERT: G 407 ARG cc_start: 0.8871 (ttt-90) cc_final: 0.8318 (ptm-80) REVERT: H 25 ASN cc_start: 0.9110 (m-40) cc_final: 0.8855 (p0) REVERT: H 28 ASP cc_start: 0.8979 (m-30) cc_final: 0.8627 (m-30) REVERT: H 50 ASP cc_start: 0.9009 (t70) cc_final: 0.8732 (t0) REVERT: H 51 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9080 (pp) REVERT: H 58 LYS cc_start: 0.9438 (mmtp) cc_final: 0.9162 (mmmm) REVERT: H 105 ARG cc_start: 0.9268 (mtm110) cc_final: 0.8797 (mtm110) REVERT: H 109 LYS cc_start: 0.9403 (mttp) cc_final: 0.9189 (mttt) REVERT: H 276 SER cc_start: 0.8491 (p) cc_final: 0.8173 (p) REVERT: H 285 ASN cc_start: 0.9461 (m-40) cc_final: 0.9206 (m-40) REVERT: H 352 GLU cc_start: 0.9264 (tm-30) cc_final: 0.9009 (tm-30) REVERT: H 355 ARG cc_start: 0.9571 (ptm-80) cc_final: 0.9171 (ptm-80) REVERT: H 395 GLU cc_start: 0.8723 (mp0) cc_final: 0.8227 (mp0) REVERT: H 399 GLU cc_start: 0.8978 (pm20) cc_final: 0.8732 (pm20) REVERT: H 404 ASP cc_start: 0.9134 (t0) cc_final: 0.8828 (t0) outliers start: 165 outliers final: 75 residues processed: 1117 average time/residue: 0.3471 time to fit residues: 599.4860 Evaluate side-chains 1017 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 935 time to evaluate : 2.429 ------------------------------------------------------------------------------- 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 66 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 312 ASN Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 49 VAL 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 104 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 180 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 282 optimal weight: 0.0470 chunk 119 optimal weight: 3.9990 chunk 225 optimal weight: 0.8980 overall best weight: 1.1680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN B 93 HIS B 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 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.104759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.084033 restraints weight = 41219.530| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.94 r_work: 0.2813 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23488 Z= 0.185 Angle : 0.685 7.565 31792 Z= 0.350 Chirality : 0.047 0.160 3656 Planarity : 0.004 0.042 4000 Dihedral : 11.939 89.298 3800 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.78 % Allowed : 21.31 % Favored : 73.91 % 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: -2.61 (0.14), residues: 2960 helix: -1.77 (0.14), residues: 1120 sheet: -2.37 (0.21), residues: 416 loop : -1.33 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 92 PHE 0.012 0.001 PHE D 401 TYR 0.020 0.002 TYR H 400 ARG 0.011 0.001 ARG F 407 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 841) hydrogen bonds : angle 5.59233 ( 2427) covalent geometry : bond 0.00434 (23480) covalent geometry : angle 0.68505 (31792) Misc. bond : bond 0.00122 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1095 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 981 time to evaluate : 2.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8800 (m-30) cc_final: 0.8478 (m-30) REVERT: A 50 ASP cc_start: 0.9093 (t0) cc_final: 0.8856 (t0) REVERT: A 51 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8921 (pp) REVERT: A 105 ARG cc_start: 0.9169 (mtm110) cc_final: 0.8895 (mtm110) REVERT: A 109 LYS cc_start: 0.9399 (mttp) cc_final: 0.9069 (mttt) REVERT: A 258 TYR cc_start: 0.9088 (t80) cc_final: 0.8854 (t80) REVERT: A 276 SER cc_start: 0.8893 (p) cc_final: 0.8636 (p) REVERT: A 285 ASN cc_start: 0.9456 (m-40) cc_final: 0.9132 (m-40) REVERT: A 352 GLU cc_start: 0.9235 (tm-30) cc_final: 0.8963 (tm-30) REVERT: A 355 ARG cc_start: 0.9490 (ptm-80) cc_final: 0.9043 (ptm-80) REVERT: A 395 GLU cc_start: 0.8845 (mp0) cc_final: 0.8195 (mp0) REVERT: A 399 GLU cc_start: 0.9002 (pm20) cc_final: 0.8760 (mp0) REVERT: A 400 TYR cc_start: 0.8634 (m-80) cc_final: 0.8424 (m-10) REVERT: A 404 ASP cc_start: 0.9155 (t0) cc_final: 0.8840 (t70) REVERT: A 438 LYS cc_start: 0.8963 (mttt) cc_final: 0.8474 (mmtt) REVERT: A 455 LYS cc_start: 0.9167 (mppt) cc_final: 0.8713 (mppt) REVERT: B 25 ASN cc_start: 0.9214 (m-40) cc_final: 0.8926 (p0) REVERT: B 28 ASP cc_start: 0.8864 (m-30) cc_final: 0.8536 (m-30) REVERT: B 50 ASP cc_start: 0.9042 (t70) cc_final: 0.8761 (t0) REVERT: B 51 LEU cc_start: 0.9285 (OUTLIER) cc_final: 0.9007 (pp) REVERT: B 66 VAL cc_start: 0.8378 (OUTLIER) cc_final: 0.8134 (p) REVERT: B 105 ARG cc_start: 0.9205 (mtm110) cc_final: 0.8737 (mtm110) REVERT: B 109 LYS cc_start: 0.9422 (mttp) cc_final: 0.9169 (mptt) REVERT: B 276 SER cc_start: 0.8884 (p) cc_final: 0.8612 (p) REVERT: B 281 ILE cc_start: 0.8945 (tp) cc_final: 0.8628 (tp) REVERT: B 285 ASN cc_start: 0.9448 (m-40) cc_final: 0.9218 (m-40) REVERT: B 352 GLU cc_start: 0.9237 (tm-30) cc_final: 0.8991 (tm-30) REVERT: B 385 MET cc_start: 0.8967 (ttm) cc_final: 0.8661 (ttm) REVERT: B 395 GLU cc_start: 0.8890 (mp0) cc_final: 0.8352 (mp0) REVERT: B 399 GLU cc_start: 0.9069 (pm20) cc_final: 0.8846 (mp0) REVERT: B 404 ASP cc_start: 0.9166 (t0) cc_final: 0.8894 (t0) REVERT: C 28 ASP cc_start: 0.8845 (m-30) cc_final: 0.8522 (m-30) REVERT: C 50 ASP cc_start: 0.9126 (t70) cc_final: 0.8838 (t0) REVERT: C 51 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8884 (pp) REVERT: C 66 VAL cc_start: 0.8314 (OUTLIER) cc_final: 0.8055 (p) REVERT: C 105 ARG cc_start: 0.9153 (mtm110) cc_final: 0.8706 (mtm110) REVERT: C 109 LYS cc_start: 0.9413 (mttp) cc_final: 0.9103 (mptt) REVERT: C 242 LYS cc_start: 0.8286 (mtpt) cc_final: 0.8084 (mttt) REVERT: C 258 TYR cc_start: 0.9050 (t80) cc_final: 0.8839 (t80) REVERT: C 276 SER cc_start: 0.8628 (p) cc_final: 0.8356 (p) REVERT: C 281 ILE cc_start: 0.9030 (tp) cc_final: 0.8822 (tt) REVERT: C 352 GLU cc_start: 0.9235 (tm-30) cc_final: 0.8945 (tm-30) REVERT: C 355 ARG cc_start: 0.9590 (ptm-80) cc_final: 0.9384 (ptm-80) REVERT: C 385 MET cc_start: 0.8899 (ttm) cc_final: 0.8320 (ttp) REVERT: C 395 GLU cc_start: 0.8889 (mp0) cc_final: 0.8283 (mp0) REVERT: C 399 GLU cc_start: 0.8979 (pm20) cc_final: 0.8666 (mp0) REVERT: C 404 ASP cc_start: 0.9216 (t0) cc_final: 0.8957 (t0) REVERT: D 25 ASN cc_start: 0.9178 (m-40) cc_final: 0.8924 (p0) REVERT: D 28 ASP cc_start: 0.8839 (m-30) cc_final: 0.8496 (m-30) REVERT: D 51 LEU cc_start: 0.9325 (OUTLIER) cc_final: 0.8946 (pp) REVERT: D 105 ARG cc_start: 0.9251 (mtm110) cc_final: 0.8960 (mtm110) REVERT: D 108 LYS cc_start: 0.9517 (OUTLIER) cc_final: 0.9183 (tppt) REVERT: D 276 SER cc_start: 0.8730 (p) cc_final: 0.8439 (p) REVERT: D 285 ASN cc_start: 0.9469 (m-40) cc_final: 0.9139 (m-40) REVERT: D 332 ILE cc_start: 0.8957 (pp) cc_final: 0.8667 (pp) REVERT: D 352 GLU cc_start: 0.9182 (tm-30) cc_final: 0.8891 (tm-30) REVERT: D 355 ARG cc_start: 0.9395 (ptm-80) cc_final: 0.9167 (ptm-80) REVERT: D 395 GLU cc_start: 0.8875 (mp0) cc_final: 0.8234 (mp0) REVERT: D 399 GLU cc_start: 0.8992 (pm20) cc_final: 0.8734 (pm20) REVERT: D 404 ASP cc_start: 0.9171 (t0) cc_final: 0.8892 (t0) REVERT: D 438 LYS cc_start: 0.8369 (mmtt) cc_final: 0.8015 (mmtm) REVERT: D 512 ARG cc_start: 0.8177 (ptm160) cc_final: 0.7941 (ptm160) REVERT: E 28 ASP cc_start: 0.8862 (m-30) cc_final: 0.8479 (m-30) REVERT: E 51 LEU cc_start: 0.9425 (OUTLIER) cc_final: 0.9075 (pp) REVERT: E 105 ARG cc_start: 0.9164 (mtm110) cc_final: 0.8907 (mtm110) REVERT: E 109 LYS cc_start: 0.9406 (mttp) cc_final: 0.8916 (tmtt) REVERT: E 258 TYR cc_start: 0.9077 (t80) cc_final: 0.8825 (t80) REVERT: E 276 SER cc_start: 0.8733 (p) cc_final: 0.8447 (p) REVERT: E 285 ASN cc_start: 0.9447 (m-40) cc_final: 0.9228 (m-40) REVERT: E 352 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8940 (tm-30) REVERT: E 355 ARG cc_start: 0.9481 (ptm-80) cc_final: 0.9061 (ptm-80) REVERT: E 385 MET cc_start: 0.8883 (ttm) cc_final: 0.8475 (ttm) REVERT: E 386 MET cc_start: 0.9267 (mtm) cc_final: 0.8845 (mtm) REVERT: E 395 GLU cc_start: 0.8825 (mp0) cc_final: 0.8222 (mp0) REVERT: E 399 GLU cc_start: 0.9049 (pm20) cc_final: 0.8774 (pm20) REVERT: E 400 TYR cc_start: 0.8562 (m-80) cc_final: 0.7866 (m-10) REVERT: E 404 ASP cc_start: 0.9244 (t0) cc_final: 0.8976 (t70) REVERT: E 407 ARG cc_start: 0.9023 (ttt-90) cc_final: 0.8456 (ttt-90) REVERT: E 476 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8954 (mt) REVERT: E 512 ARG cc_start: 0.7890 (ttm-80) cc_final: 0.7362 (ttm-80) REVERT: F 28 ASP cc_start: 0.8889 (m-30) cc_final: 0.8573 (m-30) REVERT: F 51 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8901 (pp) REVERT: F 105 ARG cc_start: 0.9221 (mtm110) cc_final: 0.8834 (mtm110) REVERT: F 108 LYS cc_start: 0.9500 (OUTLIER) cc_final: 0.9218 (tppt) REVERT: F 276 SER cc_start: 0.8733 (p) cc_final: 0.8421 (p) REVERT: F 281 ILE cc_start: 0.8995 (tp) cc_final: 0.8711 (tt) REVERT: F 285 ASN cc_start: 0.9442 (m-40) cc_final: 0.9167 (m-40) REVERT: F 352 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8916 (tm-30) REVERT: F 355 ARG cc_start: 0.9490 (ptm-80) cc_final: 0.9190 (ptm-80) REVERT: F 385 MET cc_start: 0.8835 (ttm) cc_final: 0.8410 (ttm) REVERT: F 395 GLU cc_start: 0.8882 (mp0) cc_final: 0.8283 (mp0) REVERT: F 399 GLU cc_start: 0.9122 (pm20) cc_final: 0.8844 (pm20) REVERT: F 404 ASP cc_start: 0.9228 (t0) cc_final: 0.8989 (t0) REVERT: G 28 ASP cc_start: 0.8944 (m-30) cc_final: 0.8703 (m-30) REVERT: G 50 ASP cc_start: 0.9031 (t70) cc_final: 0.8742 (t0) REVERT: G 51 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.9034 (pp) REVERT: G 105 ARG cc_start: 0.9073 (mtm110) cc_final: 0.8494 (mtm110) REVERT: G 108 LYS cc_start: 0.9569 (OUTLIER) cc_final: 0.9320 (mttm) REVERT: G 258 TYR cc_start: 0.9147 (t80) cc_final: 0.8912 (t80) REVERT: G 259 ARG cc_start: 0.9444 (ttm-80) cc_final: 0.9241 (ttm-80) REVERT: G 285 ASN cc_start: 0.9418 (m-40) cc_final: 0.9134 (m-40) REVERT: G 352 GLU cc_start: 0.9251 (tm-30) cc_final: 0.9014 (tm-30) REVERT: G 355 ARG cc_start: 0.9460 (ptm-80) cc_final: 0.9062 (ptm-80) REVERT: G 385 MET cc_start: 0.8815 (ttm) cc_final: 0.8514 (ttm) REVERT: G 395 GLU cc_start: 0.8830 (mp0) cc_final: 0.8223 (mp0) REVERT: G 399 GLU cc_start: 0.9071 (pm20) cc_final: 0.8778 (pm20) REVERT: G 400 TYR cc_start: 0.8500 (m-80) cc_final: 0.8075 (m-80) REVERT: G 404 ASP cc_start: 0.9264 (t0) cc_final: 0.8937 (t70) REVERT: G 407 ARG cc_start: 0.8927 (ttt-90) cc_final: 0.8268 (ptm-80) REVERT: G 449 ASP cc_start: 0.9329 (p0) cc_final: 0.9035 (p0) REVERT: G 510 GLU cc_start: 0.8058 (tp30) cc_final: 0.7748 (tp30) REVERT: H 25 ASN cc_start: 0.9220 (m-40) cc_final: 0.8926 (p0) REVERT: H 28 ASP cc_start: 0.8970 (m-30) cc_final: 0.8669 (m-30) REVERT: H 50 ASP cc_start: 0.9034 (t70) cc_final: 0.8749 (t0) REVERT: H 51 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8936 (pp) REVERT: H 66 VAL cc_start: 0.8385 (OUTLIER) cc_final: 0.8123 (p) REVERT: H 105 ARG cc_start: 0.9236 (mtm110) cc_final: 0.8881 (mtm110) REVERT: H 256 ASP cc_start: 0.9257 (m-30) cc_final: 0.8865 (p0) REVERT: H 276 SER cc_start: 0.8673 (p) cc_final: 0.8440 (p) REVERT: H 285 ASN cc_start: 0.9452 (m-40) cc_final: 0.9196 (m-40) REVERT: H 352 GLU cc_start: 0.9283 (tm-30) cc_final: 0.9046 (tm-30) REVERT: H 385 MET cc_start: 0.8923 (ttm) cc_final: 0.8516 (ttm) REVERT: H 395 GLU cc_start: 0.8800 (mp0) cc_final: 0.8254 (mp0) REVERT: H 399 GLU cc_start: 0.8958 (pm20) cc_final: 0.8711 (pm20) REVERT: H 400 TYR cc_start: 0.8592 (m-80) cc_final: 0.7963 (m-10) REVERT: H 404 ASP cc_start: 0.9181 (t0) cc_final: 0.8902 (t0) REVERT: H 407 ARG cc_start: 0.8909 (ttt-90) cc_final: 0.8407 (ttt-90) outliers start: 114 outliers final: 67 residues processed: 1020 average time/residue: 0.3378 time to fit residues: 535.9430 Evaluate side-chains 972 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 890 time to evaluate : 2.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU 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 66 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 66 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 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 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 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 78 MET 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 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 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 108 LYS Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 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 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 237 optimal weight: 3.9990 chunk 241 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 240 optimal weight: 0.7980 chunk 262 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 254 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 chunk 279 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 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 D 312 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 ** 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 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.108443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.087260 restraints weight = 41281.805| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 4.00 r_work: 0.2841 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.3327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23488 Z= 0.143 Angle : 0.651 8.331 31792 Z= 0.331 Chirality : 0.046 0.155 3656 Planarity : 0.004 0.038 4000 Dihedral : 11.533 89.251 3770 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.33 % Allowed : 23.32 % Favored : 71.35 % 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: -2.25 (0.14), residues: 2960 helix: -1.44 (0.14), residues: 1120 sheet: -2.10 (0.20), residues: 464 loop : -1.13 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 92 PHE 0.012 0.001 PHE C 401 TYR 0.017 0.001 TYR F 258 ARG 0.012 0.001 ARG F 407 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 841) hydrogen bonds : angle 5.37521 ( 2427) covalent geometry : bond 0.00339 (23480) covalent geometry : angle 0.65133 (31792) Misc. bond : bond 0.00079 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1110 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 983 time to evaluate : 2.604 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8742 (m-30) cc_final: 0.8463 (m-30) REVERT: A 105 ARG cc_start: 0.9176 (mtm110) cc_final: 0.8944 (mtm110) REVERT: A 242 LYS cc_start: 0.7964 (tttt) cc_final: 0.7550 (tttt) REVERT: A 258 TYR cc_start: 0.9110 (t80) cc_final: 0.8858 (t80) REVERT: A 274 ASP cc_start: 0.9124 (t0) cc_final: 0.8924 (t0) REVERT: A 276 SER cc_start: 0.8830 (p) cc_final: 0.8568 (p) REVERT: A 285 ASN cc_start: 0.9462 (m-40) cc_final: 0.9149 (m-40) REVERT: A 352 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8945 (tm-30) REVERT: A 362 ILE cc_start: 0.8135 (mt) cc_final: 0.7901 (mt) REVERT: A 385 MET cc_start: 0.8938 (ttm) cc_final: 0.8371 (ttm) REVERT: A 395 GLU cc_start: 0.8855 (mp0) cc_final: 0.8199 (mp0) REVERT: A 399 GLU cc_start: 0.9016 (pm20) cc_final: 0.8781 (mp0) REVERT: A 404 ASP cc_start: 0.9217 (t0) cc_final: 0.8937 (t70) REVERT: A 438 LYS cc_start: 0.9006 (mttt) cc_final: 0.8533 (mmtt) REVERT: A 455 LYS cc_start: 0.9183 (mppt) cc_final: 0.8750 (mppt) REVERT: B 25 ASN cc_start: 0.9239 (m-40) cc_final: 0.8943 (p0) REVERT: B 28 ASP cc_start: 0.8849 (m-30) cc_final: 0.8526 (m-30) REVERT: B 50 ASP cc_start: 0.9091 (t70) cc_final: 0.8801 (t0) REVERT: B 51 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8859 (pp) REVERT: B 88 ILE cc_start: 0.9128 (tp) cc_final: 0.8812 (tp) REVERT: B 109 LYS cc_start: 0.9436 (mttp) cc_final: 0.9185 (mttm) REVERT: B 276 SER cc_start: 0.8783 (p) cc_final: 0.8494 (p) REVERT: B 285 ASN cc_start: 0.9443 (m-40) cc_final: 0.9110 (m-40) REVERT: B 352 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8967 (tm-30) REVERT: B 385 MET cc_start: 0.8949 (ttm) cc_final: 0.8592 (ttm) REVERT: B 395 GLU cc_start: 0.8837 (mp0) cc_final: 0.8175 (mp0) REVERT: B 399 GLU cc_start: 0.9053 (pm20) cc_final: 0.8798 (pm20) REVERT: B 404 ASP cc_start: 0.9173 (t0) cc_final: 0.8882 (t0) REVERT: C 28 ASP cc_start: 0.8787 (m-30) cc_final: 0.8505 (m-30) REVERT: C 51 LEU cc_start: 0.9303 (OUTLIER) cc_final: 0.8940 (pp) REVERT: C 66 VAL cc_start: 0.8236 (OUTLIER) cc_final: 0.7938 (p) REVERT: C 105 ARG cc_start: 0.9151 (mtm110) cc_final: 0.8690 (mtm110) REVERT: C 109 LYS cc_start: 0.9417 (mttp) cc_final: 0.9124 (mptt) REVERT: C 242 LYS cc_start: 0.8268 (mtpt) cc_final: 0.8040 (mttt) REVERT: C 258 TYR cc_start: 0.9084 (t80) cc_final: 0.8810 (t80) REVERT: C 276 SER cc_start: 0.8519 (p) cc_final: 0.8231 (p) REVERT: C 279 ASN cc_start: 0.8923 (t0) cc_final: 0.8042 (t0) REVERT: C 352 GLU cc_start: 0.9196 (tm-30) cc_final: 0.8910 (tm-30) REVERT: C 355 ARG cc_start: 0.9531 (ptm-80) cc_final: 0.9309 (ptm-80) REVERT: C 395 GLU cc_start: 0.8849 (mp0) cc_final: 0.8357 (mp0) REVERT: C 399 GLU cc_start: 0.9137 (pm20) cc_final: 0.8806 (mp0) REVERT: C 404 ASP cc_start: 0.9242 (t0) cc_final: 0.8986 (t0) REVERT: C 407 ARG cc_start: 0.9038 (ttt-90) cc_final: 0.8389 (ttt-90) REVERT: C 409 LYS cc_start: 0.8789 (ttmm) cc_final: 0.8277 (tttt) REVERT: C 449 ASP cc_start: 0.9483 (p0) cc_final: 0.9099 (p0) REVERT: C 510 GLU cc_start: 0.8110 (tp30) cc_final: 0.7813 (tp30) REVERT: D 25 ASN cc_start: 0.9208 (m-40) cc_final: 0.8959 (p0) REVERT: D 28 ASP cc_start: 0.8854 (m-30) cc_final: 0.8544 (m-30) REVERT: D 51 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9043 (pp) REVERT: D 108 LYS cc_start: 0.9559 (OUTLIER) cc_final: 0.9256 (tppt) REVERT: D 256 ASP cc_start: 0.9309 (m-30) cc_final: 0.8861 (p0) REVERT: D 276 SER cc_start: 0.8734 (p) cc_final: 0.8432 (p) REVERT: D 285 ASN cc_start: 0.9464 (m-40) cc_final: 0.9147 (m110) REVERT: D 332 ILE cc_start: 0.8953 (pp) cc_final: 0.8664 (pp) REVERT: D 352 GLU cc_start: 0.9177 (tm-30) cc_final: 0.8901 (tm-30) REVERT: D 395 GLU cc_start: 0.8890 (mp0) cc_final: 0.8235 (mp0) REVERT: D 399 GLU cc_start: 0.8961 (pm20) cc_final: 0.8722 (pm20) REVERT: D 400 TYR cc_start: 0.8271 (m-10) cc_final: 