Starting phenix.real_space_refine on Thu Mar 5 15:06:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u8e_20687/03_2026/6u8e_20687.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u8e_20687/03_2026/6u8e_20687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6u8e_20687/03_2026/6u8e_20687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u8e_20687/03_2026/6u8e_20687.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6u8e_20687/03_2026/6u8e_20687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u8e_20687/03_2026/6u8e_20687.map" } resolution = 3.03 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= 0.049 sd= 2.559 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 14440 2.51 5 N 3912 2.21 5 O 4464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22984 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "B" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "C" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "D" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "E" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "F" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "G" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} Chain breaks: 2 Chain: "H" Number of atoms: 2806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 375, 2806 Classifications: {'peptide': 375} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 362} 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: 4.90, per 1000 atoms: 0.21 Number of scatterers: 22984 At special positions: 0 Unit cell: (122.85, 122.85, 120.75, 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 4464 8.00 N 3912 7.00 C 14440 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: 1.57 Conformation dependent library (CDL) restraints added in 1.2 seconds 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5376 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 32 sheets defined 40.6% alpha, 11.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 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: 3.780A pdb=" N ALA A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 110 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 266 removed outlier: 3.530A pdb=" N LEU A 260 " --> pdb=" O ASP A 256 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 4.060A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 removed outlier: 3.518A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 338 Processing helix chain 'A' and resid 342 through 355 removed outlier: 3.818A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.690A pdb=" N ILE A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 455 Processing helix chain 'A' and resid 456 through 472 Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 502 removed outlier: 3.505A pdb=" N GLY A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) Processing helix 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: 3.779A pdb=" N ALA B 81 " --> pdb=" O GLY B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 110 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 266 removed outlier: 3.529A pdb=" N LEU B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 265 " --> pdb=" O ASP B 261 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 removed outlier: 4.059A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 removed outlier: 3.519A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 338 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.817A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.692A pdb=" N ILE B 373 " --> pdb=" O ASN B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 455 Processing helix chain 'B' and resid 456 through 472 Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 502 removed outlier: 3.505A pdb=" N GLY B 502 " --> pdb=" O GLN B 498 " (cutoff:3.500A) Processing helix 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: 3.779A pdb=" N ALA C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 