Starting phenix.real_space_refine on Sat Jul 4 20:58:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6u8s_20691/07_2026/6u8s_20691.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u8s_20691/07_2026/6u8s_20691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6u8s_20691/07_2026/6u8s_20691.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6u8s_20691/07_2026/6u8s_20691.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u8s_20691/07_2026/6u8s_20691.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u8s_20691/07_2026/6u8s_20691.map" model { file = "/net/cci-nas-00/data/ceres_data/6u8s_20691/07_2026/6u8s_20691.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u8s_20691/07_2026/6u8s_20691.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.054 sd= 2.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 144 5.16 5 C 14512 2.51 5 N 3920 2.21 5 O 4480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23080 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "B" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "C" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "D" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "E" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "F" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "G" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "H" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 4.43, per 1000 atoms: 0.19 Number of scatterers: 23080 At special positions: 0 Unit cell: (122.85, 122.85, 118.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 144 16.00 P 24 15.00 O 4480 8.00 N 3920 7.00 C 14512 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 1.1 seconds 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5392 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 32 sheets defined 41.5% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.523A pdb=" N ILE A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 75 through 85 removed outlier: 3.530A pdb=" N THR A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 109 removed outlier: 3.612A pdb=" N LYS A 108 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 256 through 267 removed outlier: 4.110A pdb=" N LEU A 262 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.700A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 342 through 355 removed outlier: 3.849A pdb=" N SER A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 378 removed outlier: 3.855A pdb=" N ILE A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 420 removed outlier: 4.109A pdb=" N MET A 420 " --> pdb=" O LEU A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 502 removed outlier: 3.589A pdb=" N GLY A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 6 removed outlier: 3.523A pdb=" N ILE B 6 " --> pdb=" O ALA B 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2 through 6' Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 75 through 85 removed outlier: 3.530A pdb=" N THR B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 removed outlier: 3.613A pdb=" N LYS B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 255 No H-bonds generated for 'chain 'B' and resid 253 through 255' Processing helix chain 'B' and resid 256 through 267 removed outlier: 4.112A pdb=" N LEU B 262 " --> pdb=" O TYR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.701A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.849A pdb=" N SER B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 378 removed outlier: 3.854A pdb=" N ILE B 373 " --> pdb=" O ASN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 420 removed outlier: 4.110A pdb=" N MET B 420 " --> pdb=" O LEU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 502 removed outlier: 3.588A pdb=" N GLY B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 6 removed outlier: 3.523A pdb=" N ILE C 6 " --> pdb=" O ALA C 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2 through 6' Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 75 through 85 removed outlier: 3.530A pdb=" N THR C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 109 removed outlier: 3.612A pdb=" N LYS C 108 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 255 No H-bonds generated for 'chain 'C' and resid 253 through 255' Processing helix chain 'C' and resid 256 through 267 removed outlier: 4.111A pdb=" N LEU C 262 " --> pdb=" O TYR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.700A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 342 through 355 removed outlier: 3.848A pdb=" N SER C 351 " --> pdb=" O VAL C 347 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 378 removed outlier: 3.855A pdb=" N ILE C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 420 removed outlier: 4.109A pdb=" N MET C 420 " --> pdb=" O LEU C 417 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 502 removed outlier: 3.589A pdb=" N GLY C 502 " --> pdb=" O GLN C 498 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 6 removed outlier: 3.523A pdb=" N ILE D 6 " --> pdb=" O ALA D 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2 through 6' Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 75 through 85 removed outlier: 3.530A pdb=" N THR D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 109 removed outlier: 3.612A pdb=" N LYS D 108 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 255 No H-bonds generated for 'chain 'D' and resid 253 through 255' Processing helix chain 'D' and resid 256 through 267 removed outlier: 4.111A pdb=" N LEU D 262 " --> pdb=" O TYR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.700A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 315 Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 342 through 355 removed outlier: 3.849A pdb=" N SER D 351 " --> pdb=" O VAL D 347 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 378 removed outlier: 3.855A pdb=" N ILE D 373 " --> pdb=" O ASN D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 420 removed outlier: 4.109A pdb=" N MET D 420 " --> pdb=" O LEU D 417 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 502 removed outlier: 3.589A pdb=" N GLY D 502 " --> pdb=" O GLN D 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 6 removed outlier: 3.523A pdb=" N ILE E 6 " --> pdb=" O ALA E 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2 through 6' Processing helix chain 'E' and resid 19 through 24 Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 75 through 85 removed outlier: 3.530A pdb=" N THR E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 109 removed outlier: 3.613A pdb=" N LYS E 108 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 255 No H-bonds generated for 'chain 'E' and resid 253 through 255' Processing helix chain 'E' and resid 256 through 267 removed outlier: 4.111A pdb=" N LEU E 262 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 removed outlier: 3.701A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 315 Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 342 through 355 removed outlier: 3.848A pdb=" N SER E 351 " --> pdb=" O VAL E 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 378 removed outlier: 3.855A pdb=" N ILE E 373 " --> pdb=" O ASN E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 420 removed outlier: 4.109A pdb=" N MET E 420 " --> pdb=" O LEU E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 502 removed outlier: 3.589A pdb=" N GLY E 502 " --> pdb=" O GLN E 498 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 6 removed outlier: 3.523A pdb=" N ILE F 6 " --> pdb=" O ALA F 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2 through 6' Processing helix chain 'F' and resid 19 through 24 Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 75 through 85 removed outlier: 3.530A pdb=" N THR F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 109 removed outlier: 3.613A pdb=" N LYS F 108 " --> pdb=" O VAL F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 255 No H-bonds generated for 'chain 'F' and resid 253 through 255' Processing helix chain 'F' and resid 256 through 267 removed outlier: 4.112A pdb=" N LEU F 262 " --> pdb=" O TYR F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 removed outlier: 3.700A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS F 293 " --> pdb=" O TYR F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 315 Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 342 through 355 removed outlier: 3.849A pdb=" N SER F 351 " --> pdb=" O VAL F 347 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 378 removed outlier: 3.855A pdb=" N ILE F 373 " --> pdb=" O ASN F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 420 removed outlier: 4.109A pdb=" N MET F 420 " --> pdb=" O LEU F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 502 removed outlier: 3.588A pdb=" N GLY F 502 " --> pdb=" O GLN F 498 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 removed outlier: 3.522A pdb=" N ILE G 6 " --> pdb=" O ALA G 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 6' Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 75 through 85 removed outlier: 3.530A pdb=" N THR G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 109 removed outlier: 3.613A pdb=" N LYS G 108 " --> pdb=" O VAL G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 255 No H-bonds generated for 'chain 'G' and resid 253 through 255' Processing helix chain 'G' and resid 256 through 267 removed outlier: 4.112A pdb=" N LEU G 262 " --> pdb=" O TYR G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 removed outlier: 3.700A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS G 293 " --> pdb=" O TYR G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 315 Processing helix chain 'G' and resid 332 through 338 Processing helix chain 'G' and resid 342 through 355 removed outlier: 3.849A pdb=" N SER G 351 " --> pdb=" O VAL G 347 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 378 removed outlier: 3.855A pdb=" N ILE G 373 " --> pdb=" O ASN G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 420 removed outlier: 4.109A pdb=" N MET G 420 " --> pdb=" O LEU G 417 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 502 removed outlier: 3.588A pdb=" N GLY G 502 " --> pdb=" O GLN G 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 6 removed outlier: 3.523A pdb=" N ILE H 6 " --> pdb=" O ALA H 