0.7597 (m-10) REVERT: D 404 ASP cc_start: 0.9212 (t0) cc_final: 0.8955 (t0) REVERT: D 407 ARG cc_start: 0.8959 (ttt90) cc_final: 0.8664 (ttt90) REVERT: D 438 LYS cc_start: 0.8510 (mmtt) cc_final: 0.8162 (mmtm) REVERT: E 28 ASP cc_start: 0.8872 (m-30) cc_final: 0.8517 (m-30) REVERT: E 105 ARG cc_start: 0.9152 (mtm110) cc_final: 0.8885 (mtm110) REVERT: E 109 LYS cc_start: 0.9423 (mttp) cc_final: 0.8951 (tmtt) REVERT: E 258 TYR cc_start: 0.9095 (t80) cc_final: 0.8840 (t80) REVERT: E 276 SER cc_start: 0.8746 (p) cc_final: 0.8451 (p) REVERT: E 285 ASN cc_start: 0.9449 (m-40) cc_final: 0.9237 (m-40) REVERT: E 352 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8960 (tm-30) REVERT: E 385 MET cc_start: 0.8969 (ttm) cc_final: 0.8460 (ttm) REVERT: E 395 GLU cc_start: 0.8835 (mp0) cc_final: 0.8236 (mp0) REVERT: E 399 GLU cc_start: 0.9065 (pm20) cc_final: 0.8820 (pm20) REVERT: E 404 ASP cc_start: 0.9264 (t0) cc_final: 0.8993 (t70) REVERT: E 510 GLU cc_start: 0.8340 (tp30) cc_final: 0.8065 (tp30) REVERT: F 28 ASP cc_start: 0.8921 (m-30) cc_final: 0.8623 (m-30) REVERT: F 51 LEU cc_start: 0.9187 (OUTLIER) cc_final: 0.8787 (pp) REVERT: F 105 ARG cc_start: 0.9209 (mtm110) cc_final: 0.8963 (mtm110) REVERT: F 108 LYS cc_start: 0.9508 (OUTLIER) cc_final: 0.9295 (tppt) REVERT: F 109 LYS cc_start: 0.9483 (mptt) cc_final: 0.9192 (mttm) REVERT: F 276 SER cc_start: 0.8530 (p) cc_final: 0.8219 (p) REVERT: F 279 ASN cc_start: 0.8976 (t0) cc_final: 0.8149 (t0) REVERT: F 281 ILE cc_start: 0.9034 (tp) cc_final: 0.8742 (tt) REVERT: F 285 ASN cc_start: 0.9462 (m-40) cc_final: 0.9218 (m-40) REVERT: F 332 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8503 (pp) REVERT: F 352 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8944 (tm-30) REVERT: F 355 ARG cc_start: 0.9444 (ptm-80) cc_final: 0.9126 (ptm-80) REVERT: F 385 MET cc_start: 0.8829 (ttm) cc_final: 0.8398 (ttm) REVERT: F 393 THR cc_start: 0.9119 (p) cc_final: 0.8310 (p) REVERT: F 395 GLU cc_start: 0.8860 (mp0) cc_final: 0.8160 (mp0) REVERT: F 399 GLU cc_start: 0.9075 (pm20) cc_final: 0.8813 (pm20) REVERT: F 404 ASP cc_start: 0.9234 (t0) cc_final: 0.8957 (t70) REVERT: G 28 ASP cc_start: 0.8925 (m-30) cc_final: 0.8682 (m-30) REVERT: G 50 ASP cc_start: 0.9083 (t70) cc_final: 0.8777 (t0) REVERT: G 51 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.8998 (pp) REVERT: G 98 GLU cc_start: 0.9405 (mp0) cc_final: 0.9202 (mp0) REVERT: G 258 TYR cc_start: 0.9146 (t80) cc_final: 0.8882 (t80) REVERT: G 285 ASN cc_start: 0.9427 (m-40) cc_final: 0.9151 (m-40) REVERT: G 299 VAL cc_start: 0.9403 (m) cc_final: 0.9153 (p) REVERT: G 352 GLU cc_start: 0.9175 (tm-30) cc_final: 0.8917 (tm-30) REVERT: G 385 MET cc_start: 0.8860 (ttm) cc_final: 0.8534 (ttm) REVERT: G 395 GLU cc_start: 0.8862 (mp0) cc_final: 0.8355 (mp0) REVERT: G 399 GLU cc_start: 0.9086 (pm20) cc_final: 0.8818 (pm20) REVERT: G 400 TYR cc_start: 0.8456 (m-80) cc_final: 0.7576 (m-80) REVERT: G 404 ASP cc_start: 0.9289 (t0) cc_final: 0.8982 (t70) REVERT: G 407 ARG cc_start: 0.8880 (ttt-90) cc_final: 0.8496 (ttt-90) REVERT: G 510 GLU cc_start: 0.8056 (tp30) cc_final: 0.7753 (tp30) REVERT: H 25 ASN cc_start: 0.9235 (m-40) cc_final: 0.8948 (p0) REVERT: H 28 ASP cc_start: 0.8895 (m-30) cc_final: 0.8612 (m-30) REVERT: H 50 ASP cc_start: 0.9026 (t70) cc_final: 0.8802 (t0) REVERT: H 51 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8864 (pp) REVERT: H 66 VAL cc_start: 0.8356 (OUTLIER) cc_final: 0.7889 (p) REVERT: H 105 ARG cc_start: 0.9185 (mtm110) cc_final: 0.8880 (mtm110) REVERT: H 276 SER cc_start: 0.8736 (p) cc_final: 0.8422 (p) REVERT: H 285 ASN cc_start: 0.9445 (m-40) cc_final: 0.9125 (m110) REVERT: H 352 GLU cc_start: 0.9257 (tm-30) cc_final: 0.9015 (tm-30) REVERT: H 385 MET cc_start: 0.8979 (ttm) cc_final: 0.8547 (ttm) REVERT: H 395 GLU cc_start: 0.8809 (mp0) cc_final: 0.8250 (mp0) REVERT: H 399 GLU cc_start: 0.8951 (pm20) cc_final: 0.8732 (pm20) REVERT: H 400 TYR cc_start: 0.8524 (m-80) cc_final: 0.7940 (m-10) REVERT: H 404 ASP cc_start: 0.9201 (t0) cc_final: 0.8929 (t0) REVERT: H 407 ARG cc_start: 0.8966 (ttt-90) cc_final: 0.8355 (ttt-90) REVERT: H 512 ARG cc_start: 0.7926 (ttm-80) cc_final: 0.7468 (ptm160) outliers start: 127 outliers final: 71 residues processed: 1034 average time/residue: 0.3437 time to fit residues: 559.5653 Evaluate side-chains 997 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 915 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 377 LEU Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 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 417 LEU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 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 260 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 297 LEU 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 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 513 LEU Chi-restraints excluded: chain G residue 51 LEU 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 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 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 251 optimal weight: 4.9990 chunk 110 optimal weight: 0.0170 chunk 229 optimal weight: 0.9980 chunk 136 optimal weight: 0.8980 chunk 168 optimal weight: 3.9990 chunk 199 optimal weight: 0.7980 chunk 264 optimal weight: 4.9990 chunk 295 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 220 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 overall best weight: 0.7218 ------------------------------------------------------------------------------- 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 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** H 498 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.107904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.087697 restraints weight = 40993.099| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 3.85 r_work: 0.2859 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23488 Z= 0.142 Angle : 0.655 8.469 31792 Z= 0.330 Chirality : 0.046 0.155 3656 Planarity : 0.004 0.037 4000 Dihedral : 11.096 89.557 3761 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.70 % Allowed : 25.04 % Favored : 69.25 % 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: -2.00 (0.15), residues: 2960 helix: -1.26 (0.15), residues: 1120 sheet: -1.96 (0.23), residues: 368 loop : -1.07 (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 B 401 TYR 0.019 0.001 TYR A 400 ARG 0.012 0.001 ARG B 105 Details of bonding type rmsd hydrogen bonds : bond 0.03402 ( 841) hydrogen bonds : angle 5.26715 ( 2427) covalent geometry : bond 0.00334 (23480) covalent geometry : angle 0.65486 (31792) Misc. bond : bond 0.00076 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1111 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 975 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8763 (m-30) cc_final: 0.8519 (m-30) REVERT: A 51 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.8970 (pp) REVERT: A 109 LYS cc_start: 0.9605 (mmmt) cc_final: 0.9014 (tptt) REVERT: A 256 ASP cc_start: 0.9308 (m-30) cc_final: 0.8882 (p0) REVERT: A 274 ASP cc_start: 0.9126 (t0) cc_final: 0.8920 (t0) REVERT: A 276 SER cc_start: 0.8810 (p) cc_final: 0.8530 (p) REVERT: A 285 ASN cc_start: 0.9479 (m-40) cc_final: 0.9162 (m110) REVERT: A 325 MET cc_start: 0.8682 (ptm) cc_final: 0.8436 (ptt) REVERT: A 352 GLU cc_start: 0.9249 (tm-30) cc_final: 0.8988 (tm-30) REVERT: A 385 MET cc_start: 0.8984 (ttm) cc_final: 0.8453 (ttm) REVERT: A 395 GLU cc_start: 0.8887 (mp0) cc_final: 0.8327 (mp0) REVERT: A 400 TYR cc_start: 0.8520 (m-10) cc_final: 0.8130 (m-10) REVERT: A 404 ASP cc_start: 0.9157 (t0) cc_final: 0.8852 (t0) REVERT: A 406 ILE cc_start: 0.9053 (mp) cc_final: 0.8844 (mp) REVERT: A 407 ARG cc_start: 0.8894 (tmt90) cc_final: 0.8672 (ttt90) REVERT: A 409 LYS cc_start: 0.8742 (ttmp) cc_final: 0.8121 (tttt) REVERT: A 438 LYS cc_start: 0.8974 (mttt) cc_final: 0.8568 (mmtt) REVERT: A 455 LYS cc_start: 0.9179 (mppt) cc_final: 0.8749 (mppt) REVERT: A 510 GLU cc_start: 0.8123 (tp30) cc_final: 0.7923 (tp30) REVERT: B 25 ASN cc_start: 0.9260 (m-40) cc_final: 0.8956 (p0) REVERT: B 28 ASP cc_start: 0.8796 (m-30) cc_final: 0.8527 (m-30) REVERT: B 50 ASP cc_start: 0.9107 (t70) cc_final: 0.8850 (t0) REVERT: B 51 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8902 (pp) REVERT: B 105 ARG cc_start: 0.9174 (mtm110) cc_final: 0.8945 (mtm110) REVERT: B 109 LYS cc_start: 0.9461 (mttp) cc_final: 0.9218 (mptt) REVERT: B 276 SER cc_start: 0.8778 (p) cc_final: 0.8494 (p) REVERT: B 285 ASN cc_start: 0.9460 (m-40) cc_final: 0.9127 (m110) REVERT: B 332 ILE cc_start: 0.9098 (OUTLIER) cc_final: 0.8819 (pp) REVERT: B 352 GLU cc_start: 0.9277 (tm-30) cc_final: 0.9042 (tm-30) REVERT: B 385 MET cc_start: 0.8944 (ttm) cc_final: 0.8466 (ttm) REVERT: B 395 GLU cc_start: 0.8827 (mp0) cc_final: 0.8252 (mp0) REVERT: B 399 GLU cc_start: 0.8952 (pm20) cc_final: 0.8736 (pm20) REVERT: B 400 TYR cc_start: 0.8456 (m-80) cc_final: 0.8210 (m-10) REVERT: B 404 ASP