110 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 266 removed outlier: 3.530A pdb=" N LEU C 260 " --> pdb=" O ASP C 256 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLN C 265 " --> pdb=" O ASP C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 removed outlier: 4.059A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 removed outlier: 3.518A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 338 Processing helix chain 'C' and resid 342 through 355 removed outlier: 3.817A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.690A pdb=" N ILE C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 455 Processing helix chain 'C' and resid 456 through 472 Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 502 removed outlier: 3.506A pdb=" N GLY C 502 " --> pdb=" O GLN C 498 " (cutoff:3.500A) Processing helix 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: 3.779A pdb=" N ALA D 81 " --> pdb=" O GLY D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 110 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 266 removed outlier: 3.529A pdb=" N LEU D 260 " --> pdb=" O ASP D 256 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN D 265 " --> pdb=" O ASP D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 4.060A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 315 removed outlier: 3.518A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 338 Processing helix chain 'D' and resid 342 through 355 removed outlier: 3.818A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.691A pdb=" N ILE D 373 " --> pdb=" O ASN D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 455 Processing helix chain 'D' and resid 456 through 472 Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 502 removed outlier: 3.506A pdb=" N GLY D 502 " --> pdb=" O GLN D 498 " (cutoff:3.500A) Processing helix 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: 3.779A pdb=" N ALA E 81 " --> pdb=" O GLY E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 110 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 266 removed outlier: 3.530A pdb=" N LEU E 260 " --> pdb=" O ASP E 256 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN E 265 " --> pdb=" O ASP E 261 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 removed outlier: 4.060A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 315 removed outlier: 3.518A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 338 Processing helix chain 'E' and resid 342 through 355 removed outlier: 3.817A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 removed outlier: 3.692A pdb=" N ILE E 373 " --> pdb=" O ASN E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 455 Processing helix chain 'E' and resid 456 through 472 Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 502 removed outlier: 3.505A pdb=" N GLY E 502 " --> pdb=" O GLN E 498 " (cutoff:3.500A) Processing helix 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: 3.779A pdb=" N ALA F 81 " --> pdb=" O GLY F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 110 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 266 removed outlier: 3.529A pdb=" N LEU F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN F 265 " --> pdb=" O ASP F 261 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 removed outlier: 4.059A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS F 293 " --> pdb=" O TYR F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 315 removed outlier: 3.517A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 338 Processing helix chain 'F' and resid 342 through 355 removed outlier: 3.818A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 removed outlier: 3.691A pdb=" N ILE F 373 " --> pdb=" O ASN F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 455 Processing helix chain 'F' and resid 456 through 472 Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 502 removed outlier: 3.505A pdb=" N GLY F 502 " --> pdb=" O GLN F 498 " (cutoff:3.500A) Processing helix 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: 3.779A pdb=" N ALA G 81 " --> pdb=" O GLY G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 110 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 266 removed outlier: 3.530A pdb=" N LEU G 260 " --> pdb=" O ASP G 256 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN G 265 " --> pdb=" O ASP G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 removed outlier: 4.059A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LYS G 293 " --> pdb=" O TYR G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 315 removed outlier: 3.518A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 338 Processing helix chain 'G' and resid 342 through 355 removed outlier: 3.817A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 removed outlier: 3.691A pdb=" N ILE G 373 " --> pdb=" O ASN G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 455 Processing helix chain 'G' and resid 456 through 472 Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 502 removed outlier: 3.506A pdb=" N GLY G 502 " --> pdb=" O GLN G 498 " (cutoff:3.500A) Processing helix 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: 3.779A pdb=" N ALA H 81 " --> pdb=" O GLY H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 110 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 266 removed outlier: 3.529A pdb=" N LEU H 260 " --> pdb=" O ASP H 256 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN H 265 " --> pdb=" O ASP H 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 removed outlier: 4.059A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS H 293 " --> pdb=" O TYR H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 315 removed outlier: 3.518A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 338 Processing helix chain 'H' and resid 342 through 355 removed outlier: 3.818A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 removed outlier: 3.691A pdb=" N ILE H 373 " --> pdb=" O ASN H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 455 Processing helix chain 'H' and resid 456 through 472 Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 502 removed outlier: 3.505A 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: 6.441A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA A 320 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLY A 302 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG A 322 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.888A pdb=" N SER A 444 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.736A 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: 3.683A pdb=" N SER A 508 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.822A 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: 6.441A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA B 320 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLY B 302 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG B 322 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.727A pdb=" N SER B 508 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 3.864A 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: 6.440A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA C 320 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N GLY C 302 " --> pdb=" O ALA C 320 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG C 322 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.706A pdb=" N SER C 508 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 3.856A 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: 6.440A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA D 320 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N GLY D 302 " --> pdb=" O ALA D 320 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG D 322 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (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: 6.440A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA E 320 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLY E 302 " --> pdb=" O ALA E 320 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG E 322 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.865A pdb=" N SER E 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) removed outlier: 3.723A 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: 3.717A pdb=" N SER E 508 " --> pdb=" O ALA F 446 " (cutoff:3.500A) removed outlier: 3.863A 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: 6.441A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ALA F 320 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLY F 302 " --> pdb=" O ALA F 320 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG F 322 " --> pdb=" O GLY F 302 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 508 through 510 removed outlier: 3.699A pdb=" N SER F 508 " --> pdb=" O ALA G 446 " (cutoff:3.500A) removed outlier: 3.844A 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: 6.441A pdb=" N VAL G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N MET G 385 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA G 320 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLY G 302 " --> pdb=" O ALA G 320 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG G 322 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 508 through 510 removed outlier: 3.724A pdb=" N SER G 508 " --> pdb=" O ALA H 446 " (cutoff:3.500A) removed outlier: 3.863A 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: 6.441A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA H 320 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N GLY H 302 " --> pdb=" O ALA H 320 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ARG H 322 " --> pdb=" O GLY H 302 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) 881 hydrogen bonds defined for protein. 2547 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: 4.35 Time building geometry restraints manager: 2.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 3832 1.30 - 1.43: 5675 1.43 - 1.55: 13573 1.55 - 1.68: 56 1.68 - 1.81: 240 Bond restraints: 23376 Sorted by residual: bond pdb=" C3D NAD F 602 " pdb=" C4D NAD F 602 " ideal model delta sigma weight residual 1.531 1.298 0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C3D NAD G 602 " pdb=" C4D NAD G 602 " ideal model delta sigma weight residual 1.531 1.298 0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C3D NAD E 602 " pdb=" C4D NAD E 602 " ideal model delta sigma weight residual 1.531 1.298 0.233 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C3D NAD A 602 " pdb=" C4D NAD A 602 " ideal model delta sigma weight residual 1.531 1.298 0.233 2.00e-02 2.50e+03 1.35e+02 bond pdb=" C3D NAD B 602 " pdb=" C4D NAD B 602 " ideal model delta sigma weight residual 1.531 1.299 0.232 2.00e-02 2.50e+03 1.35e+02 ... (remaining 23371 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.33: 30885 3.33 - 6.65: 627 6.65 - 9.98: 88 9.98 - 13.30: 16 13.30 - 16.63: 24 Bond angle restraints: 31640 Sorted by residual: angle pdb=" N1A NAD G 602 " pdb=" C6A NAD G 602 " pdb=" N6A NAD G 602 " ideal model delta sigma weight residual 119.35 102.72 16.63 3.00e+00 1.11e-01 3.07e+01 angle pdb=" N1A NAD C 602 " pdb=" C6A NAD C 602 " pdb=" N6A NAD C 602 " ideal model delta sigma weight residual 119.35 102.73 16.62 3.00e+00 1.11e-01 3.07e+01 angle pdb=" N1A NAD B 602 " pdb=" C6A NAD B 602 " pdb=" N6A NAD B 602 " ideal model delta sigma weight residual 119.35 102.75 16.60 3.00e+00 1.11e-01 3.06e+01 angle pdb=" N1A NAD E 602 " pdb=" C6A NAD E 602 " pdb=" N6A NAD E 602 " ideal model delta sigma weight residual 119.35 102.76 16.59 3.00e+00 1.11e-01 3.06e+01 angle pdb=" N1A NAD H 602 " pdb=" C6A NAD H 602 " pdb=" N6A NAD H 602 " ideal model delta sigma weight residual 119.35 102.77 16.58 3.00e+00 1.11e-01 3.05e+01 ... (remaining 31635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.40: 13604 28.40 - 56.81: 