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 2 through 6' Processing helix chain 'H' and resid 19 through 24 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 75 through 85 removed outlier: 3.530A pdb=" N THR H 85 " --> pdb=" O ALA H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 109 removed outlier: 3.613A pdb=" N LYS H 108 " --> pdb=" O VAL H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 255 No H-bonds generated for 'chain 'H' and resid 253 through 255' Processing helix chain 'H' and resid 256 through 267 removed outlier: 4.111A pdb=" N LEU H 262 " --> pdb=" O TYR H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 removed outlier: 3.700A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS H 293 " --> pdb=" O TYR H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 315 Processing helix chain 'H' and resid 332 through 338 Processing helix chain 'H' and resid 342 through 355 removed outlier: 3.848A pdb=" N SER H 351 " --> pdb=" O VAL H 347 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 378 removed outlier: 3.855A pdb=" N ILE H 373 " --> pdb=" O ASN H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 420 removed outlier: 4.109A pdb=" N MET H 420 " --> pdb=" O LEU H 417 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 502 removed outlier: 3.589A pdb=" N GLY H 502 " --> pdb=" O GLN H 498 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.588A pdb=" N VAL A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL A 299 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ARG A 322 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY A 301 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE A 91 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.585A pdb=" N SER A 444 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER D 508 " --> pdb=" O ALA A 446 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.638A pdb=" N SER A 508 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER B 444 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.588A pdb=" N VAL B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL B 299 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ARG B 322 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY B 301 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE B 91 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.646A pdb=" N SER B 508 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER C 444 " --> pdb=" O GLU B 510 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.588A pdb=" N VAL C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL C 299 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ARG C 322 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY C 301 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE C 91 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.640A pdb=" N SER C 508 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER D 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.588A pdb=" N VAL D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL D 299 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ARG D 322 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY D 301 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N ILE D 91 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AB9, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC1, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.589A pdb=" N VAL E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL E 299 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ARG E 322 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY E 301 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE E 91 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.587A pdb=" N SER E 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER H 508 " --> pdb=" O ALA E 446 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.624A pdb=" N SER E 508 " --> pdb=" O ALA F 446 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER F 444 " --> pdb=" O GLU E 510 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AC5, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC6, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.589A pdb=" N VAL F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL F 299 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ARG F 322 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N GLY F 301 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE F 91 " --> pdb=" O ALA F 249 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 508 through 510 removed outlier: 3.739A pdb=" N SER F 508 " --> pdb=" O ALA G 446 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER G 444 " --> pdb=" O GLU F 510 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AC9, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AD1, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.589A pdb=" N VAL G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N MET G 385 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL G 299 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ARG G 322 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY G 301 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N ILE G 91 " --> pdb=" O ALA G 249 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 508 through 510 removed outlier: 3.574A pdb=" N SER G 508 " --> pdb=" O ALA H 446 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N SER H 444 " --> pdb=" O GLU G 510 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AD4, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.588A pdb=" N VAL H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.066A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL H 299 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N ARG H 322 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLY H 301 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N ILE H 91 " --> pdb=" O ALA H 249 " (cutoff:3.500A) 841 hydrogen bonds defined for protein. 2427 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.79 Time building geometry restraints manager: 2.52 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: 12812 17.68 - 35.36: 636 35.36 - 53.04: 296 53.04 - 70.72: 88 70.72 - 88.41: 16 Dihedral angle restraints: 13848 sinusoidal: 5344 harmonic: 8504 Sorted by residual: dihedral pdb=" CA LEU B 235 " pdb=" C LEU B 235 " pdb=" N ALA B 236 " pdb=" CA ALA B 236 " ideal model delta harmonic sigma weight residual -180.00 -157.62 -22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU F 235 " pdb=" C LEU F 235 " pdb=" N ALA F 236 " pdb=" CA ALA F 236 " ideal model delta harmonic sigma weight residual -180.00 -157.65 -22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU H 235 " pdb=" C LEU H 235 " pdb=" N ALA H 236 " pdb=" CA ALA H 236 " ideal model delta harmonic sigma weight residual 180.00 -157.67 -22.33 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 13845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.630 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: 0.340 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.140 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.050 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.230 23488 Z= 0.593 Angle : 1.355 16.360 31792 Z= 0.676 Chirality : 0.066 0.354 3656 Planarity : 0.007 0.056 4000 Dihedral : 14.271 88.405 8456 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 9.06 % Allowed : 8.05 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.07 (0.12), residues: 2960 helix: -3.47 (0.10), residues: 1064 sheet: -2.58 (0.18), residues: 456 loop : -1.97 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG C 407 TYR 0.019 0.003 TYR H 484 PHE 0.019 0.003 PHE B 401 HIS 0.007 0.001 HIS G 92 Details of bonding type rmsd/Z covalent geometry : bond 0.01240 / 0.59 (23480) covalent geometry : angle 1.35527 / 0.68 (31792) hydrogen bonds : bond 0.20259 / 13.20 ( 841) hydrogen bonds : angle 8.62652 / 5.94 ( 2427) Misc. bond : bond 0.00121 / 0.06 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 216 poor density : 1262 time to evaluate : 0.867 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8607 (m-30) cc_final: 0.8120 (m-30) REVERT: A 42 ILE cc_start: 0.8958 (pp) cc_final: 0.8739 (pt) REVERT: A 105 ARG cc_start: 0.9037 (mtm110) cc_final: 0.8664 (mtm110) REVERT: A 109 LYS cc_start: 0.9327 (mttp) cc_final: 0.9019 (mttt) REVERT: A 275 SER cc_start: 0.9145 (t) cc_final: 0.8857 (t) REVERT: A 276 SER cc_start: 0.8619 (p) cc_final: 0.8363 (p) REVERT: A 285 ASN cc_start: 0.9360 (m-40) cc_final: 0.9010 (m-40) REVERT: A 352 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8551 (tm-30) REVERT: A 395 GLU cc_start: 0.8753 (mp0) cc_final: 0.7955 (mp0) REVERT: A 399 GLU cc_start: 0.8555 (pm20) cc_final: 0.8294 (pm20) REVERT: A 404 ASP cc_start: 0.8922 (t0) cc_final: 0.8599 (t0) REVERT: B 25 ASN cc_start: 0.9039 (m110) cc_final: 0.8822 (p0) REVERT: B 28 ASP cc_start: 0.8633 (m-30) cc_final: 0.8182 (m-30) REVERT: B 50 ASP cc_start: 0.8853 (t70) cc_final: 0.8577 (t70) REVERT: B 105 ARG cc_start: 0.9104 (mtm110) cc_final: 0.8763 (mtm110) REVERT: B 106 LYS cc_start: 0.9576 (mtpt) cc_final: 0.9173 (mtpp) REVERT: B 109 LYS cc_start: 0.9364 (mttp) cc_final: 0.9106 (mttt) REVERT: B 274 ASP cc_start: 0.8815 (t0) cc_final: 0.8562 (t0) REVERT: B 276 SER cc_start: 0.8583 (p) cc_final: 0.8344 (p) REVERT: B 281 ILE cc_start: 0.9093 (tp) cc_final: 0.8879 (tp) REVERT: B 285 ASN cc_start: 0.9345 (m-40) cc_final: 0.9143 (m-40) REVERT: B 313 LEU cc_start: 0.9393 (mt) cc_final: 0.9130 (mp) REVERT: B 352 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8602 (tm-30) REVERT: B 395 GLU cc_start: 0.8812 (mp0) cc_final: 0.8116 (mp0) REVERT: B 399 GLU cc_start: 0.8567 (pm20) cc_final: 0.8336 (pm20) REVERT: B 400 TYR cc_start: 0.8116 (m-80) cc_final: 0.7864 (m-80) REVERT: B 404 ASP cc_start: 0.8929 (t0) cc_final: 0.8588 (t0) REVERT: C 28 ASP cc_start: 0.8626 (m-30) cc_final: 0.8172 (m-30) REVERT: C 50 ASP cc_start: 0.8882 (t70) cc_final: 0.8667 (t70) REVERT: C 93 HIS cc_start: 0.9315 (p-80) cc_final: 0.9064 (p90) REVERT: C 105 ARG cc_start: 0.9010 (mtm110) cc_final: 0.8809 (mtm110) REVERT: C 109 LYS cc_start: 0.9343 (mttp) cc_final: 0.8537 (tptt) REVERT: C 259 ARG cc_start: 0.9026 (mtp85) cc_final: 0.8702 (ttm-80) REVERT: C 276 SER cc_start: 0.8550 (p) cc_final: 0.8259 (p) REVERT: C 284 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.9057 (pp) REVERT: C 285 ASN cc_start: 0.9364 (m-40) cc_final: 0.9022 (m-40) REVERT: C 352 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8517 (tm-30) REVERT: C 395 GLU cc_start: 0.8717 (mp0) cc_final: 0.7976 (mp0) REVERT: C 399 GLU cc_start: 0.8520 (pm20) cc_final: 0.8273 (pm20) REVERT: D 28 ASP cc_start: 0.8619 (m-30) cc_final: 0.8136 (m-30) REVERT: D 42 ILE cc_start: 0.9050 (pp) cc_final: 0.8841 (pt) REVERT: D 50 ASP cc_start: 0.8855 (t70) cc_final: 0.8601 (t70) REVERT: D 84 LEU cc_start: 0.8648 (mm) cc_final: 0.8332 (tp) REVERT: D 106 LYS cc_start: 0.9634 (mtpt) cc_final: 0.9247 (mtpp) REVERT: D 108 LYS cc_start: 0.9548 (OUTLIER) cc_final: 0.9337 (mttm) REVERT: D 109 LYS cc_start: 0.9352 (mttp) cc_final: 0.8715 (tptt) REVERT: D 275 SER cc_start: 0.9145 (t) cc_final: 0.8847 (t) REVERT: D 276 SER cc_start: 0.8599 (p) cc_final: 0.8302 (p) REVERT: D 285 ASN cc_start: 0.9375 (m-40) cc_final: 0.9038 (m-40) REVERT: D 352 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8519 (tm-30) REVERT: D 368 GLN cc_start: 0.9008 (mt0) cc_final: 0.8514 (mp10) REVERT: D 395 GLU cc_start: 0.8842 (mp0) cc_final: 0.8082 (mp0) REVERT: D 399 GLU cc_start: 0.8541 (pm20) cc_final: 0.8271 (pm20) REVERT: D 400 TYR cc_start: 0.8114 (m-80) cc_final: 0.7912 (m-80) REVERT: D 404 ASP cc_start: 0.8879 (t0) cc_final: 0.8576 (t0) REVERT: E 28 ASP cc_start: 0.8644 (m-30) cc_final: 0.8180 (m-30) REVERT: E 91 ILE cc_start: 0.8356 (mp) cc_final: 0.8154 (mp) REVERT: E 105 ARG cc_start: 0.9009 (mtm110) cc_final: 0.8796 (mtm110) REVERT: E 109 LYS cc_start: 0.9325 (mttp) cc_final: 0.8559 (tptt) REVERT: E 276 SER cc_start: 0.8599 (p) cc_final: 0.8354 (p) REVERT: E 285 ASN cc_start: 0.9343 (m-40) cc_final: 0.9005 (m-40) REVERT: E 352 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8496 (tm-30) REVERT: E 368 GLN cc_start: 0.9006 (mt0) cc_final: 0.8425 (mp10) REVERT: E 395 GLU cc_start: 0.8722 (mp0) cc_final: 0.7922 (mp0) REVERT: E 399 GLU cc_start: 0.8591 (pm20) cc_final: 0.8315 (pm20) REVERT: E 482 MET cc_start: 0.8964 (mtp) cc_final: 0.8706 (mtp) REVERT: F 28 ASP cc_start: 0.8611 (m-30) cc_final: 0.8112 (m-30) REVERT: F 50 ASP cc_start: 0.8882 (t70) cc_final: 0.8629 (t70) REVERT: F 84 LEU cc_start: 0.8760 (mm) cc_final: 0.8407 (tp) REVERT: F 98 GLU cc_start: 0.9347 (mp0) cc_final: 0.9105 (mp0) REVERT: F 108 LYS cc_start: 0.9564 (OUTLIER) cc_final: 0.9351 (mttm) REVERT: F 109 LYS cc_start: 0.9356 (mttp) cc_final: 0.9095 (mttm) REVERT: F 276 SER cc_start: 0.8565 (p) cc_final: 0.8326 (p) REVERT: F 281 ILE cc_start: 0.9082 (tp) cc_final: 0.8713 (tp) REVERT: F 285 ASN cc_start: 0.9295 (m-40) cc_final: 0.8982 (m110) REVERT: F 352 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8662 (tm-30) REVERT: F 368 GLN cc_start: 0.8986 (mt0) cc_final: 0.8453 (mp10) REVERT: F 395 GLU cc_start: 0.8842 (mp0) cc_final: 0.8137 (mp0) REVERT: F 399 GLU cc_start: 0.8650 (pm20) cc_final: 0.8331 (pm20) REVERT: F 400 TYR cc_start: 0.8125 (m-80) cc_final: 0.7886 (m-80) REVERT: F 404 ASP cc_start: 0.8959 (t0) cc_final: 0.8649 (t0) REVERT: F 482 MET cc_start: 0.8900 (mtp) cc_final: 0.8635 (mtp) REVERT: G 28 ASP cc_start: 0.8672 (m-30) cc_final: 0.8218 (m-30) REVERT: G 50 ASP cc_start: 0.8817 (t70) cc_final: 0.8577 (t0) REVERT: G 93 HIS cc_start: 0.9352 (p-80) cc_final: 0.9128 (p90) REVERT: G 98 GLU cc_start: 0.9286 (mp0) cc_final: 0.9051 (mp0) REVERT: G 108 LYS cc_start: 0.9630 (OUTLIER) cc_final: 0.9405 (mttm) REVERT: G 109 LYS cc_start: 0.9314 (mttp) cc_final: 0.8811 (tptt) REVERT: G 261 ASP cc_start: 0.9392 (p0) cc_final: 0.9154 (p0) REVERT: G 275 SER cc_start: 0.9061 (t) cc_final: 0.8741 (t) REVERT: G 276 SER cc_start: 0.8709 (p) cc_final: 0.8431 (p) REVERT: G 281 ILE cc_start: 0.9291 (tp) cc_final: 0.8928 (tp) REVERT: G 285 ASN cc_start: 0.9335 (m-40) cc_final: 0.8961 (m-40) REVERT: G 352 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8478 (tm-30) REVERT: G 395 GLU cc_start: 0.8755 (mp0) cc_final: 0.7978 (mp0) REVERT: G 399 GLU cc_start: 0.8459 (pm20) cc_final: 0.8212 (pm20) REVERT: G 406 ILE cc_start: 0.9345 (mp) cc_final: 0.9117 (mm) REVERT: G 482 MET cc_start: 0.9001 (mtp) cc_final: 0.8759 (mtp) REVERT: H 25 ASN cc_start: 0.9057 (m110) cc_final: 0.8830 (p0) REVERT: H 28 ASP cc_start: 0.8708 (m-30) cc_final: 0.8264 (m-30) REVERT: H 50 ASP cc_start: 0.8832 (t70) cc_final: 0.8563 (t70) REVERT: H 84 LEU cc_start: 0.8553 (mm) cc_final: 0.8239 (tp) REVERT: H 98 GLU cc_start: 0.9370 (mp0) cc_final: 0.9124 (mp0) REVERT: H 105 ARG cc_start: 0.9143 (mtm110) cc_final: 0.8796 (mtm110) REVERT: H 106 LYS cc_start: 0.9586 (mtpt) cc_final: 0.9214 (mtpp) REVERT: H 109 LYS cc_start: 0.9339 (mttp) cc_final: 0.9071 (mttt) REVERT: H 274 ASP cc_start: 0.8788 (t0) cc_final: 0.8548 (t0) REVERT: H 276 SER cc_start: 0.8614 (p) cc_final: 0.8276 (p) REVERT: H 281 ILE cc_start: 0.9197 (tp) cc_final: 0.8989 (tp) REVERT: H 285 ASN cc_start: 0.9406 (m-40) cc_final: 0.9184 (m110) REVERT: H 352 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8654 (tm-30) REVERT: H 395 GLU cc_start: 0.8790 (mp0) cc_final: 0.8073 (mp0) REVERT: H 399 GLU cc_start: 0.8502 (pm20) cc_final: 0.8278 (pm20) REVERT: H 400 TYR cc_start: 0.8104 (m-80) cc_final: 0.7875 (m-80) REVERT: H 482 MET cc_start: 0.8871 (mtp) cc_final: 0.8605 (mtp) outliers start: 216 outliers final: 108 residues processed: 1332 average time/residue: 0.1489 time to fit residues: 314.0840 Evaluate side-chains 1055 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 943 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 479 VAL Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 505 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 290 ILE Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 505 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 479 VAL Chi-restraints excluded: chain G residue 505 SER Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 505 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN A 25 ASN A 48 GLN A 93 HIS A 277 GLN A 309 GLN A 312 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN B 25 ASN B 48 GLN B 277 GLN B 309 GLN B 312 ASN B 343 GLN C 22 GLN C 25 ASN C 48 GLN C 243 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN D 22 GLN D 25 ASN D 48 GLN D 93 HIS D 277 GLN ** D 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 309 GLN D 312 ASN D 343 GLN E 22 GLN E 25 ASN E 48 GLN E 93 HIS E 243 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 ASN E 334 GLN F 22 GLN F 48 GLN F 93 HIS ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN F 498 GLN G 22 GLN G 48 GLN G 243 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN H 22 GLN H 25 ASN H 48 GLN H 93 HIS ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN H 334 GLN H 343 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.108360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.087197 restraints weight = 41471.364| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 4.13 r_work: 0.2848 rms_B_bonded: 4.54 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23488 Z= 0.164 Angle : 0.734 8.218 31792 Z= 0.368 Chirality : 0.047 0.166 3656 Planarity : 0.005 0.042 4000 Dihedral : 11.683 89.978 3525 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 6.92 % Allowed : 18.29 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.22 (0.13), residues: 2960 helix: -2.27 (0.12), residues: 1120 sheet: -2.69 (0.18), residues: 464 loop : -1.64 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 407 TYR 0.019 0.002 TYR G 400 PHE 0.017 0.001 PHE E 401 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (23480) covalent geometry : angle 0.73399 / 0.37 (31792) hydrogen bonds : bond 0.04187 / 2.75 ( 841) hydrogen bonds : angle 6.07408 / 4.15 ( 2427) Misc. bond : bond 0.00028 / 0.01 ( 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 1214 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 1049 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8034 (t0) cc_final: 0.7788 (t0) REVERT: A 28 ASP cc_start: 0.8830 (m-30) cc_final: 0.8517 (m-30) REVERT: A 50 ASP cc_start: 0.9029 (t0) cc_final: 0.8794 (t0) REVERT: A 105 ARG cc_start: 0.9161 (mtm110) cc_final: 0.8926 (mtm110) REVERT: A 109 LYS cc_start: 0.9411 (mttp) cc_final: 0.8779 (tptt) REVERT: A 276 SER cc_start: 0.8760 (p) cc_final: 0.8509 (p) REVERT: A 285 ASN cc_start: 0.9444 (m-40) cc_final: 0.9075 (m-40) REVERT: A 352 GLU cc_start: 0.9161 (tm-30) cc_final: 0.8855 (tm-30) REVERT: A 395 GLU cc_start: 0.8750 (mp0) cc_final: 0.8138 (mp0) REVERT: A 399 GLU cc_start: 0.8990 (pm20) cc_final: 0.8719 (mp0) REVERT: A 404 ASP cc_start: 0.9121 (t0) cc_final: 0.8814 (t0) REVERT: A 512 ARG cc_start: 0.7785 (ttm-80) cc_final: 0.7475 (ptm160) REVERT: B 25 ASN cc_start: 0.9101 (m-40) cc_final: 0.8839 (p0) REVERT: B 28 ASP cc_start: 0.8875 (m-30) cc_final: 0.8548 (m-30) REVERT: B 50 ASP cc_start: 0.9051 (t70) cc_final: 0.8751 (t0) REVERT: B 58 LYS cc_start: 0.9446 (mmtp) cc_final: 0.9186 (mmmm) REVERT: B 66 VAL cc_start: 0.8466 (OUTLIER) cc_final: 0.8256 (p) REVERT: B 105 ARG cc_start: 0.9198 (mtm110) cc_final: 0.8881 (mtm110) REVERT: B 109 LYS cc_start: 0.9400 (mttp) cc_final: 0.9003 (mttp) REVERT: B 276 SER cc_start: 0.8832 (p) cc_final: 0.8563 (p) REVERT: B 281 ILE cc_start: 0.8915 (tp) cc_final: 0.8579 (tt) REVERT: B 285 ASN cc_start: 0.9438 (m-40) cc_final: 0.9212 (m-40) REVERT: B 352 GLU cc_start: 0.9227 (tm-30) cc_final: 0.8974 (tm-30) REVERT: B 385 MET cc_start: 0.8875 (ttm) cc_final: 0.8559 (ttp) REVERT: B 395 GLU cc_start: 0.8860 (mp0) cc_final: 0.8363 (mp0) REVERT: B 399 GLU cc_start: 0.9062 (pm20) cc_final: 0.8829 (mp0) REVERT: B 400 TYR cc_start: 0.8417 (m-80) cc_final: 0.7531 (m-80) REVERT: B 404 ASP cc_start: 0.9138 (t0) cc_final: 0.8857 (t0) REVERT: B 407 ARG cc_start: 0.8779 (ttt-90) cc_final: 0.7758 (ttt-90) REVERT: B 449 ASP cc_start: 0.9275 (p0) cc_final: 0.9014 (p0) REVERT: B 461 ILE cc_start: 0.9159 (pp) cc_final: 0.8954 (pp) REVERT: B 512 ARG cc_start: 0.7797 (ttm-80) cc_final: 0.7532 (ptm160) REVERT: C 28 ASP cc_start: 0.8897 (m-30) cc_final: 0.8538 (m-30) REVERT: C 50 ASP cc_start: 0.9028 (t70) cc_final: 0.8735 (t0) REVERT: C 58 LYS cc_start: 0.9359 (mmtp) cc_final: 0.9097 (mmmm) REVERT: C 66 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8260 (p) REVERT: C 105 ARG cc_start: 0.9158 (mtm110) cc_final: 0.8893 (mtm110) REVERT: C 109 LYS cc_start: 0.9413 (mttp) cc_final: 