cc_start: 0.9170 (t0) cc_final: 0.8920 (t0) REVERT: B 407 ARG cc_start: 0.9104 (ttt90) cc_final: 0.8740 (ttt90) REVERT: B 410 LYS cc_start: 0.8796 (ptmt) cc_final: 0.8529 (ptmt) REVERT: C 28 ASP cc_start: 0.8815 (m-30) cc_final: 0.8570 (m-30) REVERT: C 51 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9041 (pp) REVERT: C 66 VAL cc_start: 0.8217 (OUTLIER) cc_final: 0.7840 (p) REVERT: C 105 ARG cc_start: 0.9128 (mtm110) cc_final: 0.8640 (mtm110) REVERT: C 109 LYS cc_start: 0.9400 (mttp) cc_final: 0.9121 (mptt) REVERT: C 242 LYS cc_start: 0.8355 (mtpt) cc_final: 0.8131 (mttt) REVERT: C 258 TYR cc_start: 0.9096 (t80) cc_final: 0.8805 (t80) REVERT: C 276 SER cc_start: 0.8425 (p) cc_final: 0.8111 (p) REVERT: C 279 ASN cc_start: 0.9031 (t0) cc_final: 0.8214 (t0) REVERT: C 332 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8795 (pp) REVERT: C 352 GLU cc_start: 0.9246 (tm-30) cc_final: 0.9008 (tm-30) REVERT: C 395 GLU cc_start: 0.8859 (mp0) cc_final: 0.8376 (mp0) REVERT: C 399 GLU cc_start: 0.9128 (pm20) cc_final: 0.8872 (mp0) REVERT: C 404 ASP cc_start: 0.9161 (t0) cc_final: 0.8901 (t0) REVERT: C 510 GLU cc_start: 0.8187 (tp30) cc_final: 0.7899 (tp30) REVERT: D 25 ASN cc_start: 0.9237 (m-40) cc_final: 0.8991 (p0) REVERT: D 28 ASP cc_start: 0.8808 (m-30) cc_final: 0.8555 (m-30) REVERT: D 50 ASP cc_start: 0.9020 (t70) cc_final: 0.8796 (t0) REVERT: D 51 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9143 (pp) REVERT: D 105 ARG cc_start: 0.9245 (mtm110) cc_final: 0.9016 (mtm110) REVERT: D 256 ASP cc_start: 0.9268 (m-30) cc_final: 0.8733 (p0) REVERT: D 276 SER cc_start: 0.8738 (p) cc_final: 0.8448 (p) REVERT: D 285 ASN cc_start: 0.9481 (m-40) cc_final: 0.9147 (m110) REVERT: D 332 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8772 (pp) REVERT: D 352 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8908 (tm-30) REVERT: D 395 GLU cc_start: 0.8905 (mp0) cc_final: 0.8168 (mp0) REVERT: D 399 GLU cc_start: 0.8970 (pm20) cc_final: 0.8723 (pm20) REVERT: D 404 ASP cc_start: 0.9173 (t0) cc_final: 0.8926 (t0) REVERT: D 407 ARG cc_start: 0.8949 (ttt90) cc_final: 0.8692 (ttt90) REVERT: D 438 LYS cc_start: 0.8540 (mmtt) cc_final: 0.8190 (mmtm) REVERT: E 28 ASP cc_start: 0.8853 (m-30) cc_final: 0.8587 (m-30) REVERT: E 51 LEU cc_start: 0.9291 (OUTLIER) cc_final: 0.9005 (pp) REVERT: E 105 ARG cc_start: 0.9116 (mtm110) cc_final: 0.8845 (mtm110) REVERT: E 109 LYS cc_start: 0.9402 (mttp) cc_final: 0.8970 (tmtt) REVERT: E 258 TYR cc_start: 0.9093 (t80) cc_final: 0.8821 (t80) REVERT: E 276 SER cc_start: 0.8799 (p) cc_final: 0.8556 (p) REVERT: E 285 ASN cc_start: 0.9465 (m-40) cc_final: 0.9159 (m-40) REVERT: E 332 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8801 (pp) REVERT: E 352 GLU cc_start: 0.9282 (tm-30) cc_final: 0.9033 (tm-30) REVERT: E 355 ARG cc_start: 0.9287 (ptm-80) cc_final: 0.9027 (ptm-80) REVERT: E 385 MET cc_start: 0.9007 (ttm) cc_final: 0.8533 (ttm) REVERT: E 395 GLU cc_start: 0.8833 (mp0) cc_final: 0.8365 (mp0) REVERT: E 404 ASP cc_start: 0.9208 (t0) cc_final: 0.8907 (t70) REVERT: E 406 ILE cc_start: 0.9066 (mp) cc_final: 0.8858 (mp) REVERT: E 407 ARG cc_start: 0.8925 (ttt90) cc_final: 0.8557 (ttt-90) REVERT: F 28 ASP cc_start: 0.8873 (m-30) cc_final: 0.8626 (m-30) REVERT: F 51 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8964 (pp) REVERT: F 105 ARG cc_start: 0.9170 (mtm110) cc_final: 0.8796 (mtm110) REVERT: F 109 LYS cc_start: 0.9458 (mptt) cc_final: 0.9249 (mttt) REVERT: F 276 SER cc_start: 0.8475 (p) cc_final: 0.8158 (p) REVERT: F 279 ASN cc_start: 0.9060 (t0) cc_final: 0.8265 (t0) REVERT: F 285 ASN cc_start: 0.9484 (m-40) cc_final: 0.9209 (m-40) REVERT: F 332 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.8620 (pp) REVERT: F 352 GLU cc_start: 0.9247 (tm-30) cc_final: 0.8971 (tm-30) REVERT: F 355 ARG cc_start: 0.9473 (ptm-80) cc_final: 0.9147 (ptm-80) REVERT: F 385 MET cc_start: 0.8893 (ttm) cc_final: 0.8342 (ttm) REVERT: F 395 GLU cc_start: 0.8869 (mp0) cc_final: 0.8156 (mp0) REVERT: F 399 GLU cc_start: 0.9082 (pm20) cc_final: 0.8821 (pm20) REVERT: F 404 ASP cc_start: 0.9178 (t0) cc_final: 0.8936 (t70) REVERT: G 21 GLN cc_start: 0.9093 (pt0) cc_final: 0.8772 (tm-30) REVERT: G 28 ASP cc_start: 0.8920 (m-30) cc_final: 0.8719 (m-30) REVERT: G 50 ASP cc_start: 0.9140 (t70) cc_final: 0.8867 (t0) REVERT: G 51 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8852 (pp) REVERT: G 256 ASP cc_start: 0.9352 (m-30) cc_final: 0.9058 (p0) REVERT: G 258 TYR cc_start: 0.9136 (t80) cc_final: 0.8823 (t80) REVERT: G 285 ASN cc_start: 0.9411 (m-40) cc_final: 0.9118 (m110) REVERT: G 299 VAL cc_start: 0.9435 (m) cc_final: 0.9152 (p) REVERT: G 352 GLU cc_start: 0.9224 (tm-30) cc_final: 0.8945 (tm-30) REVERT: G 385 MET cc_start: 0.9028 (ttm) cc_final: 0.8536 (ttm) REVERT: G 395 GLU cc_start: 0.8809 (mp0) cc_final: 0.8347 (mp0) REVERT: G 399 GLU cc_start: 0.9061 (pm20) cc_final: 0.8825 (pm20) REVERT: G 400 TYR cc_start: 0.8478 (m-80) cc_final: 0.7589 (m-80) REVERT: G 404 ASP cc_start: 0.9233 (t0) cc_final: 0.8925 (t70) REVERT: G 407 ARG cc_start: 0.9079 (ttt-90) cc_final: 0.8686 (ttt-90) REVERT: G 510 GLU cc_start: 0.8354 (tp30) cc_final: 0.7920 (tp30) REVERT: H 25 ASN cc_start: 0.9249 (m-40) cc_final: 0.8963 (p0) REVERT: H 28 ASP cc_start: 0.8888 (m-30) cc_final: 0.8642 (m-30) REVERT: H 50 ASP cc_start: 0.9039 (t70) cc_final: 0.8789 (t0) REVERT: H 51 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.9007 (pp) REVERT: H 88 ILE cc_start: 0.9173 (tp) cc_final: 0.8863 (tp) REVERT: H 105 ARG cc_start: 0.9174 (mtm110) cc_final: 0.8868 (mtm110) REVERT: H 276 SER cc_start: 0.8867 (p) cc_final: 0.8558 (p) REVERT: H 285 ASN cc_start: 0.9456 (m-40) cc_final: 0.9158 (m110) REVERT: H 332 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8629 (pp) REVERT: H 335 GLU cc_start: 0.8634 (tm-30) cc_final: 0.7940 (tm-30) REVERT: H 352 GLU cc_start: 0.9284 (tm-30) cc_final: 0.9039 (tm-30) REVERT: H 355 ARG cc_start: 0.9309 (ptm-80) cc_final: 0.8873 (ptm-80) REVERT: H 385 MET cc_start: 0.8998 (ttm) cc_final: 0.8437 (ttm) REVERT: H 395 GLU cc_start: 0.8834 (mp0) cc_final: 0.8291 (mp0) REVERT: H 399 GLU cc_start: 0.8937 (pm20) cc_final: 0.8720 (pm20) REVERT: H 404 ASP cc_start: 0.9159 (t0) cc_final: 0.8877 (t0) REVERT: H 410 LYS cc_start: 0.8724 (ptmt) cc_final: 0.8432 (ptmt) REVERT: H 512 ARG cc_start: 0.7985 (ttm-80) cc_final: 0.7714 (ptm160) outliers start: 136 outliers final: 86 residues processed: 1032 average time/residue: 0.3299 time to fit residues: 534.8408 Evaluate side-chains 1008 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 907 time to evaluate : 2.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 VAL 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 65 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 45 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 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 45 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 282 PHE 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 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 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 260 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 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 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 297 LEU Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 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 178 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 295 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 68 optimal weight: 0.0980 chunk 255 optimal weight: 0.8980 chunk 154 optimal weight: 0.8980 chunk 250 optimal weight: 0.7980 chunk 234 optimal weight: 2.9990 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 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.108424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.088127 restraints weight = 40336.746| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 3.81 r_work: 0.2865 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23488 Z= 0.142 Angle : 0.662 8.325 31792 Z= 0.334 Chirality : 0.046 0.178 3656 Planarity : 0.004 0.038 4000 Dihedral : 10.698 89.870 3745 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.70 % Allowed : 26.17 % Favored : 68.12 % 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: -1.18 (0.15), residues: 1120 sheet: -1.83 (0.24), residues: 368 loop : -1.02 (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 C 401 TYR 0.019 0.001 TYR A 258 ARG 0.008 0.001 ARG G 105 Details of bonding type rmsd hydrogen bonds : bond 0.03281 ( 841) hydrogen bonds : angle 5.16480 ( 2427) covalent geometry : bond 0.00337 (23480) covalent geometry : angle 0.66162 (31792) Misc. bond : bond 0.00077 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 136 poor density : 960 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8746 (m-30) cc_final: 0.8544 (m-30) REVERT: A 51 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.8997 (pp) REVERT: A 98 GLU cc_start: 0.9442 (mp0) cc_final: 