568 56.81 - 85.21: 24 85.21 - 113.62: 0 113.62 - 142.02: 4 Dihedral angle restraints: 14200 sinusoidal: 5728 harmonic: 8472 Sorted by residual: dihedral pdb=" C5' IMP A 601 " pdb=" O5' IMP A 601 " pdb=" P IMP A 601 " pdb=" O2P IMP A 601 " ideal model delta sinusoidal sigma weight residual -168.07 -26.05 -142.02 1 2.00e+01 2.50e-03 4.29e+01 dihedral pdb=" C5' IMP B 601 " pdb=" O5' IMP B 601 " pdb=" P IMP B 601 " pdb=" O2P IMP B 601 " ideal model delta sinusoidal sigma weight residual -168.07 -26.07 -142.00 1 2.00e+01 2.50e-03 4.29e+01 dihedral pdb=" C5' IMP D 601 " pdb=" O5' IMP D 601 " pdb=" P IMP D 601 " pdb=" O2P IMP D 601 " ideal model delta sinusoidal sigma weight residual -168.07 -26.07 -142.00 1 2.00e+01 2.50e-03 4.29e+01 ... (remaining 14197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2651 0.065 - 0.130: 856 0.130 - 0.195: 109 0.195 - 0.260: 16 0.260 - 0.326: 16 Chirality restraints: 3648 Sorted by residual: chirality pdb=" C3D NAD E 602 " pdb=" C2D NAD E 602 " pdb=" C4D NAD E 602 " pdb=" O3D NAD E 602 " both_signs ideal model delta sigma weight residual False -2.73 -2.40 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" C3D NAD A 602 " pdb=" C2D NAD A 602 " pdb=" C4D NAD A 602 " pdb=" O3D NAD A 602 " both_signs ideal model delta sigma weight residual False -2.73 -2.40 -0.32 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C3D NAD G 602 " pdb=" C2D NAD G 602 " pdb=" C4D NAD G 602 " pdb=" O3D NAD G 602 " both_signs ideal model delta sigma weight residual False -2.73 -2.40 -0.32 2.00e-01 2.50e+01 2.64e+00 ... (remaining 3645 not shown) Planarity restraints: 3976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL E 13 " -0.014 2.00e-02 2.50e+03 2.82e-02 7.98e+00 pdb=" C VAL E 13 " 0.049 2.00e-02 2.50e+03 pdb=" O VAL E 13 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO E 14 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL D 13 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" C VAL D 13 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL D 13 " 0.018 2.00e-02 2.50e+03 pdb=" N PRO D 14 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 13 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.93e+00 pdb=" C VAL C 13 " -0.049 2.00e-02 2.50e+03 pdb=" O VAL C 13 " 0.018 2.00e-02 2.50e+03 pdb=" N PRO C 14 " 0.016 2.00e-02 2.50e+03 ... (remaining 3973 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 6917 2.80 - 3.32: 20808 3.32 - 3.85: 39248 3.85 - 4.37: 47025 4.37 - 4.90: 79269 Nonbonded interactions: 193267 Sorted by model distance: nonbonded pdb=" OD1 ASP G 261 " pdb=" OH TYR G 294 " model vdw 2.274 3.040 nonbonded pdb=" OD1 ASP F 261 " pdb=" OH TYR F 294 " model vdw 2.274 3.040 nonbonded pdb=" OD1 ASP H 261 " pdb=" OH TYR H 294 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASP E 261 " pdb=" OH TYR E 294 " model vdw 2.275 3.040 nonbonded pdb=" OD1 ASP C 261 " pdb=" OH TYR C 294 " model vdw 2.275 3.040 ... (remaining 193262 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.450 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: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 21.100 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.015 0.270 23384 Z= 0.816 Angle : 1.250 16.626 31640 Z= 0.626 Chirality : 0.064 0.326 3648 Planarity : 0.006 0.046 3976 Dihedral : 13.483 142.020 8824 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 2.02 % Allowed : 6.19 % Favored : 91.79 % 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: -3.92 (0.12), residues: 2952 helix: -3.05 (0.10), residues: 1080 sheet: -3.20 (0.20), residues: 496 loop : -1.79 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG B 322 TYR 0.017 0.003 TYR F 484 PHE 0.021 0.003 PHE A 401 HIS 0.007 0.003 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.01393 (23376) covalent geometry : angle 1.24962 (31640) hydrogen bonds : bond 0.22392 ( 881) hydrogen bonds : angle 8.58230 ( 2547) Misc. bond : bond 0.26927 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 