0.9015 (mttp) REVERT: C 276 SER cc_start: 0.8710 (p) cc_final: 0.8458 (p) REVERT: C 285 ASN cc_start: 0.9470 (m-40) cc_final: 0.9174 (m-40) REVERT: C 352 GLU cc_start: 0.9120 (tm-30) cc_final: 0.8845 (tm-30) REVERT: C 385 MET cc_start: 0.8879 (ttm) cc_final: 0.8513 (ttp) REVERT: C 395 GLU cc_start: 0.8841 (mp0) cc_final: 0.8310 (mp0) REVERT: C 399 GLU cc_start: 0.8974 (pm20) cc_final: 0.8703 (mp0) REVERT: C 400 TYR cc_start: 0.8637 (m-80) cc_final: 0.7499 (m-10) REVERT: C 407 ARG cc_start: 0.8949 (ttt-90) cc_final: 0.8001 (ttt-90) REVERT: C 449 ASP cc_start: 0.9326 (p0) cc_final: 0.8921 (p0) REVERT: C 512 ARG cc_start: 0.7774 (ttm-80) cc_final: 0.7558 (ptm160) REVERT: D 1 MET cc_start: 0.5980 (ptp) cc_final: 0.5744 (ptp) REVERT: D 28 ASP cc_start: 0.8859 (m-30) cc_final: 0.8519 (m-30) REVERT: D 47 ASP cc_start: 0.9147 (p0) cc_final: 0.8898 (p0) REVERT: D 50 ASP cc_start: 0.9022 (t70) cc_final: 0.8741 (t0) REVERT: D 58 LYS cc_start: 0.9436 (mmtp) cc_final: 0.9179 (mmmm) REVERT: D 105 ARG cc_start: 0.9242 (mtm110) cc_final: 0.8821 (mtm110) REVERT: D 108 LYS cc_start: 0.9585 (OUTLIER) cc_final: 0.9323 (tppt) REVERT: D 258 TYR cc_start: 0.9207 (t80) cc_final: 0.8998 (t80) REVERT: D 275 SER cc_start: 0.9039 (t) cc_final: 0.8821 (t) REVERT: D 276 SER cc_start: 0.8710 (p) cc_final: 0.8504 (p) REVERT: D 285 ASN cc_start: 0.9443 (m-40) cc_final: 0.9075 (m-40) REVERT: D 312 ASN cc_start: 0.9061 (OUTLIER) cc_final: 0.8832 (t0) REVERT: D 352 GLU cc_start: 0.9161 (tm-30) cc_final: 0.8846 (tm-30) REVERT: D 355 ARG cc_start: 0.9600 (ptm-80) cc_final: 0.9288 (ptm-80) REVERT: D 385 MET cc_start: 0.8949 (ttm) cc_final: 0.8623 (ttp) REVERT: D 395 GLU cc_start: 0.8838 (mp0) cc_final: 0.8224 (mp0) REVERT: D 399 GLU cc_start: 0.9051 (pm20) cc_final: 0.8777 (pm20) REVERT: D 404 ASP cc_start: 0.9105 (t0) cc_final: 0.8809 (t0) REVERT: D 461 ILE cc_start: 0.9162 (pp) cc_final: 0.8957 (pp) REVERT: E 28 ASP cc_start: 0.8898 (m-30) cc_final: 0.8520 (m-30) REVERT: E 58 LYS cc_start: 0.9315 (mmtp) cc_final: 0.9011 (mmmm) REVERT: E 105 ARG cc_start: 0.9152 (mtm110) cc_final: 0.8905 (mtm110) REVERT: E 109 LYS cc_start: 0.9392 (mttp) cc_final: 0.8885 (tmtt) REVERT: E 274 ASP cc_start: 0.9097 (t0) cc_final: 0.8886 (t0) REVERT: E 276 SER cc_start: 0.8714 (p) cc_final: 0.8433 (p) REVERT: E 281 ILE cc_start: 0.8792 (tp) cc_final: 0.8082 (tt) REVERT: E 285 ASN cc_start: 0.9411 (m-40) cc_final: 0.9040 (m-40) REVERT: E 322 ARG cc_start: 0.8194 (ppp80) cc_final: 0.7895 (ptm160) REVERT: E 352 GLU cc_start: 0.9158 (tm-30) cc_final: 0.8927 (tm-30) REVERT: E 385 MET cc_start: 0.8872 (ttm) cc_final: 0.8652 (ttp) REVERT: E 386 MET cc_start: 0.9311 (mtm) cc_final: 0.8981 (mtm) REVERT: E 395 GLU cc_start: 0.8727 (mp0) cc_final: 0.8076 (mp0) REVERT: E 399 GLU cc_start: 0.8948 (pm20) cc_final: 0.8673 (pm20) REVERT: E 400 TYR cc_start: 0.8638 (m-80) cc_final: 0.7650 (m-10) REVERT: E 407 ARG cc_start: 0.9023 (ttt-90) cc_final: 0.8295 (ttt-90) REVERT: E 438 LYS cc_start: 0.8176 (mmtt) cc_final: 0.7881 (mttp) REVERT: E 512 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7516 (ttm-80) REVERT: F 28 ASP cc_start: 0.8869 (m-30) cc_final: 0.8505 (m-30) REVERT: F 47 ASP cc_start: 0.9159 (p0) cc_final: 0.8939 (p0) REVERT: F 105 ARG cc_start: 0.9230 (mtm110) cc_final: 0.8952 (mtm110) REVERT: F 108 LYS cc_start: 0.9582 (OUTLIER) cc_final: 0.9305 (tppt) REVERT: F 109 LYS cc_start: 0.9391 (mttp) cc_final: 0.9160 (mtmm) REVERT: F 274 ASP cc_start: 0.9032 (t0) cc_final: 0.8808 (t0) REVERT: F 276 SER cc_start: 0.8757 (p) cc_final: 0.8486 (p) REVERT: F 279 ASN cc_start: 0.8918 (t0) cc_final: 0.8679 (t0) REVERT: F 281 ILE cc_start: 0.8914 (tp) cc_final: 0.8596 (tt) REVERT: F 285 ASN cc_start: 0.9399 (m-40) cc_final: 0.9157 (m110) REVERT: F 322 ARG cc_start: 0.8108 (ppp80) cc_final: 0.7546 (ptm160) REVERT: F 352 GLU cc_start: 0.9148 (tm-30) cc_final: 0.8920 (tm-30) REVERT: F 385 MET cc_start: 0.8958 (ttm) cc_final: 0.8369 (ttp) REVERT: F 395 GLU cc_start: 0.8849 (mp0) cc_final: 0.8153 (mp0) REVERT: F 399 GLU cc_start: 0.9072 (pm20) cc_final: 0.8777 (pm20) REVERT: F 404 ASP cc_start: 0.9192 (t0) cc_final: 0.8942 (t0) REVERT: F 461 ILE cc_start: 0.9138 (pp) cc_final: 0.8938 (pp) REVERT: F 512 ARG cc_start: 0.7683 (ttm-80) cc_final: 0.7151 (ptm160) REVERT: G 28 ASP cc_start: 0.8958 (m-30) cc_final: 0.8671 (m-30) REVERT: G 50 ASP cc_start: 0.9015 (t70) cc_final: 0.8730 (t0) REVERT: G 51 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9094 (pp) REVERT: G 105 ARG cc_start: 0.9165 (mtm110) cc_final: 0.8528 (mtm110) REVERT: G 108 LYS cc_start: 0.9628 (OUTLIER) cc_final: 0.9335 (mttm) REVERT: G 109 LYS cc_start: 0.9344 (mttp) cc_final: 0.9119 (mttt) REVERT: G 275 SER cc_start: 0.8964 (t) cc_final: 0.8726 (t) REVERT: G 285 ASN cc_start: 0.9342 (m-40) cc_final: 0.8973 (m-40) REVERT: G 352 GLU cc_start: 0.9152 (tm-30) cc_final: 0.8922 (tm-30) REVERT: G 395 GLU cc_start: 0.8751 (mp0) cc_final: 0.8155 (mp0) REVERT: G 399 GLU cc_start: 0.9012 (pm20) cc_final: 0.8699 (pm20) REVERT: G 400 TYR cc_start: 0.8492 (m-80) cc_final: 0.8038 (m-80) REVERT: G 407 ARG cc_start: 0.8937 (ttt-90) cc_final: 0.8384 (ptm-80) REVERT: G 512 ARG cc_start: 0.7577 (ttm-80) cc_final: 0.7353 (ptm160) REVERT: H 25 ASN cc_start: 0.9114 (m-40) cc_final: 0.8856 (p0) REVERT: H 28 ASP cc_start: 0.8983 (m-30) cc_final: 0.8648 (m-30) REVERT: H 50 ASP cc_start: 0.9023 (t70) cc_final: 0.8709 (t0) REVERT: H 58 LYS cc_start: 0.9448 (mmtp) cc_final: 0.9178 (mmmm) REVERT: H 105 ARG cc_start: 0.9261 (mtm110) cc_final: 0.8784 (mtm110) REVERT: H 109 LYS cc_start: 0.9403 (mttp) cc_final: 0.9199 (mttt) REVERT: H 276 SER cc_start: 0.8672 (p) cc_final: 0.8379 (p) REVERT: H 285 ASN cc_start: 0.9464 (m-40) cc_final: 0.9210 (m-40) REVERT: H 352 GLU cc_start: 0.9284 (tm-30) cc_final: 0.9045 (tm-30) REVERT: H 395 GLU cc_start: 0.8739 (mp0) cc_final: 0.8236 (mp0) REVERT: H 399 GLU cc_start: 0.8983 (pm20) cc_final: 0.8744 (pm20) outliers start: 165 outliers final: 77 residues processed: 1111 average time/residue: 0.1472 time to fit residues: 256.1745 Evaluate side-chains 1018 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 934 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 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 235 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 108 LYS Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 282 PHE Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 282 PHE Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 282 PHE Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 245 LEU 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 406 ILE Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 146 optimal weight: 2.9990 chunk 152 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 262 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 248 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 22 GLN ** A 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN B 93 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN C 93 HIS ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN E 22 GLN E 93 HIS ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 ASN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 HIS ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN F 498 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 ASN ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN H 22 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.102483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.082023 restraints weight = 41762.038| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.89 r_work: 0.2776 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 23488 Z= 0.217 Angle : 0.714 7.538 31792 Z= 0.363 Chirality : 0.048 0.160 3656 Planarity : 0.005 0.045 4000 Dihedral : 9.932 89.817 3401 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 5.45 % Allowed : 21.22 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.14), residues: 2960 helix: -1.65 (0.14), residues: 1120 sheet: -2.29 (0.20), residues: 464 loop : -1.32 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 407 TYR 0.020 0.002 TYR H 400 PHE 0.012 0.001 PHE H 401 HIS 0.003 0.001 HIS H 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00509 / 0.22 (23480) covalent geometry : angle 0.71398 / 0.36 (31792) hydrogen bonds : bond 0.03957 / 2.58 ( 841) hydrogen bonds : angle 5.55249 / 3.79 ( 2427) Misc. bond : bond 0.00139 / 0.07 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 963 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8786 (m-30) cc_final: 0.8496 (m-30) REVERT: A 50 ASP cc_start: 0.9102 (t0) cc_final: 0.8839 (t0) REVERT: A 51 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9023 (pp) REVERT: A 66 VAL cc_start: 0.8285 (OUTLIER) cc_final: 0.8059 (p) REVERT: A 105 ARG cc_start: 0.9193 (mtm110) cc_final: 0.8700 (mtm110) REVERT: A 109 LYS cc_start: 0.9415 (mttp) cc_final: 0.9168 (mptt) REVERT: A 242 LYS cc_start: 0.8236 (mtpt) cc_final: 0.7990 (mttt) REVERT: A 258 TYR cc_start: 0.9093 (t80) cc_final: 0.8846 (t80) REVERT: A 276 SER cc_start: 0.9087 (p) cc_final: 0.8834 (p) REVERT: A 285 ASN cc_start: 0.9460 (m-40) cc_final: 0.9152 (m-40) REVERT: A 352 GLU cc_start: 0.9256 (tm-30) cc_final: 0.8998 (tm-30) REVERT: A 355 ARG cc_start: 0.9495 (ptm-80) cc_final: 0.9041 (ptm-80) REVERT: A 385 MET cc_start: 0.8975 (ttm) cc_final: 0.8708 (ttm) REVERT: A 395 GLU cc_start: 0.8871 (mp0) cc_final: 0.8123 (mp0) REVERT: A 400 TYR cc_start: 0.8551 (m-80) cc_final: 0.8095 (m-10) REVERT: A 404 ASP cc_start: 0.9182 (t0) cc_final: 0.8877 (t70) REVERT: A 407 ARG cc_start: 0.9007 (ttt-90) cc_final: 0.8252 (ttt-90) REVERT: A 438 LYS cc_start: 0.9006 (mttt) cc_final: 0.8538 (mmtt) REVERT: A 449 ASP cc_start: 0.9442 (p0) cc_final: 0.9168 (p0) REVERT: A 455 LYS cc_start: 0.9168 (mppt) cc_final: 0.8715 (mppt) REVERT: B 28 ASP cc_start: 0.8869 (m-30) cc_final: 0.8582 (m-30) REVERT: B 50 ASP cc_start: 0.9038 (t70) cc_final: 0.8825 (t0) REVERT: B 51 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9065 (pp) REVERT: B 66 VAL cc_start: 0.8471 (OUTLIER) cc_final: 0.8245 (p) REVERT: B 105 ARG cc_start: 0.9218 (mtm110) cc_final: 0.8751 (mtm110) REVERT: B 109 LYS cc_start: 0.9443 (mttp) cc_final: 0.9205 (mptt) REVERT: B 258 TYR cc_start: 0.9111 (t80) cc_final: 0.8887 (t80) REVERT: B 276 SER cc_start: 0.9094 (p) cc_final: 0.8838 (p) REVERT: B 281 