0.9231 (mp0) REVERT: A 109 LYS cc_start: 0.9641 (mmmt) cc_final: 0.9025 (tptt) REVERT: A 256 ASP cc_start: 0.9330 (m-30) cc_final: 0.8826 (p0) REVERT: A 274 ASP cc_start: 0.9159 (t0) cc_final: 0.8921 (t0) REVERT: A 276 SER cc_start: 0.8766 (p) cc_final: 0.8488 (p) REVERT: A 285 ASN cc_start: 0.9491 (m-40) cc_final: 0.9169 (m110) REVERT: A 335 GLU cc_start: 0.8516 (tm-30) cc_final: 0.7863 (tm-30) REVERT: A 352 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8945 (tm-30) REVERT: A 385 MET cc_start: 0.8921 (ttm) cc_final: 0.8411 (ttm) REVERT: A 395 GLU cc_start: 0.8949 (mp0) cc_final: 0.8354 (mp0) REVERT: A 400 TYR cc_start: 0.8420 (m-10) cc_final: 0.8051 (m-10) REVERT: A 404 ASP cc_start: 0.9202 (t0) cc_final: 0.8922 (t0) REVERT: A 407 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8627 (ttt90) REVERT: A 438 LYS cc_start: 0.9039 (mttt) cc_final: 0.8576 (mmtt) REVERT: A 510 GLU cc_start: 0.8117 (tp30) cc_final: 0.7819 (tp30) REVERT: A 512 ARG cc_start: 0.7848 (ttm-80) cc_final: 0.7461 (ttm-80) REVERT: B 25 ASN cc_start: 0.9303 (m-40) cc_final: 0.9011 (p0) REVERT: B 28 ASP cc_start: 0.8770 (m-30) cc_final: 0.8542 (m-30) REVERT: B 50 ASP cc_start: 0.9074 (t70) cc_final: 0.8805 (t0) REVERT: B 51 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8877 (pp) REVERT: B 105 ARG cc_start: 0.9181 (mtm110) cc_final: 0.8933 (mtm110) REVERT: B 109 LYS cc_start: 0.9450 (mttp) cc_final: 0.9167 (mtmm) REVERT: B 274 ASP cc_start: 0.9120 (t0) cc_final: 0.8919 (t0) REVERT: B 276 SER cc_start: 0.8710 (p) cc_final: 0.8436 (p) REVERT: B 285 ASN cc_start: 0.9472 (m-40) cc_final: 0.9181 (m110) REVERT: B 332 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8799 (pp) REVERT: B 352 GLU cc_start: 0.9217 (tm-30) cc_final: 0.8964 (tm-30) REVERT: B 385 MET cc_start: 0.8915 (ttm) cc_final: 0.8470 (ttm) REVERT: B 395 GLU cc_start: 0.8864 (mp0) cc_final: 0.8287 (mp0) REVERT: B 404 ASP cc_start: 0.9192 (t0) cc_final: 0.8925 (t70) REVERT: B 407 ARG cc_start: 0.9143 (ttt90) cc_final: 0.8915 (ttt90) REVERT: B 410 LYS cc_start: 0.8730 (ptmt) cc_final: 0.8479 (ptmt) REVERT: C 28 ASP cc_start: 0.8788 (m-30) cc_final: 0.8569 (m-30) REVERT: C 51 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8750 (pp) REVERT: C 66 VAL cc_start: 0.7785 (OUTLIER) cc_final: 0.7562 (p) REVERT: C 98 GLU cc_start: 0.9402 (mp0) cc_final: 0.9172 (mp0) REVERT: C 105 ARG cc_start: 0.9074 (mtm110) cc_final: 0.8842 (mtm110) REVERT: C 258 TYR cc_start: 0.9122 (t80) cc_final: 0.8820 (t80) REVERT: C 276 SER cc_start: 0.8389 (p) cc_final: 0.8079 (p) REVERT: C 279 ASN cc_start: 0.9061 (t0) cc_final: 0.8262 (t0) REVERT: C 325 MET cc_start: 0.8558 (ptm) cc_final: 0.8297 (ptt) REVERT: C 332 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8451 (pp) REVERT: C 335 GLU cc_start: 0.8561 (tm-30) cc_final: 0.7807 (tm-30) REVERT: C 385 MET cc_start: 0.8942 (ttm) cc_final: 0.8640 (ttm) REVERT: C 395 GLU cc_start: 0.8877 (mp0) cc_final: 0.8388 (mp0) REVERT: C 399 GLU cc_start: 0.9191 (pm20) cc_final: 0.8915 (mp0) REVERT: C 404 ASP cc_start: 0.9208 (t0) cc_final: 0.8957 (t0) REVERT: C 510 GLU cc_start: 0.8221 (tp30) cc_final: 0.7940 (tp30) REVERT: D 25 ASN cc_start: 0.9241 (m-40) cc_final: 0.8989 (p0) REVERT: D 28 ASP cc_start: 0.8788 (m-30) cc_final: 0.8555 (m-30) REVERT: D 50 ASP cc_start: 0.9014 (t70) cc_final: 0.8747 (t0) REVERT: D 51 LEU cc_start: 0.9447 (OUTLIER) cc_final: 0.9195 (pp) REVERT: D 105 ARG cc_start: 0.9252 (mtm110) cc_final: 0.9049 (mtm110) REVERT: D 276 SER cc_start: 0.8732 (p) cc_final: 0.8462 (p) REVERT: D 285 ASN cc_start: 0.9492 (m-40) cc_final: 0.9208 (m110) REVERT: D 332 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8779 (pp) REVERT: D 352 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8884 (tm-30) REVERT: D 395 GLU cc_start: 0.8816 (mp0) cc_final: 0.8134 (mp0) REVERT: D 399 GLU cc_start: 0.9098 (pm20) cc_final: 0.8837 (pm20) REVERT: D 400 TYR cc_start: 0.8438 (m-10) cc_final: 0.7841 (m-10) REVERT: D 404 ASP cc_start: 0.9185 (t0) cc_final: 0.8930 (t0) REVERT: D 407 ARG cc_start: 0.8933 (ttt90) cc_final: 0.8676 (ttt90) REVERT: D 438 LYS cc_start: 0.8546 (mmtt) cc_final: 0.8244 (mmtm) REVERT: E 21 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8659 (tm-30) REVERT: E 25 ASN cc_start: 0.9201 (m-40) cc_final: 0.8839 (m-40) REVERT: E 28 ASP cc_start: 0.8838 (m-30) cc_final: 0.8596 (m-30) REVERT: E 51 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8961 (pp) REVERT: E 105 ARG cc_start: 0.9119 (mtm110) cc_final: 0.8851 (mtm110) REVERT: E 258 TYR cc_start: 0.9082 (t80) cc_final: 0.8839 (t80) REVERT: E 276 SER cc_start: 0.8773 (p) cc_final: 0.8467 (p) REVERT: E 285 ASN cc_start: 0.9474 (m-40) cc_final: 0.9141 (m-40) REVERT: E 332 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8466 (pp) REVERT: E 335 GLU cc_start: 0.8656 (tm-30) cc_final: 0.7908 (tm-30) REVERT: E 352 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8972 (tm-30) REVERT: E 355 ARG cc_start: 0.9262 (ptm-80) cc_final: 0.8963 (ptm-80) REVERT: E 385 MET cc_start: 0.8998 (ttm) cc_final: 0.8506 (ttm) REVERT: E 395 GLU cc_start: 0.8813 (mp0) cc_final: 0.8376 (mp0) REVERT: E 404 ASP cc_start: 0.9220 (t0) cc_final: 0.8954 (t70) REVERT: E 406 ILE cc_start: 0.9070 (mp) cc_final: 0.8789 (mp) REVERT: F 21 GLN cc_start: 0.9065 (pt0) cc_final: 0.8666 (tm-30) REVERT: F 28 ASP cc_start: 0.8844 (m-30) cc_final: 0.8635 (m-30) REVERT: F 51 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.9007 (pp) REVERT: F 105 ARG cc_start: 0.9144 (mtm110) cc_final: 0.8942 (mtm110) REVERT: F 109 LYS cc_start: 0.9463 (mptt) cc_final: 0.9053 (mtmm) REVERT: F 274 ASP cc_start: 0.9057 (t0) cc_final: 0.8850 (t0) REVERT: F 276 SER cc_start: 0.8431 (p) cc_final: 0.8119 (p) REVERT: F 279 ASN cc_start: 0.9057 (t0) cc_final: 0.8289 (t0) REVERT: F 285 ASN cc_start: 0.9506 (m-40) cc_final: 0.9241 (m-40) REVERT: F 332 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8547 (pp) REVERT: F 352 GLU cc_start: 0.9231 (tm-30) cc_final: 0.8970 (tm-30) REVERT: F 385 MET cc_start: 0.8798 (ttm) cc_final: 0.8270 (ttm) REVERT: F 395 GLU cc_start: 0.8789 (mp0) cc_final: 0.8222 (mp0) REVERT: F 399 GLU cc_start: 0.9108 (pm20) cc_final: 0.8845 (pm20) REVERT: F 404 ASP cc_start: 0.9171 (t0) cc_final: 0.8924 (t70) REVERT: G 21 GLN cc_start: 0.9136 (pt0) cc_final: 0.8751 (tm-30) REVERT: G 50 ASP cc_start: 0.9140 (t70) cc_final: 0.8869 (t0) REVERT: G 51 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8937 (pp) REVERT: G 256 ASP cc_start: 0.9325 (m-30) cc_final: 0.8835 (p0) REVERT: G 258 TYR cc_start: 0.9144 (t80) cc_final: 0.8800 (t80) REVERT: G 285 ASN cc_start: 0.9409 (m-40) cc_final: 0.9124 (m110) REVERT: G 286 MET cc_start: 0.9519 (tpp) cc_final: 0.9205 (ttp) REVERT: G 325 MET cc_start: 0.8605 (ptm) cc_final: 0.8389 (ptt) REVERT: G 332 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8511 (pp) REVERT: G 335 GLU cc_start: 0.8618 (tm-30) cc_final: 0.7862 (tm-30) REVERT: G 352 GLU cc_start: 0.9222 (tm-30) cc_final: 0.8942 (tm-30) REVERT: G 385 MET cc_start: 0.8944 (ttm) cc_final: 0.8456 (ttm) REVERT: G 395 GLU cc_start: 0.8798 (mp0) cc_final: 0.8357 (mp0) REVERT: G 399 GLU cc_start: 0.9101 (pm20) cc_final: 0.8874 (pm20) REVERT: G 404 ASP cc_start: 0.9252 (t0) cc_final: 0.8935 (t70) REVERT: G 510 GLU cc_start: 0.8403 (tp30) cc_final: 0.8062 (tp30) REVERT: H 25 ASN cc_start: 0.9271 (m-40) cc_final: 0.8984 (p0) REVERT: H 28 ASP cc_start: 0.8870 (m-30) cc_final: 0.8652 (m-30) REVERT: H 50 ASP cc_start: 0.9066 (t70) cc_final: 0.8833 (t0) REVERT: H 51 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8860 (pp) REVERT: H 105 ARG cc_start: 0.9163 (mtm110) cc_final: 0.8853 (mtm110) REVERT: H 276 SER cc_start: 0.8836 (p) cc_final: 0.8541 (p) REVERT: H 285 ASN cc_start: 0.9450 (m-40) cc_final: 0.9196 (m110) REVERT: H 332 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8620 (pp) REVERT: H 335 GLU cc_start: 0.8616 (tm-30) cc_final: 0.7971 (tm-30) REVERT: H 352 GLU cc_start: 0.9254 (tm-30) cc_final: 0.9012 (tm-30) REVERT: H 355 ARG cc_start: 0.9283 (ptm-80) cc_final: 0.8860 (ptm-80) REVERT: H 385 MET cc_start: 0.8897 (ttm) cc_final: 0.8383 (ttm) REVERT: H 395 GLU cc_start: 0.8880 (mp0) cc_final: 0.8352 (mp0) REVERT: H 399 GLU cc_start: 0.8914 (pm20) cc_final: 0.8578 (mp0) REVERT: H 404 ASP cc_start: 0.9218 (t0) cc_final: 0.8961 (t0) REVERT: H 409 LYS cc_start: 0.8722 (ttmp) cc_final: 0.8007 (tttt) REVERT: H 410 LYS cc_start: 0.8672 (ptmt) cc_final: 0.8407 (ptmt) REVERT: H 512 ARG cc_start: 0.7908 (ttm-80) cc_final: 0.7665 (ptm160) outliers start: 136 outliers final: 91 residues processed: 1018 average time/residue: 0.3319 time to fit residues: 530.9011 Evaluate side-chains 1017 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 908 time to evaluate : 2.