827 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 779 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6631 (mt) REVERT: A 269 ASP cc_start: 0.8427 (m-30) cc_final: 0.7973 (m-30) REVERT: A 329 SER cc_start: 0.9362 (p) cc_final: 0.9030 (p) REVERT: A 399 GLU cc_start: 0.8353 (pm20) cc_final: 0.8021 (pm20) REVERT: A 417 LEU cc_start: 0.8685 (pt) cc_final: 0.8482 (pp) REVERT: A 482 MET cc_start: 0.8835 (mtp) cc_final: 0.8537 (mtm) REVERT: A 483 MET cc_start: 0.9303 (tmm) cc_final: 0.8318 (tmm) REVERT: A 487 GLU cc_start: 0.8832 (tt0) cc_final: 0.8474 (tt0) REVERT: A 512 ARG cc_start: 0.8654 (mtp-110) cc_final: 0.8334 (ttp-110) REVERT: B 16 ASP cc_start: 0.8699 (t0) cc_final: 0.8430 (t0) REVERT: B 28 ASP cc_start: 0.8693 (m-30) cc_final: 0.8386 (m-30) REVERT: B 84 LEU cc_start: 0.7159 (OUTLIER) cc_final: 0.6614 (mt) REVERT: B 243 GLN cc_start: 0.8219 (mt0) cc_final: 0.7702 (mt0) REVERT: B 254 GLU cc_start: 0.8938 (tp30) cc_final: 0.8673 (tp30) REVERT: B 269 ASP cc_start: 0.8524 (m-30) cc_final: 0.8094 (m-30) REVERT: B 329 SER cc_start: 0.9409 (p) cc_final: 0.9081 (p) REVERT: B 399 GLU cc_start: 0.8422 (pm20) cc_final: 0.8083 (pm20) REVERT: B 417 LEU cc_start: 0.8699 (pt) cc_final: 0.8470 (pt) REVERT: B 482 MET cc_start: 0.8728 (mtp) cc_final: 0.8438 (mtm) REVERT: B 483 MET cc_start: 0.9439 (tmm) cc_final: 0.8409 (tmm) REVERT: B 487 GLU cc_start: 0.8768 (tt0) cc_final: 0.8393 (tt0) REVERT: C 28 ASP cc_start: 0.8708 (m-30) cc_final: 0.8504 (m-30) REVERT: C 62 LYS cc_start: 0.8509 (mmtp) cc_final: 0.8214 (mmtm) REVERT: C 84 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.6799 (mt) REVERT: C 269 ASP cc_start: 0.8490 (m-30) cc_final: 0.8042 (m-30) REVERT: C 329 SER cc_start: 0.9366 (p) cc_final: 0.9081 (p) REVERT: C 399 GLU cc_start: 0.8319 (pm20) cc_final: 0.8023 (pm20) REVERT: C 482 MET cc_start: 0.8865 (mtp) cc_final: 0.8614 (mtm) REVERT: C 487 GLU cc_start: 0.8819 (tt0) cc_final: 0.8495 (tt0) REVERT: C 512 ARG cc_start: 0.8601 (mtp-110) cc_final: 0.8386 (ttp-110) REVERT: D 28 ASP cc_start: 0.8726 (m-30) cc_final: 0.8495 (m-30) REVERT: D 102 ASN cc_start: 0.9046 (t0) cc_final: 0.8741 (t0) REVERT: D 108 LYS cc_start: 0.8929 (tttt) cc_final: 0.8723 (tptt) REVERT: D 269 ASP cc_start: 0.8520 (m-30) cc_final: 0.8101 (m-30) REVERT: D 329 SER cc_start: 0.9364 (p) cc_final: 0.9056 (p) REVERT: D 399 GLU cc_start: 0.8355 (pm20) cc_final: 0.8054 (pm20) REVERT: D 482 MET cc_start: 0.8815 (mtp) cc_final: 0.8551 (mtm) REVERT: D 487 GLU cc_start: 0.8792 (tt0) cc_final: 0.8463 (tt0) REVERT: E 16 ASP cc_start: 0.8555 (t0) cc_final: 0.8250 (t0) REVERT: E 28 ASP cc_start: 0.8685 (m-30) cc_final: 0.8431 (m-30) REVERT: E 62 LYS cc_start: 0.8477 (mmtp) cc_final: 0.8275 (mmtp) REVERT: E 84 LEU cc_start: 0.7193 (OUTLIER) cc_final: 0.6713 (mt) REVERT: E 269 ASP cc_start: 0.8428 (m-30) cc_final: 0.7990 (m-30) REVERT: E 329 SER cc_start: 0.9354 (p) cc_final: 0.9030 (p) REVERT: E 399 GLU cc_start: 0.8327 (pm20) cc_final: 0.8006 (pm20) REVERT: E 417 LEU cc_start: 0.8635 (pt) cc_final: 0.8415 (pp) REVERT: E 482 MET cc_start: 0.8839 (mtp) cc_final: 0.8574 (mtm) REVERT: E 483 MET cc_start: 0.9435 (tmm) cc_final: 0.8387 (tmm) REVERT: E 487 GLU cc_start: 0.8830 (tt0) cc_final: 0.8489 (tt0) REVERT: E 512 ARG cc_start: 0.8660 (mtp-110) cc_final: 0.8455 (ttp-110) REVERT: F 28 ASP cc_start: 0.8700 (m-30) cc_final: 0.8433 (m-30) REVERT: F 84 LEU cc_start: 0.7010 (OUTLIER) cc_final: 0.6485 (mt) REVERT: F 102 ASN cc_start: 0.9010 (t0) cc_final: 0.8685 (t0) REVERT: F 108 LYS cc_start: 0.8911 (tttt) cc_final: 0.8706 (tptt) REVERT: F 269 ASP cc_start: 0.8530 (m-30) cc_final: 0.8106 (m-30) REVERT: F 329 SER cc_start: 0.9380 (p) cc_final: 0.9046 (p) REVERT: F 399 GLU cc_start: 0.8394 (pm20) cc_final: 0.8050 (pm20) REVERT: F 417 LEU cc_start: 0.8625 (pt) cc_final: 0.8424 (pt) REVERT: F 482 MET cc_start: 0.8749 (mtp) cc_final: 0.8464 (mtm) REVERT: F 483 MET cc_start: 0.9435 (tmm) cc_final: 0.8401 (tmm) REVERT: F 487 GLU cc_start: 0.8800 (tt0) cc_final: 0.8455 (tt0) REVERT: G 16 ASP cc_start: 0.8594 (t0) cc_final: 0.8296 (t0) REVERT: G 28 ASP cc_start: 0.8700 (m-30) cc_final: 0.8462 (m-30) REVERT: G 84 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6624 (mt) REVERT: G 254 GLU cc_start: 0.8868 (tp30) cc_final: 0.8660 (tp30) REVERT: G 269 ASP cc_start: 0.8460 (m-30) cc_final: 0.8012 (m-30) REVERT: G 329 SER cc_start: 0.9346 (p) cc_final: 0.9009 (p) REVERT: G 399 GLU cc_start: 0.8350 (pm20) cc_final: 0.8000 (pm20) REVERT: G 482 MET cc_start: 0.8877 (mtp) cc_final: 0.8577 (mtm) REVERT: G 487 GLU cc_start: 0.8838 (tt0) cc_final: 0.8490 (tt0) REVERT: G 512 ARG cc_start: 0.8635 (mtp-110) cc_final: 0.8382 (ttp-110) REVERT: H 28 ASP cc_start: 0.8703 (m-30) cc_final: 0.8421 (m-30) REVERT: H 78 MET cc_start: 0.9092 (tpt) cc_final: 0.8863 (tpp) REVERT: H 105 ARG cc_start: 0.8595 (tmm160) cc_final: 0.8391 (ttp80) REVERT: H 329 SER cc_start: 0.9398 (p) cc_final: 0.9082 (p) REVERT: H 399 GLU cc_start: 0.8349 (pm20) cc_final: 0.8057 (pm20) REVERT: H 482 MET cc_start: 0.8775 (mtp) cc_final: 0.8513 (mtm) REVERT: H 483 MET cc_start: 0.9416 (tmm) cc_final: 0.8445 (tmm) REVERT: H 487 GLU cc_start: 0.8792 (tt0) cc_final: 0.8435 (tt0) outliers start: 48 outliers final: 6 residues processed: 814 average time/residue: 0.1580 time to fit residues: 199.0450 Evaluate side-chains 540 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 528 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 84 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 48 GLN A 243 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN B 48 GLN B 102 ASN B 253 HIS ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN C 48 GLN C 243 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN D 48 GLN D 243 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN E 48 GLN E 243 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 498 GLN F 48 GLN F 243 GLN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN G 48 GLN G 243 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 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 48 GLN H 243 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 498 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.104764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.086343 restraints weight = 33183.494| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 3.22 r_work: 0.2775 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23384 Z= 0.145 Angle : 0.572 6.593 31640 Z= 0.302 Chirality : 0.043 0.152 3648 Planarity : 0.004 0.041 3976 Dihedral : 10.098 62.401 3730 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.37 % Allowed : 10.02 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.54 (0.13), residues: 2952 helix: -1.16 (0.14), residues: 1144 sheet: -2.74 (0.18), residues: 544 loop : -1.49 (0.15), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 105 TYR 0.021 0.002 TYR A 12 PHE 0.013 0.001 PHE D 401 HIS 0.004 0.001 HIS F 92 Details of bonding type rmsd covalent geometry : bond 0.00341 (23376) covalent geometry : angle 0.57249 (31640) hydrogen bonds : bond 0.03430 ( 881) hydrogen bonds : angle 5.49575 ( 2547) Misc. bond : bond 0.00032 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 683 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 603 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6484 (mt) REVERT: A 269 ASP cc_start: 0.8738 (m-30) cc_final: 0.8354 (m-30) REVERT: A 271 VAL cc_start: 0.8957 (m) cc_final: 0.8734 (p) REVERT: A 329 SER cc_start: 0.9610 (p) cc_final: 0.9353 (p) REVERT: A 399 GLU cc_start: 0.8687 (pm20) cc_final: 0.8313 (pm20) REVERT: A 483 MET cc_start: 0.9309 (tmm) cc_final: 0.8363 (tmm) REVERT: A 487 GLU cc_start: 0.9139 (tt0) cc_final: 0.8800 (tt0) REVERT: A 512 ARG cc_start: 0.8936 (mtp-110) cc_final: 0.8531 (ttp-110) REVERT: B 16 ASP cc_start: 0.8935 (t0) cc_final: 0.8648 (t0) REVERT: B 28 ASP