ILE cc_start: 0.8965 (tp) cc_final: 0.8659 (tp) REVERT: B 285 ASN cc_start: 0.9451 (m-40) cc_final: 0.9228 (m-40) REVERT: B 352 GLU cc_start: 0.9255 (tm-30) cc_final: 0.9013 (tm-30) REVERT: B 395 GLU cc_start: 0.8918 (mp0) cc_final: 0.8356 (mp0) REVERT: B 399 GLU cc_start: 0.9066 (pm20) cc_final: 0.8841 (pm20) REVERT: B 404 ASP cc_start: 0.9173 (t0) cc_final: 0.8905 (t0) REVERT: B 438 LYS cc_start: 0.9007 (mtpt) cc_final: 0.8480 (mmtt) REVERT: C 28 ASP cc_start: 0.8830 (m-30) cc_final: 0.8530 (m-30) REVERT: C 50 ASP cc_start: 0.9128 (t70) cc_final: 0.8863 (t0) REVERT: C 51 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8937 (pp) REVERT: C 66 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.8078 (p) REVERT: C 105 ARG cc_start: 0.9163 (mtm110) cc_final: 0.8698 (mtm110) REVERT: C 109 LYS cc_start: 0.9402 (mttp) cc_final: 0.9146 (mptt) REVERT: C 258 TYR cc_start: 0.9070 (t80) cc_final: 0.8764 (t80) REVERT: C 276 SER cc_start: 0.8896 (p) cc_final: 0.8619 (p) REVERT: C 279 ASN cc_start: 0.9141 (t0) cc_final: 0.8053 (t0) REVERT: C 281 ILE cc_start: 0.9034 (OUTLIER) cc_final: 0.8809 (tt) REVERT: C 285 ASN cc_start: 0.9496 (m-40) cc_final: 0.9296 (m-40) REVERT: C 352 GLU cc_start: 0.9267 (tm-30) cc_final: 0.8995 (tm-30) REVERT: C 355 ARG cc_start: 0.9591 (ptm-80) cc_final: 0.9383 (ptm-80) REVERT: C 395 GLU cc_start: 0.8927 (mp0) cc_final: 0.8356 (mp0) REVERT: C 438 LYS cc_start: 0.9085 (mtpp) cc_final: 0.8614 (mmtt) REVERT: D 25 ASN cc_start: 0.9180 (m-40) cc_final: 0.8905 (p0) REVERT: D 28 ASP cc_start: 0.8832 (m-30) cc_final: 0.8521 (m-30) REVERT: D 51 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9008 (pp) REVERT: D 105 ARG cc_start: 0.9195 (mtm110) cc_final: 0.8848 (mtm110) REVERT: D 109 LYS cc_start: 0.9397 (mttt) cc_final: 0.9121 (mttt) REVERT: D 258 TYR cc_start: 0.9209 (t80) cc_final: 0.8982 (t80) REVERT: D 276 SER cc_start: 0.8934 (p) cc_final: 0.8655 (p) REVERT: D 285 ASN cc_start: 0.9452 (m-40) cc_final: 0.9194 (m-40) REVERT: D 332 ILE cc_start: 0.8976 (pp) cc_final: 0.8689 (pp) REVERT: D 352 GLU cc_start: 0.9242 (tm-30) cc_final: 0.8969 (tm-30) REVERT: D 385 MET cc_start: 0.8993 (ttm) cc_final: 0.8529 (ttm) REVERT: D 395 GLU cc_start: 0.8885 (mp0) cc_final: 0.8226 (mp0) REVERT: D 399 GLU cc_start: 0.8992 (pm20) cc_final: 0.8737 (pm20) REVERT: D 404 ASP cc_start: 0.9182 (t0) cc_final: 0.8907 (t0) REVERT: D 438 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8110 (mmtm) REVERT: E 28 ASP cc_start: 0.8858 (m-30) cc_final: 0.8539 (m-30) REVERT: E 51 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9121 (pp) REVERT: E 98 GLU cc_start: 0.9474 (mp0) cc_final: 0.9266 (mp0) REVERT: E 105 ARG cc_start: 0.9174 (mtm110) cc_final: 0.8919 (mtm110) REVERT: E 109 LYS cc_start: 0.9418 (mttp) cc_final: 0.8956 (tmtt) REVERT: E 258 TYR cc_start: 0.9088 (t80) cc_final: 0.8813 (t80) REVERT: E 274 ASP cc_start: 0.9096 (t0) cc_final: 0.8854 (t0) REVERT: E 276 SER cc_start: 0.8926 (p) cc_final: 0.8623 (p) REVERT: E 279 ASN cc_start: 0.9091 (t0) cc_final: 0.8049 (t0) REVERT: E 285 ASN cc_start: 0.9434 (m-40) cc_final: 0.9205 (m-40) REVERT: E 322 ARG cc_start: 0.8448 (ppp80) cc_final: 0.8162 (ptm160) REVERT: E 352 GLU cc_start: 0.9274 (tm-30) cc_final: 0.8997 (tm-30) REVERT: E 355 ARG cc_start: 0.9503 (ptm-80) cc_final: 0.9079 (ptm-80) REVERT: E 386 MET cc_start: 0.9253 (mtm) cc_final: 0.8774 (mtm) REVERT: E 395 GLU cc_start: 0.8809 (mp0) cc_final: 0.8207 (mp0) REVERT: E 399 GLU cc_start: 0.8966 (pm20) cc_final: 0.8682 (pm20) REVERT: E 400 TYR cc_start: 0.8485 (m-80) cc_final: 0.7695 (m-10) REVERT: E 407 ARG cc_start: 0.9115 (ttt-90) cc_final: 0.8602 (ttt-90) REVERT: F 28 ASP cc_start: 0.8918 (m-30) cc_final: 0.8629 (m-30) REVERT: F 51 LEU cc_start: 0.9207 (OUTLIER) cc_final: 0.8918 (pp) REVERT: F 80 ILE cc_start: 0.9299 (pp) cc_final: 0.9098 (pp) REVERT: F 108 LYS cc_start: 0.9503 (OUTLIER) cc_final: 0.9221 (mttm) REVERT: F 109 LYS cc_start: 0.9418 (mttp) cc_final: 0.9206 (mttm) REVERT: F 258 TYR cc_start: 0.9201 (t80) cc_final: 0.8976 (t80) REVERT: F 274 ASP cc_start: 0.9015 (t0) cc_final: 0.8763 (t0) REVERT: F 276 SER cc_start: 0.8926 (p) cc_final: 0.8633 (p) REVERT: F 281 ILE cc_start: 0.9015 (tp) cc_final: 0.8757 (tt) REVERT: F 285 ASN cc_start: 0.9444 (m-40) cc_final: 0.9185 (m-40) REVERT: F 322 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.7723 (ptm160) REVERT: F 352 GLU cc_start: 0.9244 (tm-30) cc_final: 0.9001 (tm-30) REVERT: F 355 ARG cc_start: 0.9499 (ptm-80) cc_final: 0.9183 (ptm-80) REVERT: F 385 MET cc_start: 0.8896 (ttm) cc_final: 0.8578 (ttp) REVERT: F 395 GLU cc_start: 0.8905 (mp0) cc_final: 0.8201 (mp0) REVERT: F 399 GLU cc_start: 0.8999 (pm20) cc_final: 0.8729 (pm20) REVERT: F 404 ASP cc_start: 0.9216 (t0) cc_final: 0.8979 (t0) REVERT: G 28 ASP cc_start: 0.8956 (m-30) cc_final: 0.8723 (m-30) REVERT: G 50 ASP cc_start: 0.9015 (t70) cc_final: 0.8711 (t0) REVERT: G 51 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9112 (pp) REVERT: G 105 ARG cc_start: 0.9047 (mtm110) cc_final: 0.8745 (mtm110) REVERT: G 108 LYS cc_start: 0.9550 (OUTLIER) cc_final: 0.9290 (mttm) REVERT: G 109 LYS cc_start: 0.9354 (mttp) cc_final: 0.9078 (mttm) REVERT: G 258 TYR cc_start: 0.9170 (t80) cc_final: 0.8949 (t80) REVERT: G 299 VAL cc_start: 0.9418 (m) cc_final: 0.9154 (p) REVERT: G 352 GLU cc_start: 0.9275 (tm-30) cc_final: 0.9041 (tm-30) REVERT: G 355 ARG cc_start: 0.9393 (ptm-80) cc_final: 0.9083 (ptm-80) REVERT: G 385 MET cc_start: 0.8871 (ttm) cc_final: 0.8374 (ttm) REVERT: G 395 GLU cc_start: 0.8824 (mp0) cc_final: 0.8196 (mp0) REVERT: G 399 GLU cc_start: 0.9083 (pm20) cc_final: 0.8785 (pm20) REVERT: G 400 TYR cc_start: 0.8399 (m-80) cc_final: 0.7942 (m-80) REVERT: G 407 ARG cc_start: 0.8855 (ttt-90) cc_final: 0.8253 (ptm-80) REVERT: G 449 ASP cc_start: 0.9322 (p0) cc_final: 0.9039 (p0) REVERT: G 510 GLU cc_start: 0.8063 (tp30) cc_final: 0.7825 (tp30) REVERT: H 28 ASP cc_start: 0.8946 (m-30) cc_final: 0.8694 (m-30) REVERT: H 50 ASP cc_start: 0.9087 (t70) cc_final: 0.8863 (t0) REVERT: H 51 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9023 (pp) REVERT: H 66 VAL cc_start: 0.8420 (OUTLIER) cc_final: 0.8024 (p) REVERT: H 68 SER cc_start: 0.9149 (t) cc_final: 0.8904 (t) REVERT: H 105 ARG cc_start: 0.9235 (mtm110) cc_final: 0.8862 (mtm110) REVERT: H 258 TYR cc_start: 0.9096 (t80) cc_final: 0.8864 (t80) REVERT: H 276 SER cc_start: 0.8855 (p) cc_final: 0.8614 (p) REVERT: H 285 ASN cc_start: 0.9453 (m-40) cc_final: 0.9191 (m-40) REVERT: H 352 GLU cc_start: 0.9303 (tm-30) cc_final: 0.9077 (tm-30) REVERT: H 395 GLU cc_start: 0.8803 (mp0) cc_final: 0.8155 (mp0) REVERT: H 399 GLU cc_start: 0.8913 (pm20) cc_final: 0.8658 (pm20) outliers start: 130 outliers final: 72 residues processed: 1011 average time/residue: 0.1436 time to fit residues: 228.5914 Evaluate side-chains 963 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 875 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 281 ILE Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 322 ARG Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 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 327 SER Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 347 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 290 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 chunk 225 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 280 optimal weight: 0.9990 chunk 219 optimal weight: 0.9980 chunk 229 optimal weight: 0.8980 chunk 228 optimal weight: 0.6980 chunk 214 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 265 GLN D 303 ASN D 312 ASN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 ASN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 ASN ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 498 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.106560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.085645 restraints weight = 41507.080| |-----------------------------------------------------------------------------| r_work (start): 0.2976 rms_B_bonded: 3.96 r_work: 0.2815 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23488 Z= 0.148 Angle : 0.666 8.543 31792 Z= 0.336 Chirality : 0.046 0.155 3656 Planarity : 0.004 0.040 4000 Dihedral : 9.480 89.837 3370 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.54 % Allowed : 22.73 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.14), residues: 2960 helix: -1.33 (0.15), residues: 1120 sheet: -2.14 (0.21), residues: 464 loop : -1.16 (0.16), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 407 TYR 0.017 0.001 TYR H 400 PHE 0.015 0.001 PHE B 401 HIS 0.003 0.001 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.15 (23480) covalent geometry : angle 0.66632 / 0.34 (31792) hydrogen bonds : bond 0.03528 / 2.30 ( 841) hydrogen bonds : angle 5.36914 / 3.66 ( 2427) Misc. bond : bond 0.00080 / 0.04 ( 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: 132 poor density : 978 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8740 (m-30) cc_final: 0.8495 (m-30) REVERT: A 50 ASP cc_start: 0.9103 (t0) cc_final: 0.8898 (t0) REVERT: A 66 VAL cc_start: 0.8318 (OUTLIER) cc_final: 0.8108 (p) REVERT: A 105 ARG cc_start: 0.9192 (mtm110) cc_final: 0.8676 (mtm110) REVERT: A 109 LYS cc_start: 0.9423 (mttp) cc_final: 0.9183 (mptt) REVERT: A 258 TYR cc_start: 0.9112 (t80) cc_final: 0.8860 (t80) REVERT: A 276 SER cc_start: 0.9055 (p) cc_final: 0.8807 (p) REVERT: A 285 ASN cc_start: 0.9471 (m-40) cc_final: 0.9252 (m-40) REVERT: A 352 GLU cc_start: 0.9221 (tm-30) cc_final: 0.8965 (tm-30) REVERT: A 385 MET cc_start: 0.8983 (ttm) cc_final: 0.8593 (ttm) REVERT: A 395 GLU cc_start: 0.8848 (mp0) cc_final: 0.8250 (mp0) REVERT: A 399 GLU cc_start: 0.8896 (pm20) cc_final: 0.8683 (mp0) REVERT: A 400 TYR cc_start: 0.8367 (m-80) cc_final: 0.7554 (m-10) REVERT: A 404 ASP cc_start: 0.9193 (t0) cc_final: 0.8899 (t70) REVERT: A 407 ARG cc_start: 0.8968 (ttt-90) cc_final: 0.8594 (ttt-90) REVERT: A 438 LYS cc_start: 0.8991 (mttt) cc_final: 0.8530 (mmtt) REVERT: A 455 LYS cc_start: 0.9185 (mppt) cc_final: 0.8758 (mppt) REVERT: B 25 ASN cc_start: 0.9043 (m-40) cc_final: 0.8760 (p0) REVERT: B 28 ASP cc_start: 0.8791 (m-30) cc_final: 0.8533 (m-30) REVERT: B 50 ASP cc_start: 0.9029 (t70) cc_final: 0.8736 (t0) REVERT: B 51 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9013 (pp) REVERT: B 66 VAL cc_start: 0.8260 (OUTLIER) cc_final: 0.7937 (p) REVERT: B 105 ARG cc_start: 0.9212 (mtm110) cc_final: 0.8740 (mtm110) REVERT: B 109 LYS cc_start: 0.9446 (mttp) cc_final: 0.9216 (mptt) REVERT: B 258 TYR cc_start: 0.9105 (t80) cc_final: 0.8807 (t80) REVERT: B 276 SER cc_start: 0.9050 (p) cc_final: 0.8794 (p) REVERT: B 285 ASN cc_start: 0.9446 (m-40) cc_final: 0.9217 (m-40) REVERT: B 352 GLU cc_start: 0.9220 (tm-30) cc_final: 0.8989 (tm-30) REVERT: B 385 MET cc_start: 0.8962 (ttm) cc_final: 0.8342 (ttm) REVERT: B 395 GLU cc_start: 0.8831 (mp0) cc_final: 0.8250 (mp0) REVERT: B 399 GLU cc_start: 0.9082 (pm20) cc_final: 0.8824 (pm20) REVERT: B 404 ASP cc_start: 0.9193 (t0) cc_final: 0.8906 (t0) REVERT: B 438 LYS cc_start: 0.9081 (mtpt) cc_final: 0.8530 (mmtt) REVERT: C 28 ASP cc_start: 0.8747 (m-30) cc_final: 0.8491 (m-30) REVERT: C 50 ASP cc_start: 0.9154 (t70) cc_final: 0.8880 (t0) REVERT: C 51 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9016 (pp) REVERT: C 66 VAL cc_start: 0.8205 (OUTLIER) cc_final: 0.7820 (p) REVERT: C 75 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8178 (mm-30) REVERT: C 105 ARG cc_start: 0.9166 (mtm110) cc_final: 0.8679 (mtm110) REVERT: C 109 LYS cc_start: 0.9423 (mttp) cc_final: 0.9159 (mptt) REVERT: C 258 TYR cc_start: 0.9081 (t80) cc_final: 0.8754 (t80) REVERT: C 276 SER cc_start: 0.8790 (p) cc_final: 0.8505 (p) REVERT: C 279 ASN cc_start: 0.9192 (t0) cc_final: 0.8916 (t0) REVERT: C 352 GLU cc_start: 0.9230 (tm-30) cc_final: 0.8950 (tm-30) REVERT: C 355 ARG cc_start: 0.9536 (ptm-80) cc_final: 0.9319 (ptm-80) REVERT: C 395 GLU cc_start: 0.8887 (mp0) cc_final: 0.8353 (mp0) REVERT: C 400 TYR cc_start: 0.8255 (m-10) cc_final: 0.7918 (m-10) REVERT: C 409 LYS cc_start: 0.8765 (ttmp) cc_final: 0.8233 (tttt) REVERT: C 438 LYS cc_start: 0.9111 (mtpp) cc_final: 0.8616 (mmtt) REVERT: C 510 GLU cc_start: 0.8095 (tp30) cc_final: 0.7798 (tp30) REVERT: C 512 ARG cc_start: 0.7889 (ttm-80) cc_final: 0.7601 (ptm160) REVERT: D 25 ASN cc_start: 0.9220 (m-40) cc_final: 0.8968 (p0) REVERT: D 28 ASP cc_start: 0.8793 (m-30) cc_final: 0.8528 (m-30) REVERT: D 51 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9085 (pp) REVERT: D 61 LEU cc_start: 0.9148 (mt) cc_final: 0.8927 (mp) REVERT: D 105 ARG cc_start: 0.9267 (mtm110) cc_final: 0.8919 (mtm110) REVERT: D 109 LYS cc_start: 0.9425 (mttt) cc_final: 0.9219 (mttt) REVERT: D 258 TYR cc_start: 0.9192 (t80) cc_final: 0.8861 (t80) REVERT: D 276 SER cc_start: 0.8892 (p) cc_final: 0.8618 (p) REVERT: D 285 ASN cc_start: 0.9464 (m-40) cc_final: 0.9236 (m-40) REVERT: D 332 ILE cc_start: 0.8949 (pp) cc_final: 0.8669 (pp) REVERT: D 352 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8913 (tm-30) REVERT: D 355 ARG cc_start: 0.9299 (ptm-80) cc_final: 0.9086 (ptm-80) REVERT: D 385 MET cc_start: 0.9047 (ttm) cc_final: 0.8820 (ttp) REVERT: D 395 GLU cc_start: 0.8867 (mp0) cc_final: 0.8233 (mp0) REVERT: D 399 GLU cc_start: 0.8947 (pm20) cc_final: 0.8633 (pm20) REVERT: D 404 ASP cc_start: 0.9215 (t0) cc_final: 0.8952 (t0) REVERT: D 409 LYS cc_start: 0.8712 (ttmp) cc_final: 0.7999 (tttt) REVERT: D 438 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8168 (mmtm) REVERT: E 28 ASP cc_start: 0.8828 (m-30) cc_final: 0.8549 (m-30) REVERT: E 78 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.8498 (ptm) REVERT: E 105 ARG cc_start: 0.9162 (mtm110) cc_final: 0.8660 (mtm110) REVERT: E 109 LYS cc_start: 0.9421 (mttp) cc_final: 0.9167 (mptt) REVERT: E 258 TYR cc_start: 0.9092 (t80) cc_final: 0.8827 (t80) REVERT: E 274 ASP cc_start: 0.9138 (t0) cc_final: 0.8843 (t0) REVERT: E 276 SER cc_start: 0.8864 (p) cc_final: 0.8569 (p) REVERT: E 279 ASN cc_start: 0.9133 (t0) cc_final: 0.8879 (t0) REVERT: E 285 ASN cc_start: 0.9444 (m-40) cc_final: 0.9238 (m-40) REVERT: E 352 GLU cc_start: 0.9237 (tm-30) cc_final: 0.8986 (tm-30) REVERT: E 395 GLU cc_start: 0.8861 (mp0) cc_final: 0.8264 (mp0) REVERT: E 399 GLU cc_start: 0.8982 (pm20) cc_final: 0.8701 (pm20) REVERT: F 28 ASP cc_start: 0.8889 (m-30) cc_final: 0.8637 (m-30) REVERT: F 51 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8837 (pp) REVERT: F 105 ARG cc_start: 0.9205 (mtm110) cc_final: 0.8980 (mtm110) REVERT: F 108 LYS cc_start: 0.9491 (OUTLIER) cc_final: 0.9130 (tppt) REVERT: F 274 ASP cc_start: 0.9051 (t0) cc_final: 0.8815 (t0) REVERT: F 276 SER cc_start: 0.8844 (p) cc_final: 0.8548 (p) REVERT: F 279 ASN cc_start: 0.9013 (t0) cc_final: 0.8208 (t0) REVERT: F 281 ILE cc_start: 0.9027 (tp) cc_final: 0.8730 (tt) REVERT: F 285 ASN cc_start: 0.9444 (m-40) cc_final: 0.9172 (m-40) REVERT: F 332 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8553 (pp) REVERT: F 352 GLU cc_start: 0.9222 (tm-30) cc_final: 0.8963 (tm-30) REVERT: F 355 ARG cc_start: 0.9441 (ptm-80) cc_final: 0.9115 (ptm-80) REVERT: F 385 MET cc_start: 0.8918 (ttm) cc_final: 0.8472 (ttm) REVERT: F 393 THR cc_start: 0.9205 (p) cc_final: 0.8379 (p) REVERT: F 395 GLU cc_start: 0.8898 (mp0) cc_final: 0.8113 (mp0) REVERT: F 399 GLU cc_start: 0.8974 (pm20) cc_final: 0.8767 (pm20) REVERT: F 404 ASP cc_start: 0.9224 (t0) cc_final: 0.8990 (t70) REVERT: F 407 ARG cc_start: 0.8981 (ttt90) cc_final: 0.8677 (ttt90) REVERT: F 409 LYS cc_start: 0.8725 (ttmp) cc_final: 0.8053 (tttt) REVERT: G 21 GLN cc_start: 0.8993 (pt0) cc_final: 0.8531 (tm-30) REVERT: G 50 ASP cc_start: 0.9115 (t70) cc_final: 0.8843 (t0) REVERT: G 51 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8860 (pp) REVERT: G 108 LYS cc_start: 0.9568 (OUTLIER) cc_final: 0.9275 (mttm) REVERT: G 109 LYS cc_start: 0.9364 (mttp) cc_final: 0.9071 (mttm) REVERT: G 256 ASP cc_start: 0.9316 (m-30) cc_final: 0.8929 (p0) REVERT: G 258 TYR cc_start: 0.9152 (t80) cc_final: 0.8880 (t80) REVERT: G 279 ASN cc_start: 0.8986 (t0) cc_final: 0.8380 (t0) REVERT: G 299 VAL cc_start: 0.9413 (m) cc_final: 0.9184 (p) REVERT: G 352 GLU cc_start: 0.9226 (tm-30) cc_final: 0.9011 (tm-30) REVERT: G 385 MET cc_start: 0.8833 (ttm) cc_final: 0.8352 (ttm) REVERT: G 395 GLU cc_start: 0.8844 (mp0) cc_final: 0.8266 (mp0) REVERT: G 399 GLU cc_start: 0.9083 (pm20) cc_final: 0.8793 (pm20) REVERT: G 400 TYR cc_start: 0.8366 (m-80) cc_final: 0.7885 (m-80) REVERT: G 407 ARG cc_start: 0.8948 (ttt-90) cc_final: 0.8616 (ptm-80) REVERT: H 25 ASN cc_start: 0.9040 (m-40) cc_final: 0.8759 (p0) REVERT: H 28 ASP cc_start: 0.8908 (m-30) cc_final: 0.8659 (m-30) REVERT: H 51 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8870 (pp) REVERT: H 66 VAL cc_start: 0.8162 (OUTLIER) cc_final: 0.7842 (p) REVERT: H 105 ARG cc_start: 0.9179 (mtm110) cc_final: 0.8873 (mtm110) REVERT: H 258 TYR cc_start: 0.9092 (t80) cc_final: 0.8822 (t80) REVERT: H 276 SER cc_start: 0.8886 (p) cc_final: 0.8581 (p) REVERT: H 285 ASN cc_start: 0.9446 (m-40) cc_final: 0.9194 (m-40) REVERT: H 352 GLU cc_start: 0.9256 (tm-30) cc_final: 0.9025 (tm-30) REVERT: H 385 MET cc_start: 0.8838 (ttm) cc_final: 0.8409 (ttm) REVERT: H 395 GLU cc_start: 0.8814 (mp0) cc_final: 0.8242 (mp0) REVERT: H 399 GLU cc_start: 0.8922 (pm20) cc_final: 0.8676 (pm20) REVERT: H 512 ARG cc_start: 0.7961 (ttm-80) cc_final: 0.7470 (ptm160) outliers start: 132 outliers final: 70 residues processed: 1032 average time/residue: 0.1426 time to fit residues: 232.7560 Evaluate side-chains 996 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 912 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 313 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 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 297 LEU Chi-restraints excluded: chain H residue 313 LEU Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 282 optimal weight: 0.9980 chunk 142 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 261 optimal weight: 0.0060 chunk 173 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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 = 0.3317 r_free = 0.3317 target = 0.105313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.084240 restraints weight = 41375.410| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 3.99 r_work: 0.2801 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23488 Z= 0.164 Angle : 0.674 8.418 31792 Z= 0.340 Chirality : 0.047 0.154 3656 Planarity : 0.004 0.039 4000 Dihedral : 9.123 89.834 3359 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 5.79 % Allowed : 23.99 % Favored : 70.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.08 (0.15), residues: 2960 helix: -1.18 (0.15), residues: 1120 sheet: -2.05 (0.20), residues: 480 loop : -1.12 (0.16), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 105 TYR 0.014 0.001 TYR G 353 PHE 0.012 0.001 PHE H 401 HIS 0.003 0.000 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (23480) covalent geometry : angle 0.67364 / 0.34 (31792) hydrogen bonds : bond 0.03477 / 2.28 ( 841) hydrogen bonds : angle 5.30471 / 3.62 ( 2427) Misc. bond : bond 0.00092 / 0.04 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1098 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 960 time to evaluate : 0.630 Fit side-chains revert: symmetry clash REVERT: A 50 ASP cc_start: 0.9111 (t0) cc_final: 0.8864 (t0) REVERT: A 51 LEU cc_start: 0.9379 (OUTLIER) cc_final: 0.9055 (pp) REVERT: A 66 VAL cc_start: 0.8249 (OUTLIER) cc_final: 0.7954 (p) REVERT: A 105 ARG cc_start: 0.9167 (mtm110) cc_final: 0.8664 (mtm110) REVERT: A 109 LYS cc_start: 0.9437 (mttp) cc_final: 0.9183 (mptt) REVERT: A 258 TYR cc_start: 0.9124 (t80) cc_final: 0.8915 (t80) REVERT: A 276 SER cc_start: 0.9038 (p) cc_final: 0.8788 (p) REVERT: A 285 ASN cc_start: 0.9472 (m-40) cc_final: 0.9249 (m-40) REVERT: A 352 GLU cc_start: 0.9232 (tm-30) cc_final: 0.8996 (tm-30) REVERT: A 385 MET cc_start: 0.8949 (ttm) cc_final: 0.8534 (ttm) REVERT: A 395 GLU cc_start: 0.8886 (mp0) cc_final: 0.8312 (mp0) REVERT: A 404 ASP cc_start: 0.9238 (t0) cc_final: 0.8946 (t70) REVERT: A 438 LYS cc_start: 0.9027 (mttt) cc_final: 0.8535 (mmtt) REVERT: B 28 ASP cc_start: 0.8775 (m-30) cc_final: 0.8568 (m-30) REVERT: B 50 ASP cc_start: 0.9063 (t70) cc_final: 0.8819 (t0) REVERT: B 51 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9000 (pp) REVERT: B 105 ARG cc_start: 0.9227 (mtm110) cc_final: 0.8779 (mtm110) REVERT: B 258 TYR cc_start: 0.9103 (t80) cc_final: 0.8835 (t80) REVERT: B 276 SER cc_start: 0.9044 (p) cc_final: 0.8801 (p) REVERT: B 285 ASN cc_start: 0.9454 (m-40) cc_final: 0.9227 (m-40) REVERT: B 332 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8737 (pp) REVERT: B 352 GLU cc_start: 0.9236 (tm-30) cc_final: 0.9016 (tm-30) REVERT: B 385 MET cc_start: 0.8964 (ttm) cc_final: 0.8378 (ttm) REVERT: B 395 GLU cc_start: 0.8865 (mp0) cc_final: 0.8288 (mp0) REVERT: B 399 GLU cc_start: 0.8992 (pm20) cc_final: 0.8770 (pm20) REVERT: B 404 ASP cc_start: 0.9236 (t0) cc_final: 0.8993 (t0) REVERT: B 438 LYS cc_start: 0.9106 (mtpt) cc_final: 0.8544 (mmtt) REVERT: C 50 ASP cc_start: 0.9194 (t70) cc_final: 0.8931 (t0) REVERT: C 51 LEU cc_start: 0.9314 (OUTLIER) cc_final: 0.9047 (pp) REVERT: C 66 VAL cc_start: 0.8079 (OUTLIER) cc_final: 0.6987 (t) REVERT: C 105 ARG cc_start: 0.9169 (mtm110) cc_final: 0.8689 (mtm110) REVERT: C 109 LYS cc_start: 0.9437 (mttp) cc_final: 0.9174 (mptt) REVERT: C 258 TYR cc_start: 0.9062 (t80) cc_final: 0.8716 (t80) REVERT: C 276 SER cc_start: 0.8818 (p) cc_final: 0.8539 (p) REVERT: C 279 ASN cc_start: 0.9266 (t0) cc_final: 0.8268 (t0) REVERT: C 332 ILE cc_start: 0.8991 (OUTLIER) cc_final: 0.8734 (pp) REVERT: C 352 GLU cc_start: 0.9215 (tm-30) cc_final: 0.8929 (tm-30) REVERT: C 355 ARG cc_start: 0.9518 (ptm-80) cc_final: 0.9278 (ptm-80) REVERT: C 385 MET cc_start: 0.9047 (ttm) cc_final: 0.8636 (ttm) REVERT: C 395 GLU cc_start: 0.8936 (mp0) cc_final: 0.8376 (mp0) REVERT: C 407 ARG cc_start: 0.8997 (ttt90) cc_final: 0.8779 (ttt90) REVERT: C 409 LYS cc_start: 0.8793 (ttmp) cc_final: 0.8514 (ttmt) REVERT: C 438 LYS cc_start: 0.9181 (mtpp) cc_final: 0.8677 (mmtt) REVERT: C 510 GLU cc_start: 0.8117 (tp30) cc_final: 0.7827 (tp30) REVERT: D 25 ASN cc_start: 0.9236 (m-40) cc_final: 0.8977 (p0) REVERT: D 28 ASP cc_start: 0.8786 (m-30) cc_final: 0.8577 (m-30) REVERT: D 51 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9057 (pp) REVERT: D 80 ILE cc_start: 0.9277 (pp) cc_final: 0.9075 (pp) REVERT: D 84 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8240 (mm) REVERT: D 105 ARG cc_start: 0.9271 (mtm110) cc_final: 0.8715 (mtm110) REVERT: D 109 LYS cc_start: 0.9470 (mttt) cc_final: 0.9103 (mttt) REVERT: D 258 TYR cc_start: 0.9205 (t80) cc_final: 0.8958 (t80) REVERT: D 276 SER cc_start: 0.8948 (p) cc_final: 0.8709 (p) REVERT: D 279 ASN cc_start: 0.8009 (m-40) cc_final: 0.7762 (m110) REVERT: D 285 ASN cc_start: 0.9472 (m-40) cc_final: 0.9238 (m-40) REVERT: D 332 ILE cc_start: 0.8990 (OUTLIER) cc_final: 0.8719 (pp) REVERT: D 352 GLU cc_start: 0.9203 (tm-30) cc_final: 0.8934 (tm-30) REVERT: D 385 MET cc_start: 0.8997 (ttm) cc_final: 0.8768 (ttp) REVERT: D 395 GLU cc_start: 0.8907 (mp0) cc_final: 0.8245 (mp0) REVERT: D 399 GLU cc_start: 0.9078 (pm20) cc_final: 0.8716 (mp0) REVERT: D 400 TYR cc_start: 0.8392 (m-10) cc_final: 0.7983 (m-10) REVERT: D 404 ASP cc_start: 0.9226 (t0) cc_final: 0.8976 (t0) REVERT: D 407 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8566 (ttt90) REVERT: D 409 LYS cc_start: 0.8780 (ttmp) cc_final: 0.8317 (tttt) REVERT: E 28 ASP cc_start: 0.8815 (m-30) cc_final: 0.8595 (m-30) REVERT: E 51 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8804 (pp) REVERT: E 105 ARG cc_start: 0.9175 (mtm110) cc_final: 0.8677 (mtm110) REVERT: E 109 LYS cc_start: 0.9439 (mttp) cc_final: 0.9187 (mptt) REVERT: E 274 ASP cc_start: 0.9119 (t0) cc_final: 0.8886 (t0) REVERT: E 276 SER cc_start: 0.8869 (p) cc_final: 0.8580 (p) REVERT: E 279 ASN cc_start: 0.9194 (t0) cc_final: 0.8186 (t0) REVERT: E 285 ASN cc_start: 0.9452 (m-40) cc_final: 0.9235 (m-40) REVERT: E 332 ILE cc_start: 0.8933 (OUTLIER) cc_final: 0.8710 (pp) REVERT: E 352 GLU cc_start: 0.9246 (tm-30) cc_final: 0.9008 (tm-30) REVERT: E 395 GLU cc_start: 0.8877 (mp0) cc_final: 0.8337 (mp0) REVERT: E 399 GLU cc_start: 0.8963 (pm20) cc_final: 0.8723 (pm20) REVERT: E 400 TYR cc_start: 0.8281 (m-10) cc_final: 0.7442 (m-10) REVERT: E 407 ARG cc_start: 0.9112 (ttt-90) cc_final: 0.8592 (ttt-90) REVERT: F 51 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.8957 (pp) REVERT: F 70 MET cc_start: 0.9158 (mpp) cc_final: 0.8895 (mpp) REVERT: F 105 ARG cc_start: 0.9154 (mtm110) cc_final: 0.8922 (mtm110) REVERT: F 108 LYS cc_start: 0.9548 (OUTLIER) cc_final: 0.9259 (tppt) REVERT: F 109 LYS cc_start: 0.9467 (mptt) cc_final: 0.9142 (mttm) REVERT: F 274 ASP cc_start: 0.9093 (t0) cc_final: 0.8870 (t0) REVERT: F 276 SER cc_start: 0.8828 (p) cc_final: 0.8544 (p) REVERT: F 279 ASN cc_start: 0.9068 (t0) cc_final: 0.8253 (t0) REVERT: F 285 ASN cc_start: 0.9458 (m-40) cc_final: 0.9218 (m-40) REVERT: F 332 ILE cc_start: 0.8796 (OUTLIER) cc_final: 0.8564 (pp) REVERT: F 352 GLU cc_start: 0.9222 (tm-30) cc_final: 0.8984 (tm-30) REVERT: F 355 ARG cc_start: 0.9431 (ptm-80) cc_final: 0.9121 (ptm-80) REVERT: F 385 MET cc_start: 0.9032 (ttm) cc_final: 0.8440 (ttm) REVERT: F 393 THR cc_start: 0.9245 (p) cc_final: 0.8355 (p) REVERT: F 395 GLU cc_start: 0.8927 (mp0) cc_final: 0.8090 (mp0) REVERT: F 399 GLU cc_start: 0.9062 (pm20) cc_final: 0.8838 (pm20) REVERT: F 404 ASP cc_start: 0.9245 (t0) cc_final: 0.8999 (t70) REVERT: F 409 LYS cc_start: 0.8774 (ttmp) cc_final: 0.8139 (tttt) REVERT: G 21 GLN cc_start: 0.9073 (pt0) cc_final: 0.8697 (tm-30) REVERT: G 50 ASP cc_start: 0.9110 (t70) cc_final: 0.8839 (t0) REVERT: G 51 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8939 (pp) REVERT: G 258 TYR cc_start: 0.9153 (t80) cc_final: 0.8832 (t80) REVERT: G 279 ASN cc_start: 0.9043 (t0) cc_final: 0.8427 (t0) REVERT: G 299 VAL cc_start: 0.9402 (m) cc_final: 0.9163 (p) REVERT: G 332 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8773 (pp) REVERT: G 352 GLU cc_start: 0.9204 (tm-30) cc_final: 0.8936 (tm-30) REVERT: G 355 ARG cc_start: 0.9245 (ptm-80) cc_final: 0.8940 (ptm-80) REVERT: G 385 MET cc_start: 0.8947 (ttm) cc_final: 0.8438 (ttm) REVERT: G 395 GLU cc_start: 0.8841 (mp0) cc_final: 0.8333 (mp0) REVERT: G 399 GLU cc_start: 0.9122 (pm20) cc_final: 0.8840 (pm20) REVERT: G 400 TYR cc_start: 0.8399 (m-80) cc_final: 0.7858 (m-80) REVERT: G 407 ARG cc_start: 0.9072 (ttt-90) cc_final: 0.8522 (ptm-80) REVERT: H 25 ASN cc_start: 0.9082 (m-40) cc_final: 0.8764 (p0) REVERT: H 28 ASP cc_start: 0.8902 (m-30) cc_final: 0.8696 (m-30) REVERT: H 51 LEU cc_start: 0.9180 (OUTLIER) cc_final: 0.8817 (pp) REVERT: H 66 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7905 (p) REVERT: H 105 ARG cc_start: 0.9196 (mtm110) cc_final: 0.8855 (mtm110) REVERT: H 258 TYR cc_start: 0.9106 (t80) cc_final: 0.8806 (t80) REVERT: H 276 SER cc_start: 0.8969 (p) cc_final: 0.8695 (p) REVERT: H 285 ASN cc_start: 0.9458 (m-40) cc_final: 0.9194 (m-40) REVERT: H 332 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8775 (pp) REVERT: H 352 GLU cc_start: 0.9260 (tm-30) cc_final: 0.9032 (tm-30) REVERT: H 355 ARG cc_start: 0.9199 (ptm-80) cc_final: 0.8911 (ptm-80) REVERT: H 385 MET cc_start: 0.8975 (ttm) cc_final: 0.8514 (ttm) REVERT: H 395 GLU cc_start: 0.8862 (mp0) cc_final: 0.8290 (mp0) REVERT: H 410 LYS cc_start: 0.8692 (ptmt) cc_final: 0.8387 (ptmt) outliers start: 138 outliers final: 87 residues processed: 1015 average time/residue: 0.1368 time to fit residues: 220.1575 Evaluate side-chains 1027 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 919 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 250 ILE 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 332 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 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 84 LEU 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 297 LEU Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 407 ARG Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 332 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 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 82 MET Chi-restraints excluded: chain H residue 250 ILE 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 147 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 191 optimal weight: 0.5980 chunk 223 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 269 optimal weight: 0.7980 chunk 242 optimal weight: 4.9990 chunk 277 optimal weight: 0.0060 chunk 104 optimal weight: 0.4980 chunk 41 optimal weight: 4.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN B 312 ASN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 ASN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 ASN ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.106663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.085459 restraints weight = 41465.552| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 4.01 r_work: 0.2818 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23488 Z= 0.149 Angle : 0.672 8.444 31792 Z= 0.339 Chirality : 0.046 0.166 3656 Planarity : 0.004 0.044 4000 Dihedral : 8.822 89.486 3353 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 6.04 % Allowed : 25.29 % Favored : 68.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.15), residues: 2960 helix: -1.13 (0.15), residues: 1120 sheet: -1.86 (0.21), residues: 464 loop : -1.08 (0.17), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 105 TYR 0.019 0.001 TYR A 400 PHE 0.012 0.001 PHE E 401 HIS 0.002 0.000 HIS D 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (23480) covalent geometry : angle 0.67225 / 0.34 (31792) hydrogen bonds : bond 0.03345 / 2.18 ( 841) hydrogen bonds : angle 5.20444 / 3.55 ( 2427) Misc. bond : bond 0.00079 / 0.04 ( 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 1133 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 989 time to evaluate : 0.880 Fit side-chains REVERT: A 50 ASP cc_start: 0.9136 (t0) cc_final: 0.8836 (t0) REVERT: A 51 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9061 (pp) REVERT: A 105 ARG cc_start: 0.9140 (mtm110) cc_final: 0.8641 (mtm110) REVERT: A 109 LYS cc_start: 0.9438 (mttp) cc_final: 0.9187 (mptt) REVERT: A 258 TYR cc_start: 0.9153 (t80) cc_final: 0.8942 (t80) REVERT: A 276 SER cc_start: 0.9005 (p) cc_final: 0.8753 (p) REVERT: A 285 ASN cc_start: 0.9485 (m-40) cc_final: 0.9257 (m-40) REVERT: A 352 GLU cc_start: 0.9196 (tm-30) cc_final: 0.8947 (tm-30) REVERT: A 385 MET cc_start: 0.8933 (ttm) cc_final: 0.8571 (ttm) REVERT: A 395 GLU cc_start: 0.8909 (mp0) cc_final: 0.8312 (mp0) REVERT: A 404 ASP cc_start: 0.9247 (t0) cc_final: 0.8950 (t70) REVERT: A 406 ILE cc_start: 0.9076 (mp) cc_final: 0.8806 (mp) REVERT: A 438 LYS cc_start: 0.9097 (mttt) cc_final: 0.8569 (mmtt) REVERT: B 25 ASN cc_start: 0.9090 (m-40) cc_final: 0.8772 (p0) REVERT: B 50 ASP cc_start: 0.9049 (t70) cc_final: 0.8792 (t0) REVERT: B 51 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8967 (pp) REVERT: B 105 ARG cc_start: 0.9157 (mtm110) cc_final: 0.8864 (mtm110) REVERT: B 258 TYR cc_start: 0.9102 (t80) cc_final: 0.8874 (t80) REVERT: B 276 SER cc_start: 0.9032 (p) cc_final: 0.8776 (p) REVERT: B 285 ASN cc_start: 0.9462 (m-40) cc_final: 0.9224 (m-40) REVERT: B 332 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8692 (pp) REVERT: B 352 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8990 (tm-30) REVERT: B 385 MET cc_start: 0.8901 (ttm) cc_final: 0.8422 (ttm) REVERT: B 395 GLU cc_start: 0.8888 (mp0) cc_final: 0.8286 (mp0) REVERT: B 400 TYR cc_start: 0.8309 (m-10) cc_final: 0.7819 (m-10) REVERT: B 404 ASP cc_start: 0.9259 (t0) cc_final: 0.9025 (t0) REVERT: B 407 ARG cc_start: 0.8928 (ttt90) cc_final: 0.8559 (ttt90) REVERT: B 410 LYS cc_start: 0.8695 (ptmt) cc_final: 0.8402 (ptmt) REVERT: B 438 LYS cc_start: 0.9130 (mtpt) cc_final: 0.8456 (mmtm) REVERT: C 50 ASP cc_start: 0.9192 (t70) cc_final: 0.8896 (t0) REVERT: C 51 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9066 (pp) REVERT: C 66 VAL cc_start: 0.7904 (OUTLIER) cc_final: 0.6913 (t) REVERT: C 105 ARG cc_start: 0.9106 (mtm110) cc_final: 0.8606 (mtm110) REVERT: C 109 LYS cc_start: 0.9452 (mttp) cc_final: 0.9164 (mptt) REVERT: C 256 ASP cc_start: 0.9262 (m-30) cc_final: 0.8766 (p0) REVERT: C 258 TYR cc_start: 0.9088 (t80) cc_final: 0.8773 (t80) REVERT: C 276 SER cc_start: 0.8698 (p) cc_final: 0.8406 (p) REVERT: C 279 ASN cc_start: 0.9261 (t0) cc_final: 0.8268 (t0) REVERT: C 352 GLU cc_start: 0.9194 (tm-30) cc_final: 0.8893 (tm-30) REVERT: C 355 ARG cc_start: 0.9496 (ptm-80) cc_final: 0.9249 (ptm-80) REVERT: C 385 MET cc_start: 0.9041 (ttm) cc_final: 0.8593 (ttm) REVERT: C 395 GLU cc_start: 0.8937 (mp0) cc_final: 0.8248 (mp0) REVERT: C 409 LYS cc_start: 0.8804 (ttmp) cc_final: 0.8542 (ttmt) REVERT: C 438 LYS cc_start: 0.9171 (mtpp) cc_final: 0.8692 (mmtt) REVERT: C 510 GLU cc_start: 0.8152 (tp30) cc_final: 0.7867 (tp30) REVERT: D 25 ASN cc_start: 0.9231 (m-40) cc_final: 0.8978 (p0) REVERT: D 28 ASP cc_start: 0.8758 (m-30) cc_final: 0.8553 (m-30) REVERT: D 51 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9052 (pp) REVERT: D 80 ILE cc_start: 0.9273 (pp) cc_final: 0.9059 (pp) REVERT: D 84 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8219 (mm) REVERT: D 105 ARG cc_start: 0.9289 (mtm110) cc_final: 0.8883 (mtm110) REVERT: D 109 LYS cc_start: 0.9462 (mttt) cc_final: 0.9255 (mttt) REVERT: D 258 TYR cc_start: 0.9217 (t80) cc_final: 0.8955 (t80) REVERT: D 276 SER cc_start: 0.8956 (p) cc_final: 0.8727 (p) REVERT: D 285 ASN cc_start: 0.9494 (m-40) cc_final: 0.9186 (m-40) REVERT: D 332 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8749 (pp) REVERT: D 352 GLU cc_start: 0.9178 (tm-30) cc_final: 0.8875 (tm-30) REVERT: D 355 ARG cc_start: 0.9137 (ptm-80) cc_final: 0.8858 (ptm-80) REVERT: D 385 MET cc_start: 0.9003 (ttm) cc_final: 0.8772 (ttp) REVERT: D 395 GLU cc_start: 0.8934 (mp0) cc_final: 0.8271 (mp0) REVERT: D 399 GLU cc_start: 0.9116 (pm20) cc_final: 0.8786 (mp0) REVERT: D 400 TYR cc_start: 0.8378 (m-10) cc_final: 0.8049 (m-10) REVERT: D 404 ASP cc_start: 0.9227 (t0) cc_final: 0.8989 (t0) REVERT: E 21 GLN cc_start: 0.9104 (pt0) cc_final: 0.8686 (tm-30) REVERT: E 25 ASN cc_start: 0.9222 (m-40) cc_final: 0.8852 (m-40) REVERT: E 51 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8690 (pp) REVERT: E 105 ARG cc_start: 0.9117 (mtm110) cc_final: 0.8811 (mtm110) REVERT: E 274 ASP cc_start: 0.9110 (t0) cc_final: 0.8885 (t0) REVERT: E 276 SER cc_start: 0.8881 (p) cc_final: 0.8596 (p) REVERT: E 279 ASN cc_start: 0.9203 (t0) cc_final: 0.8917 (t0) REVERT: E 285 ASN cc_start: 0.9449 (m-40) cc_final: 0.9219 (m-40) REVERT: E 332 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8629 (pp) REVERT: E 352 GLU cc_start: 0.9246 (tm-30) cc_final: 0.9029 (tm-30) REVERT: E 395 GLU cc_start: 0.8870 (mp0) cc_final: 0.8333 (mp0) REVERT: E 409 LYS cc_start: 0.8734 (ttmp) cc_final: 0.8142 (ttmt) REVERT: E 510 GLU cc_start: 0.8270 (tp30) cc_final: 0.8020 (tp30) REVERT: F 21 GLN cc_start: 0.9069 (pt0) cc_final: 0.8648 (tm-30) REVERT: F 51 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9002 (pp) REVERT: F 84 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8238 (mm) REVERT: F 105 ARG cc_start: 0.9160 (mtm110) cc_final: 0.8774 (mtm110) REVERT: F 109 LYS cc_start: 0.9436 (mptt) cc_final: 0.9185 (mttt) REVERT: F 274 ASP cc_start: 0.9099 (t0) cc_final: 0.8865 (t0) REVERT: F 276 SER cc_start: 0.8728 (p) cc_final: 0.8440 (p) REVERT: F 279 ASN cc_start: 0.9103 (t0) cc_final: 0.8338 (t0) REVERT: F 285 ASN cc_start: 0.9489 (m-40) cc_final: 0.9219 (m-40) REVERT: F 332 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8529 (pp) REVERT: F 352 GLU cc_start: 0.9220 (tm-30) cc_final: 0.8977 (tm-30) REVERT: F 385 MET cc_start: 0.8992 (ttm) cc_final: 0.8467 (ttm) REVERT: F 393 THR cc_start: 0.9212 (p) cc_final: 0.8382 (p) REVERT: F 395 GLU cc_start: 0.8939 (mp0) cc_final: 0.8145 (mp0) REVERT: F 399 GLU cc_start: 0.9088 (pm20) cc_final: 0.8818 (pm20) REVERT: F 404 ASP cc_start: 0.9258 (t0) cc_final: 0.9040 (t0) REVERT: F 409 LYS cc_start: 0.8793 (ttmp) cc_final: 0.8351 (tttt) REVERT: G 21 GLN cc_start: 0.9167 (pt0) cc_final: 0.8813 (tm-30) REVERT: G 50 ASP cc_start: 0.9184 (t70) cc_final: 0.8909 (t0) REVERT: G 51 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8906 (pp) REVERT: G 105 ARG cc_start: 0.9004 (mtm110) cc_final: 0.8777 (mtm110) REVERT: G 109 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.8998 (mttm) REVERT: G 258 TYR cc_start: 0.9150 (t80) cc_final: 0.8815 (t80) REVERT: G 279 ASN cc_start: 0.9013 (t0) cc_final: 0.8419 (t0) REVERT: G 332 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8724 (pp) REVERT: G 352 GLU cc_start: 0.9211 (tm-30) cc_final: 0.8950 (tm-30) REVERT: G 385 MET cc_start: 0.8999 (ttm) cc_final: 0.8532 (ttm) REVERT: G 395 GLU cc_start: 0.8805 (mp0) cc_final: 0.8331 (mp0) REVERT: G 399 GLU cc_start: 0.9144 (pm20) cc_final: 0.8883 (pm20) REVERT: G 400 TYR cc_start: 0.8409 (m-80) cc_final: 0.7248 (m-80) REVERT: G 407 ARG cc_start: 0.9122 (ttt-90) cc_final: 0.8293 (ttt-90) REVERT: G 510 GLU cc_start: 0.8319 (tp30) cc_final: 0.7879 (tp30) REVERT: H 25 ASN cc_start: 0.9111 (m-40) cc_final: 0.8773 (p0) REVERT: H 51 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8863 (pp) REVERT: H 66 VAL cc_start: 0.8017 (OUTLIER) cc_final: 0.7813 (p) REVERT: H 84 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8153 (mm) REVERT: H 105 ARG cc_start: 0.9205 (mtm110) cc_final: 0.8897 (mtm110) REVERT: H 258 TYR cc_start: 0.9094 (t80) cc_final: 0.8812 (t80) REVERT: H 276 SER cc_start: 0.9003 (p) cc_final: 0.8803 (p) REVERT: H 285 ASN cc_start: 0.9475 (m-40) cc_final: 0.9234 (m-40) REVERT: H 332 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8751 (pp) REVERT: H 352 GLU cc_start: 0.9248 (tm-30) cc_final: 0.8997 (tm-30) REVERT: H 385 MET cc_start: 0.8918 (ttm) cc_final: 0.8505 (ttm) REVERT: H 395 GLU cc_start: 0.8884 (mp0) cc_final: 0.8286 (mp0) outliers start: 144 outliers final: 90 residues processed: 1053 average time/residue: 0.1308 time to fit residues: 219.2761 Evaluate side-chains 1032 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 922 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 313 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 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 500 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 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 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 63 THR Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 84 LEU 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 280 SER Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 309 GLN Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 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 332 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 313 LEU Chi-restraints excluded: chain F residue 332 ILE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 56 THR 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 109 LYS Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 282 PHE Chi-restraints excluded: chain H residue 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 ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 69.2913 > 50: distance: 14 - 49: 29.000 distance: 17 - 46: 26.192 distance: 33 - 39: 27.929 distance: 39 - 40: 25.069 distance: 40 - 41: 19.319 distance: 40 - 43: 26.055 distance: 41 - 42: 4.987 distance: 41 - 46: 5.460 distance: 43 - 44: 41.914 distance: 43 - 45: 35.944 distance: 47 - 48: 23.592 distance: 47 - 50: 11.654 distance: 48 - 49: 36.079 distance: 48 - 54: 32.980 distance: 50 - 51: 4.705 distance: 51 - 52: 19.087 distance: 51 - 53: 44.395 distance: 54 - 55: 9.895 distance: 55 - 56: 11.656 distance: 55 - 58: 27.847 distance: 56 - 57: 17.945 distance: 56 - 63: 22.015 distance: 58 - 59: 14.537 distance: 59 - 60: 40.902 distance: 60 - 61: 18.737 distance: 61 - 62: 5.485 distance: 63 - 64: 24.311 distance: 64 - 65: 3.078 distance: 64 - 67: 4.259 distance: 65 - 66: 44.906 distance: 65 - 70: 28.992 distance: 67 - 68: 33.519 distance: 67 - 69: 6.590 distance: 70 - 71: 15.418 distance: 70 - 76: 47.236 distance: 71 - 72: 23.832 distance: 71 - 74: 26.584 distance: 72 - 73: 24.510 distance: 72 - 77: 8.530 distance: 74 - 75: 40.767 distance: 75 - 76: 10.187 distance: 77 - 78: 23.401 distance: 78 - 79: 14.153 distance: 78 - 81: 20.620 distance: 79 - 80: 12.650 distance: 79 - 85: 17.668 distance: 81 - 82: 42.625 distance: 82 - 83: 27.064 distance: 82 - 84: 28.859 distance: 85 - 86: 12.479 distance: 86 - 87: 28.515 distance: 86 - 89: 16.583 distance: 87 - 88: 25.935 distance: 87 - 92: 8.388 distance: 89 - 90: 33.041 distance: 89 - 91: 12.267 distance: 92 - 93: 27.087 distance: 93 - 94: 20.275 distance: 93 - 96: 28.355 distance: 94 - 95: 43.733 distance: 94 - 98: 25.730 distance: 96 - 97: 39.845 distance: 98 - 99: 7.478 distance: 99 - 100: 31.508 distance: 99 - 102: 21.679 distance: 100 - 101: 43.185 distance: 100 - 104: 16.798 distance: 102 - 103: 39.325 distance: 104 - 105: 17.747 distance: 104 - 110: 7.580 distance: 105 - 106: 12.962 distance: 105 - 108: 23.077 distance: 106 - 107: 33.363 distance: 106 - 111: 7.695 distance: 108 - 109: 20.355 distance: 109 - 110: 26.010