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 82 MET 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 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 66 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 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 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 82 MET Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 260 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 377 LEU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 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 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 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 386 MET 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 65 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 MET 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 377 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 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 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 119 optimal weight: 0.5980 chunk 121 optimal weight: 0.0270 chunk 246 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 chunk 229 optimal weight: 0.8980 chunk 209 optimal weight: 2.9990 chunk 286 optimal weight: 5.9990 chunk 232 optimal weight: 0.9980 chunk 271 optimal weight: 0.4980 chunk 225 optimal weight: 1.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.109633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.089170 restraints weight = 40753.311| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.87 r_work: 0.2886 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23488 Z= 0.133 Angle : 0.670 8.167 31792 Z= 0.337 Chirality : 0.046 0.185 3656 Planarity : 0.004 0.038 4000 Dihedral : 10.439 89.713 3742 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 6.17 % Allowed : 26.59 % Favored : 67.24 % 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: -1.93 (0.15), residues: 2960 helix: -1.23 (0.15), residues: 1136 sheet: -2.02 (0.26), residues: 320 loop : -1.01 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS D 92 PHE 0.012 0.001 PHE F 401 TYR 0.019 0.001 TYR G 400 ARG 0.007 0.001 ARG F 407 Details of bonding type rmsd hydrogen bonds : bond 0.03245 ( 841) hydrogen bonds : angle 5.13641 ( 2427) covalent geometry : bond 0.00316 (23480) covalent geometry : angle 0.67031 (31792) Misc. bond : bond 0.00059 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1117 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 970 time to evaluate : 2.733 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4579 (ptp) cc_final: 0.3724 (ptm) REVERT: A 21 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8571 (tm-30) REVERT: A 28 ASP cc_start: 0.8728 (m-30) cc_final: 0.8524 (m-30) REVERT: A 51 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8811 (pp) REVERT: A 109 LYS cc_start: 0.9672 (mmmt) cc_final: 0.9103 (tptt) REVERT: A 256 ASP cc_start: 0.9293 (m-30) cc_final: 0.8763 (p0) REVERT: A 274 ASP cc_start: 0.9157 (t0) cc_final: 0.8914 (t0) REVERT: A 276 SER cc_start: 0.8711 (p) cc_final: 0.8425 (p) REVERT: A 285 ASN cc_start: 0.9495 (m-40) cc_final: 0.9216 (m110) REVERT: A 332 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8900 (pp) REVERT: A 352 GLU cc_start: 0.9211 (tm-30) cc_final: 0.8956 (tm-30) REVERT: A 355 ARG cc_start: 0.9248 (ptm-80) cc_final: 0.8918 (ptm-80) REVERT: A 385 MET cc_start: 0.8929 (ttm) cc_final: 0.8444 (ttm) REVERT: A 395 GLU cc_start: 0.8925 (mp0) cc_final: 0.8396 (mp0) REVERT: A 404 ASP cc_start: 0.9245 (t0) cc_final: 0.9011 (t0) REVERT: A 407 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8213 (ttt-90) REVERT: A 438 LYS cc_start: 0.9050 (mttt) cc_final: 0.8593 (mmtt) REVERT: A 510 GLU cc_start: 0.8097 (tp30) cc_final: 0.7750 (tp30) REVERT: B 25 ASN cc_start: 0.9317 (m-40) cc_final: 0.9047 (p0) REVERT: B 28 ASP cc_start: 0.8745 (m-30) cc_final: 0.8539 (m-30) REVERT: B 50 ASP cc_start: 0.9071 (t70) cc_final: 0.8772 (t0) REVERT: B 51 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8926 (pp) REVERT: B 99 PHE cc_start: 0.9439 (t80) cc_final: 0.9206 (t80) REVERT: B 105 ARG cc_start: 0.9100 (mtm110) cc_final: 0.8857 (mtm110) REVERT: B 109 LYS cc_start: 0.9458 (mttp) cc_final: 0.9159 (mtmm) REVERT: B 243 GLN cc_start: 0.9093 (mp10) cc_final: 0.8777 (mp10) REVERT: B 274 ASP cc_start: 0.9155 (t0) cc_final: 0.8846 (t0) REVERT: B 276 SER cc_start: 0.8767 (p) cc_final: 0.8507 (p) REVERT: B 281 ILE cc_start: 0.9035 (tp) cc_final: 0.8363 (tp) REVERT: B 285 ASN cc_start: 0.9512 (m-40) cc_final: 0.9117 (m-40) REVERT: B 332 ILE cc_start: 0.8952 (OUTLIER) cc_final: 0.8392 (pp) REVERT: B 335 GLU cc_start: 0.8642 (tm-30) cc_final: 0.7914 (tm-30) REVERT: B 352 GLU cc_start: 0.9235 (tm-30) cc_final: 0.8968 (tm-30) REVERT: B 385 MET cc_start: 0.8846 (ttm) cc_final: 0.8385 (ttm) REVERT: B 395 GLU cc_start: 0.8846 (mp0) cc_final: 0.8266 (mp0) REVERT: B 404 ASP cc_start: 0.9199 (t0) cc_final: 0.8935 (t70) REVERT: B 410 LYS cc_start: 0.8702 (ptmt) cc_final: 0.8448 (ptmt) REVERT: B 438 LYS cc_start: 0.8525 (mmtt) cc_final: 0.8156 (mmtm) REVERT: B 510 GLU cc_start: 0.8270 (tp30) cc_final: 0.7951 (tp30) REVERT: C 21 GLN cc_start: 0.9054 (pt0) cc_final: 0.8464 (tm-30) REVERT: C 28 ASP cc_start: 0.8742 (m-30) cc_final: 0.8540 (m-30) REVERT: C 51 LEU cc_start: 0.9149 (OUTLIER) cc_final: 0.8708 (pp) REVERT: C 66 VAL cc_start: 0.7705 (OUTLIER) cc_final: 0.7480 (p) REVERT: C 109 LYS cc_start: 0.9668 (mmmt) cc_final: 0.8948 (tptt) REVERT: C 256 ASP cc_start: 0.9342 (m-30) cc_final: 0.8844 (p0) REVERT: C 258 TYR cc_start: 0.9133 (t80) cc_final: 0.8807 (t80) REVERT: C 276 SER cc_start: 0.8374 (p) cc_final: 0.8060 (p) REVERT: C 279 ASN cc_start: 0.9054 (t0) cc_final: 0.8297 (t0) REVERT: C 285 ASN cc_start: 0.9346 (m-40) cc_final: 0.9122 (m-40) REVERT: C 325 MET cc_start: 0.8484 (ptm) cc_final: 0.8226 (ptt) REVERT: C 332 ILE cc_start: 0.9012 (OUTLIER) cc_final: 0.8798 (pp) REVERT: C 395 GLU cc_start: 0.8864 (mp0) cc_final: 0.8368 (mp0) REVERT: C 399 GLU cc_start: 0.9165 (pm20) cc_final: 0.8952 (pm20) REVERT: C 404 ASP cc_start: 0.9233 (t0) cc_final: 0.8994 (t0) REVERT: C 510 GLU cc_start: 0.8222 (tp30) cc_final: 0.7910 (tp30) REVERT: D 25 ASN cc_start: 0.9260 (m-40) cc_final: 0.9023 (p0) REVERT: D 28 ASP cc_start: 0.8747 (m-30) cc_final: 0.8530 (m-30) REVERT: D 50 ASP cc_start: 0.9087 (t70) cc_final: 0.8869 (t0) REVERT: D 51 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8936 (pp) REVERT: D 105 ARG cc_start: 0.9187 (mtm110) cc_final: 0.8977 (mtm110) REVERT: D 276 SER cc_start: 0.8793 (p) cc_final: 0.8528 (p) REVERT: D 285 ASN cc_start: 0.9506 (m-40) cc_final: 0.9132 (m-40) REVERT: D 332 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8753 (pp) REVERT: D 352 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8705 (tm-30) REVERT: D 355 ARG cc_start: 0.9206 (ptm-80) cc_final: 0.8909 (ptm-80) REVERT: D 395 GLU cc_start: 0.8845 (mp0) cc_final: 0.8379 (mp0) REVERT: D 399 GLU cc_start: 0.9107 (pm20) cc_final: 0.8854 (pm20) REVERT: D 400 TYR cc_start: 0.8554 (m-10) cc_final: 0.7964 (m-10) REVERT: D 404 ASP cc_start: 0.9224 (t0) cc_final: 0.8971 (t70) REVERT: D 407 ARG cc_start: 0.8954 (ttt90) cc_final: 0.8627 (ttt90) REVERT: D 438 LYS cc_start: 0.8596 (mmtt) cc_final: 0.8304 (mmtm) REVERT: E 21 GLN cc_start: 0.9084 (pt0) cc_final: 0.8654 (tm-30) REVERT: E 25 ASN cc_start: 0.9233 (m-40) cc_final: 0.8872 (m-40) REVERT: E 28 ASP cc_start: 0.8829 (m-30) cc_final: 0.8618 (m-30) REVERT: E 51 LEU cc_start: 0.9228 (OUTLIER) cc_final: 0.8950 (pp) REVERT: E 109 LYS cc_start: 0.9602 (mmmt) cc_final: 0.8965 (tptt) REVERT: E 242 LYS cc_start: 0.7984 (mttt) cc_final: 0.7487 (tttt) REVERT: E 258 TYR cc_start: 0.9098 (t80) cc_final: 0.8891 (t80) REVERT: E 285 ASN cc_start: 0.9488 (m-40) cc_final: 0.9230 (m110) REVERT: E 332 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8463 (pp) REVERT: E 335 GLU cc_start: 0.8607 (tm-30) cc_final: 0.7867 (tm-30) REVERT: E 352 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8959 (tm-30) REVERT: E 385 MET cc_start: 0.8969 (ttm) cc_final: 0.8413 (ttm) REVERT: E 395 GLU cc_start: 0.8839 (mp0) cc_final: 0.8411 (mp0) REVERT: E 404 ASP cc_start: 0.9244 (t0) cc_final: 0.8976 (t70) REVERT: E 406 ILE cc_start: 0.9083 (mp) cc_final: 0.8815 (mp) REVERT: E 407 ARG cc_start: 0.8925 (ttt90) cc_final: 0.8550 (ttt-90) REVERT: F 21 GLN cc_start: 0.9027 (pt0) cc_final: 0.8630 (tm-30) REVERT: F 51 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8765 (pp) REVERT: F 105 ARG cc_start: 0.9166 (mtm110) cc_final: 0.8792 (mtm110) REVERT: F 109 LYS cc_start: 0.9478 (mptt) cc_final: 0.9256 (mttt) REVERT: F 276 SER cc_start: 0.8384 (p) cc_final: 0.8049 (p) REVERT: F 279 ASN cc_start: 0.9070 (t0) cc_final: 0.8279 (t0) REVERT: F 285 ASN cc_start: 0.9508 (m-40) cc_final: 0.9229 (m-40) REVERT: F 332 ILE cc_start: 0.8741 (OUTLIER) cc_final: 0.8508 (pp) REVERT: F 352 GLU cc_start: 0.9189 (tm-30) cc_final: 0.8929 (tm-30) REVERT: F 355 ARG cc_start: 0.9303 (ptm-80) cc_final: 0.8907 (ptm-80) REVERT: F 385 MET cc_start: 0.8847 (ttm) cc_final: 0.8328 (ttm) REVERT: F 395 GLU cc_start: 0.8781 (mp0) cc_final: 0.8325 (mp0) REVERT: F 399 GLU cc_start: 0.9078 (pm20) cc_final: 0.8835 (pm20) REVERT: F 400 TYR cc_start: 0.8221 (m-80) cc_final: 0.7932 (m-10) REVERT: F 438 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8108 (mmtm) REVERT: F 490 PHE cc_start: 0.9564 (m-80) cc_final: 0.9259 (m-80) REVERT: G 21 GLN cc_start: 0.9138 (pt0) cc_final: 0.8769 (tm-30) REVERT: G 50 ASP cc_start: 0.9137 (t70) cc_final: 0.8846 (t0) REVERT: G 51 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.8962 (pp) REVERT: G 105 ARG cc_start: 0.8972 (ttp80) cc_final: 0.8744 (ttp80) REVERT: G 110 TYR cc_start: 0.8331 (t80) cc_final: 0.8016 (t80) REVERT: G 258 TYR cc_start: 0.9141 (t80) cc_final: 0.8793 (t80) REVERT: G 285 ASN cc_start: 0.9454 (m-40) cc_final: 0.9173 (m110) REVERT: G 332 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8531 (pp) REVERT: G 335 GLU cc_start: 0.8608 (tm-30) cc_final: 0.7853 (tm-30) REVERT: G 352 GLU cc_start: 0.9217 (tm-30) cc_final: 0.8910 (tm-30) REVERT: G 355 ARG cc_start: 0.9277 (ptm-80) cc_final: 0.8971 (ptm-80) REVERT: G 385 MET cc_start: 0.8975 (ttm) cc_final: 0.8466 (ttm) REVERT: G 395 GLU cc_start: 0.8787 (mp0) cc_final: 0.8376 (mp0) REVERT: G 399 GLU cc_start: 0.9096 (pm20) cc_final: 0.8872 (pm20) REVERT: G 400 TYR cc_start: 0.8382 (m-80) cc_final: 0.7942 (m-80) REVERT: G 404 ASP cc_start: 0.9258 (t0) cc_final: 0.8930 (t70) REVERT: G 407 ARG cc_start: 0.9145 (ttt-90) cc_final: 0.8436 (ptm-80) REVERT: G 510 GLU cc_start: 0.8392 (tp30) cc_final: 0.8056 (tp30) REVERT: H 21 GLN cc_start: 0.9166 (pt0) cc_final: 0.8763 (tm-30) REVERT: H 25 ASN cc_start: 0.9254 (m-40) cc_final: 0.8858 (p0) REVERT: H 28 ASP cc_start: 0.8866 (m-30) cc_final: 0.8662 (m-30) REVERT: H 36 LEU cc_start: 0.8262 (pp) cc_final: 0.8052 (pp) REVERT: H 50 ASP cc_start: 0.9078 (t70) cc_final: 0.8851 (t0) REVERT: H 51 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8855 (pp) REVERT: H 276 SER cc_start: 0.8820 (p) cc_final: 0.8520 (p) REVERT: H 285 ASN cc_start: 0.9489 (m-40) cc_final: 0.9182 (m-40) REVERT: H 332 ILE cc_start: 0.9113 (OUTLIER) cc_final: 0.8598 (pp) REVERT: H 335 GLU cc_start: 0.8631 (tm-30) cc_final: 0.7949 (tm-30) REVERT: H 352 GLU cc_start: 0.9246 (tm-30) cc_final: 0.8993 (tm-30) REVERT: H 355 ARG cc_start: 0.9298 (ptm-80) cc_final: 0.8880 (ptm-80) REVERT: H 385 MET cc_start: 0.8845 (ttm) cc_final: 0.8407 (ttm) REVERT: H 395 GLU cc_start: 0.8905 (mp0) cc_final: 0.8418 (mp0) REVERT: H 399 GLU cc_start: 0.8939 (pm20) cc_final: 0.8729 (mp0) REVERT: H 404 ASP cc_start: 0.9223 (t0) cc_final: 0.8920 (t70) REVERT: H 406 ILE cc_start: 0.9079 (mp) cc_final: 0.8821 (mp) REVERT: H 410 LYS cc_start: 0.8672 (ptmt) cc_final: 0.8409 (ptmt) REVERT: H 512 ARG cc_start: 0.7882 (ttm-80) cc_final: 0.7657 (ptm160) outliers start: 147 outliers final: 99 residues processed: 1032 average time/residue: 0.3320 time to fit residues: 537.0605 Evaluate side-chains 1041 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 923 time to evaluate : 2.441 ------------------------------------------------------------------------------- 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 107 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 327 SER Chi-restraints excluded: chain A residue 332 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 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 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 377 LEU 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 66 VAL Chi-restraints excluded: chain C residue 78 MET 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 260 LEU Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR 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 384 VAL 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 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 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 65 LEU Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 282 PHE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 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 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 73 VAL 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 284 ILE 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 513 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 108 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 186 optimal weight: 3.9990 chunk 182 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 chunk 45 optimal weight: 0.0980 chunk 166 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 266 optimal weight: 0.7980 chunk 232 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 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 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 HIS H 309 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.110307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.089364 restraints weight = 40477.036| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 3.91 r_work: 0.2880 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23488 Z= 0.139 Angle : 0.687 9.282 31792 Z= 0.345 Chirality : 0.046 0.191 3656 Planarity : 0.004 0.050 4000 Dihedral : 10.182 89.397 3737 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 5.96 % Allowed : 27.39 % Favored : 66.65 % 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: 1136 sheet: -1.99 (0.27), residues: 320 loop : -1.00 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 92 PHE 0.011 0.001 PHE D 401 TYR 0.015 0.001 TYR B 258 ARG 0.012 0.001 ARG H 105 Details of bonding type rmsd hydrogen bonds : bond 0.03187 ( 841) hydrogen bonds : angle 5.11008 ( 2427) covalent geometry : bond 0.00332 (23480) covalent geometry : angle 0.68668 (31792) Misc. bond : bond 0.00069 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 981 time to evaluate : 2.474 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.4173 (ptp) cc_final: 0.3580 (ptm) REVERT: A 21 GLN cc_start: 0.9035 (OUTLIER) cc_final: 0.8612 (tm-30) REVERT: A 51 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8749 (pp) REVERT: A 109 LYS cc_start: 0.9658 (mmmt) cc_final: 0.9058 (tptt) REVERT: A 256 ASP cc_start: 0.9272 (m-30) cc_final: 0.8703 (p0) REVERT: A 274 ASP cc_start: 0.9145 (t0) cc_final: 0.8910 (t0) REVERT: A 276 SER cc_start: 0.8683 (p) cc_final: 0.8415 (p) REVERT: A 285 ASN cc_start: 0.9540 (m-40) cc_final: 0.9242 (m-40) REVERT: A 332 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8516 (pp) REVERT: A 335 GLU cc_start: 0.8491 (tm-30) cc_final: 0.7749 (tm-30) REVERT: A 352 GLU cc_start: 0.9170 (tm-30) cc_final: 0.8902 (tm-30) REVERT: A 355 ARG cc_start: 0.9219 (ptm-80) cc_final: 0.8900 (ptm-80) REVERT: A 385 MET cc_start: 0.8879 (ttm) cc_final: 0.8409 (ttm) REVERT: A 395 GLU cc_start: 0.8882 (mp0) cc_final: 0.8356 (mp0) REVERT: A 400 TYR cc_start: 0.8529 (m-10) cc_final: 0.7667 (m-10) REVERT: A 407 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8436 (ttt-90) REVERT: A 438 LYS cc_start: 0.9075 (mttt) cc_final: 0.8535 (mmtm) REVERT: A 510 GLU cc_start: 0.8062 (tp30) cc_final: 0.7717 (tp30) REVERT: B 21 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8682 (tm-30) REVERT: B 25 ASN cc_start: 0.9293 (m-40) cc_final: 0.8939 (p0) REVERT: B 50 ASP cc_start: 0.9117 (t70) cc_final: 0.8916 (t0) REVERT: B 51 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8746 (pp) REVERT: B 105 ARG cc_start: 0.9104 (mtm110) cc_final: 0.8805 (mtm110) REVERT: B 276 SER cc_start: 0.8682 (p) cc_final: 0.8382 (p) REVERT: B 285 ASN cc_start: 0.9500 (m-40) cc_final: 0.9135 (m-40) REVERT: B 332 ILE cc_start: 0.8863 (OUTLIER) cc_final: 0.8294 (pp) REVERT: B 335 GLU cc_start: 0.8537 (tm-30) cc_final: 0.7842 (tm-30) REVERT: B 352 GLU cc_start: 0.9171 (tm-30) cc_final: 0.8918 (tm-30) REVERT: B 355 ARG cc_start: 0.9193 (ptm-80) cc_final: 0.8911 (ptm-80) REVERT: B 385 MET cc_start: 0.8863 (ttm) cc_final: 0.8365 (ttm) REVERT: B 388 SER cc_start: 0.9190 (p) cc_final: 0.8595 (m) REVERT: B 395 GLU cc_start: 0.8820 (mp0) cc_final: 0.8377 (mp0) REVERT: B 404 ASP cc_start: 0.9264 (t0) cc_final: 0.9001 (t70) REVERT: B 438 LYS cc_start: 0.8500 (mmtt) cc_final: 0.8126 (mmtm) REVERT: B 510 GLU cc_start: 0.8238 (tp30) cc_final: 0.7907 (tp30) REVERT: C 21 GLN cc_start: 0.9095 (OUTLIER) cc_final: 0.8576 (tm-30) REVERT: C 51 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8830 (pp) REVERT: C 66 VAL cc_start: 0.7469 (OUTLIER) cc_final: 0.6437 (t) REVERT: C 109 LYS cc_start: 0.9654 (mmmt) cc_final: 0.8985 (tptt) REVERT: C 256 ASP cc_start: 0.9347 (m-30) cc_final: 0.8801 (p0) REVERT: C 258 TYR cc_start: 0.9162 (t80) cc_final: 0.8840 (t80) REVERT: C 276 SER cc_start: 0.8321 (p) cc_final: 0.8006 (p) REVERT: C 279 ASN cc_start: 0.9027 (t0) cc_final: 0.8273 (t0) REVERT: C 325 MET cc_start: 0.8433 (ptm) cc_final: 0.8200 (ptt) REVERT: C 332 ILE cc_start: 0.8934 (OUTLIER) cc_final: 0.8418 (pp) REVERT: C 335 GLU cc_start: 0.8501 (tm-30) cc_final: 0.7791 (tm-30) REVERT: C 395 GLU cc_start: 0.8888 (mp0) cc_final: 0.8267 (mp0) REVERT: C 399 GLU cc_start: 0.9130 (pm20) cc_final: 0.8912 (pm20) REVERT: C 404 ASP cc_start: 0.9216 (t0) cc_final: 0.8960 (t0) REVERT: C 510 GLU cc_start: 0.8185 (tp30) cc_final: 0.7902 (tp30) REVERT: D 21 GLN cc_start: 0.9097 (pt0) cc_final: 0.8672 (tm-30) REVERT: D 25 ASN cc_start: 0.9289 (m-40) cc_final: 0.8931 (p0) REVERT: D 36 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8462 (pp) REVERT: D 50 ASP cc_start: 0.9051 (t70) cc_final: 0.8813 (t0) REVERT: D 51 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8857 (pp) REVERT: D 276 SER cc_start: 0.8764 (p) cc_final: 0.8490 (p) REVERT: D 285 ASN cc_start: 0.9505 (m-40) cc_final: 0.9151 (m-40) REVERT: D 332 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8413 (pp) REVERT: D 335 GLU cc_start: 0.8535 (tm-30) cc_final: 0.7791 (tm-30) REVERT: D 352 GLU cc_start: 0.9138 (tm-30) cc_final: 0.8663 (tm-30) REVERT: D 355 ARG cc_start: 0.9170 (ptm-80) cc_final: 0.8865 (ptm-80) REVERT: D 395 GLU cc_start: 0.8890 (mp0) cc_final: 0.8390 (mp0) REVERT: D 399 GLU cc_start: 0.9115 (pm20) cc_final: 0.8887 (pm20) REVERT: D 400 TYR cc_start: 0.8452 (m-10) cc_final: 0.8070 (m-10) REVERT: D 404 ASP cc_start: 0.9202 (t0) cc_final: 0.8947 (t70) REVERT: D 407 ARG cc_start: 0.8943 (ttt90) cc_final: 0.8662 (ttt-90) REVERT: D 438 LYS cc_start: 0.8618 (mmtt) cc_final: 0.8292 (mmtm) REVERT: E 21 GLN cc_start: 0.9101 (OUTLIER) cc_final: 0.8578 (tm-30) REVERT: E 51 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8888 (pp) REVERT: E 105 ARG cc_start: 0.9134 (ttp80) cc_final: 0.8915 (ttp80) REVERT: E 109 LYS cc_start: 0.9651 (mmmt) cc_final: 0.8978 (tptt) REVERT: E 258 TYR cc_start: 0.9099 (t80) cc_final: 0.8893 (t80) REVERT: E 285 ASN cc_start: 0.9521 (m-40) cc_final: 0.9282 (m110) REVERT: E 332 ILE cc_start: 0.8880 (OUTLIER) cc_final: 0.8342 (pp) REVERT: E 335 GLU cc_start: 0.8520 (tm-30) cc_final: 0.7789 (tm-30) REVERT: E 352 GLU cc_start: 0.9218 (tm-30) cc_final: 0.8832 (tm-30) REVERT: E 385 MET cc_start: 0.8799 (ttm) cc_final: 0.8274 (ttm) REVERT: E 395 GLU cc_start: 0.8821 (mp0) cc_final: 0.8364 (mp0) REVERT: E 404 ASP cc_start: 0.9253 (t0) cc_final: 0.8995 (t70) REVERT: E 406 ILE cc_start: 0.9029 (mp) cc_final: 0.8707 (mp) REVERT: F 21 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8658 (tm-30) REVERT: F 51 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8751 (pp) REVERT: F 109 LYS cc_start: 0.9484 (mptt) cc_final: 0.9159 (mttm) REVERT: F 276 SER cc_start: 0.8273 (p) cc_final: 0.7942 (p) REVERT: F 279 ASN cc_start: 0.9028 (t0) cc_final: 0.8237 (t0) REVERT: F 285 ASN cc_start: 0.9518 (m-40) cc_final: 0.9318 (m-40) REVERT: F 332 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8092 (pp) REVERT: F 335 GLU cc_start: 0.8562 (tm-30) cc_final: 0.7850 (tm-30) REVERT: F 352 GLU cc_start: 0.9177 (tm-30) cc_final: 0.8917 (tm-30) REVERT: F 355 ARG cc_start: 0.9262 (ptm-80) cc_final: 0.8879 (ptm-80) REVERT: F 385 MET cc_start: 0.8812 (ttm) cc_final: 0.8265 (ttm) REVERT: F 395 GLU cc_start: 0.8823 (mp0) cc_final: 0.8306 (mp0) REVERT: F 399 GLU cc_start: 0.9091 (pm20) cc_final: 0.8879 (pm20) REVERT: F 406 ILE cc_start: 0.9023 (mm) cc_final: 0.8758 (tp) REVERT: F 438 LYS cc_start: 0.8348 (mmtt) cc_final: 0.8044 (mmtm) REVERT: G 21 GLN cc_start: 0.9166 (pt0) cc_final: 0.8813 (tm-30) REVERT: G 50 ASP cc_start: 0.9123 (t70) cc_final: 0.8833 (t0) REVERT: G 51 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8744 (pp) REVERT: G 74 THR cc_start: 0.8161 (t) cc_final: 0.7897 (m) REVERT: G 78 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.7877 (ptm) REVERT: G 258 TYR cc_start: 0.9136 (t80) cc_final: 0.8791 (t80) REVERT: G 277 GLN cc_start: 0.8659 (tp40) cc_final: 0.8391 (tp40) REVERT: G 285 ASN cc_start: 0.9439 (m-40) cc_final: 0.9151 (m110) REVERT: G 332 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8482 (pp) REVERT: G 335 GLU cc_start: 0.8564 (tm-30) cc_final: 0.7860 (tm-30) REVERT: G 352 GLU cc_start: 0.9207 (tm-30) cc_final: 0.8946 (tm-30) REVERT: G 355 ARG cc_start: 0.9233 (ptm-80) cc_final: 0.8922 (ptm-80) REVERT: G 385 MET cc_start: 0.8994 (ttm) cc_final: 0.8443 (ttm) REVERT: G 395 GLU cc_start: 0.8771 (mp0) cc_final: 0.8370 (mp0) REVERT: G 399 GLU cc_start: 0.9065 (pm20) cc_final: 0.8795 (mp0) REVERT: G 400 TYR cc_start: 0.8439 (m-80) cc_final: 0.7652 (m-10) REVERT: G 404 ASP cc_start: 0.9286 (t0) cc_final: 0.8946 (t70) REVERT: G 407 ARG cc_start: 0.9123 (ttt-90) cc_final: 0.8645 (ttt-90) REVERT: G 510 GLU cc_start: 0.8354 (tp30) cc_final: 0.7950 (tp30) REVERT: H 21 GLN cc_start: 0.9184 (pt0) cc_final: 0.8780 (tm-30) REVERT: H 25 ASN cc_start: 0.9292 (m-40) cc_final: 0.8913 (p0) REVERT: H 50 ASP cc_start: 0.9051 (t70) cc_final: 0.8811 (t0) REVERT: H 51 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8827 (pp) REVERT: H 70 MET cc_start: 0.8914 (OUTLIER) cc_final: 0.8317 (mtp) REVERT: H 109 LYS cc_start: 0.9472 (mttt) cc_final: 0.9015 (mtmm) REVERT: H 276 SER cc_start: 0.8734 (p) cc_final: 0.8473 (p) REVERT: H 285 ASN cc_start: 0.9491 (m-40) cc_final: 0.9150 (m-40) REVERT: H 332 ILE cc_start: 0.9042 (OUTLIER) cc_final: 0.8552 (pp) REVERT: H 335 GLU cc_start: 0.8616 (tm-30) cc_final: 0.7978 (tm-30) REVERT: H 352 GLU cc_start: 0.9186 (tm-30) cc_final: 0.8975 (tm-30) REVERT: H 385 MET cc_start: 0.8799 (ttm) cc_final: 0.8309 (ttm) REVERT: H 395 GLU cc_start: 0.8912 (mp0) cc_final: 0.8443 (mp0) REVERT: H 399 GLU cc_start: 0.8979 (pm20) cc_final: 0.8773 (mp0) REVERT: H 404 ASP cc_start: 0.9271 (t0) cc_final: 0.8961 (t70) REVERT: H 406 ILE cc_start: 0.9046 (mp) cc_final: 0.8795 (mp) outliers start: 142 outliers final: 100 residues processed: 1042 average time/residue: 0.3802 time to fit residues: 636.5721 Evaluate side-chains 1056 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 930 time to evaluate : 3.702 ------------------------------------------------------------------------------- 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 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 332 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 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 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 332 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 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 66 VAL Chi-restraints excluded: chain C residue 78 MET 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 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 235 LEU Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 306 THR 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 384 VAL 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 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 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 65 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 282 PHE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 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 333 THR Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 70 MET Chi-restraints excluded: chain H residue 73 VAL 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 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.2635 > 50: distance: 14 - 49: 25.806 distance: 17 - 46: 36.837 distance: 33 - 39: 27.922 distance: 39 - 40: 36.956 distance: 40 - 41: 51.395 distance: 40 - 43: 41.766 distance: 41 - 42: 41.768 distance: 41 - 46: 30.175 distance: 43 - 44: 49.896 distance: 43 - 45: 58.535 distance: 46 - 47: 42.112 distance: 47 - 48: 41.869 distance: 47 - 50: 57.048 distance: 48 - 49: 31.582 distance: 48 - 54: 23.367 distance: 50 - 51: 11.969 distance: 51 - 52: 59.575 distance: 51 - 53: 34.402 distance: 54 - 55: 33.774 distance: 55 - 56: 42.383 distance: 55 - 58: 41.853 distance: 56 - 57: 50.853 distance: 56 - 63: 55.295 distance: 58 - 59: 58.523 distance: 59 - 60: 60.653 distance: 60 - 61: 43.580 distance: 61 - 62: 48.322 distance: 63 - 64: 32.357 distance: 64 - 65: 45.989 distance: 64 - 67: 40.079 distance: 65 - 66: 43.475 distance: 65 - 70: 56.899 distance: 67 - 68: 60.455 distance: 67 - 69: 55.480 distance: 70 - 71: 63.019 distance: 70 - 76: 46.011 distance: 71 - 72: 61.043 distance: 71 - 74: 20.928 distance: 72 - 73: 40.803 distance: 72 - 77: 15.379 distance: 74 - 75: 28.182 distance: 75 - 76: 41.852 distance: 77 - 78: 37.002 distance: 78 - 79: 40.416 distance: 78 - 81: 46.999 distance: 79 - 80: 27.922 distance: 79 - 85: 54.161 distance: 81 - 82: 31.851 distance: 82 - 83: 57.941 distance: 82 - 84: 58.996 distance: 85 - 86: 18.657 distance: 86 - 87: 29.508 distance: 86 - 89: 24.475 distance: 87 - 88: 44.479 distance: 87 - 92: 41.789 distance: 89 - 90: 54.865 distance: 89 - 91: 31.115 distance: 92 - 93: 27.150 distance: 93 - 94: 29.450 distance: 93 - 96: 24.319 distance: 94 - 95: 6.914 distance: 94 - 98: 42.726 distance: 96 - 97: 44.231 distance: 98 - 99: 37.882 distance: 99 - 100: 22.703 distance: 99 - 102: 32.532 distance: 100 - 101: 57.765 distance: 100 - 104: 20.376 distance: 102 - 103: 22.692 distance: 104 - 105: 56.955 distance: 104 - 110: 50.821 distance: 105 - 106: 57.940 distance: 105 - 108: 58.320 distance: 106 - 107: 45.116 distance: 106 - 111: 31.363 distance: 108 - 109: 55.301 distance: 109 - 110: 12.606