cc_start: 0.8871 (m-30) cc_final: 0.8524 (m-30) REVERT: B 84 LEU cc_start: 0.6833 (OUTLIER) cc_final: 0.6409 (mt) REVERT: B 269 ASP cc_start: 0.8817 (m-30) cc_final: 0.8309 (m-30) REVERT: B 277 GLN cc_start: 0.8643 (tp40) cc_final: 0.8352 (tp40) REVERT: B 300 ILE cc_start: 0.8373 (mm) cc_final: 0.8153 (mm) REVERT: B 385 MET cc_start: 0.8682 (ttm) cc_final: 0.8310 (ttp) REVERT: B 399 GLU cc_start: 0.8683 (pm20) cc_final: 0.8312 (pm20) REVERT: B 417 LEU cc_start: 0.8582 (pt) cc_final: 0.8267 (pt) REVERT: B 487 GLU cc_start: 0.9029 (tt0) cc_final: 0.8766 (tt0) REVERT: C 28 ASP cc_start: 0.8955 (m-30) cc_final: 0.8528 (m-30) REVERT: C 84 LEU cc_start: 0.6995 (OUTLIER) cc_final: 0.6621 (mt) REVERT: C 102 ASN cc_start: 0.8852 (t0) cc_final: 0.8584 (t0) REVERT: C 105 ARG cc_start: 0.8528 (tmm160) cc_final: 0.8266 (ttp80) REVERT: C 254 GLU cc_start: 0.9169 (tp30) cc_final: 0.8949 (tp30) REVERT: C 269 ASP cc_start: 0.8816 (m-30) cc_final: 0.8392 (m-30) REVERT: C 329 SER cc_start: 0.9617 (p) cc_final: 0.9389 (p) REVERT: C 399 GLU cc_start: 0.8753 (pm20) cc_final: 0.8365 (pm20) REVERT: C 483 MET cc_start: 0.9323 (tmm) cc_final: 0.8351 (tmm) REVERT: C 487 GLU cc_start: 0.9116 (tt0) cc_final: 0.8809 (tt0) REVERT: C 512 ARG cc_start: 0.8936 (mtp-110) cc_final: 0.8502 (ttp-110) REVERT: D 16 ASP cc_start: 0.8925 (t0) cc_final: 0.8588 (t0) REVERT: D 28 ASP cc_start: 0.8904 (m-30) cc_final: 0.8520 (m-30) REVERT: D 84 LEU cc_start: 0.6830 (OUTLIER) cc_final: 0.6405 (mt) REVERT: D 269 ASP cc_start: 0.8842 (m-30) cc_final: 0.8166 (m-30) REVERT: D 399 GLU cc_start: 0.8678 (pm20) cc_final: 0.8278 (pm20) REVERT: D 417 LEU cc_start: 0.8630 (pt) cc_final: 0.8290 (pt) REVERT: D 483 MET cc_start: 0.9352 (tmm) cc_final: 0.8257 (tmm) REVERT: D 487 GLU cc_start: 0.9067 (tt0) cc_final: 0.8793 (tt0) REVERT: E 16 ASP cc_start: 0.8878 (t0) cc_final: 0.8604 (t0) REVERT: E 28 ASP cc_start: 0.8955 (m-30) cc_final: 0.8533 (m-30) REVERT: E 62 LYS cc_start: 0.8192 (mmtp) cc_final: 0.7811 (mmmt) REVERT: E 84 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6539 (mt) REVERT: E 269 ASP cc_start: 0.8774 (m-30) cc_final: 0.8394 (m-30) REVERT: E 300 ILE cc_start: 0.8543 (mm) cc_final: 0.8326 (mm) REVERT: E 385 MET cc_start: 0.8603 (ttm) cc_final: 0.8244 (ttp) REVERT: E 399 GLU cc_start: 0.8687 (pm20) cc_final: 0.8319 (pm20) REVERT: E 483 MET cc_start: 0.9382 (tmm) cc_final: 0.8424 (tmm) REVERT: E 487 GLU cc_start: 0.9097 (tt0) cc_final: 0.8835 (tt0) REVERT: E 512 ARG cc_start: 0.8959 (mtp-110) cc_final: 0.8603 (ttp-110) REVERT: F 16 ASP cc_start: 0.8790 (t0) cc_final: 0.8528 (t0) REVERT: F 28 ASP cc_start: 0.8952 (m-30) cc_final: 0.8514 (m-30) REVERT: F 84 LEU cc_start: 0.6496 (OUTLIER) cc_final: 0.6069 (mt) REVERT: F 254 GLU cc_start: 0.9209 (tp30) cc_final: 0.8982 (tp30) REVERT: F 269 ASP cc_start: 0.8923 (m-30) cc_final: 0.8250 (m-30) REVERT: F 271 VAL cc_start: 0.8959 (m) cc_final: 0.8750 (p) REVERT: F 300 ILE cc_start: 0.8454 (mm) cc_final: 0.8235 (mm) REVERT: F 385 MET cc_start: 0.8638 (ttm) cc_final: 0.8278 (ttp) REVERT: F 399 GLU cc_start: 0.8678 (pm20) cc_final: 0.8285 (pm20) REVERT: F 417 LEU cc_start: 0.8595 (pt) cc_final: 0.8282 (pt) REVERT: F 487 GLU cc_start: 0.9092 (tt0) cc_final: 0.8821 (tt0) REVERT: G 16 ASP cc_start: 0.8929 (t0) cc_final: 0.8666 (t0) REVERT: G 84 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.6143 (mt) REVERT: G 254 GLU cc_start: 0.9070 (tp30) cc_final: 0.8708 (tp30) REVERT: G 269 ASP cc_start: 0.8764 (m-30) cc_final: 0.8381 (m-30) REVERT: G 300 ILE cc_start: 0.8605 (mm) cc_final: 0.8382 (mm) REVERT: G 385 MET cc_start: 0.8577 (ttm) cc_final: 0.8214 (ttp) REVERT: G 399 GLU cc_start: 0.8696 (pm20) cc_final: 0.8329 (pm20) REVERT: G 483 MET cc_start: 0.9331 (tmm) cc_final: 0.8326 (tmm) REVERT: G 487 GLU cc_start: 0.9115 (tt0) cc_final: 0.8840 (tt0) REVERT: G 512 ARG cc_start: 0.8860 (mtp-110) cc_final: 0.8453 (ttp-110) REVERT: H 16 ASP cc_start: 0.8917 (t0) cc_final: 0.8548 (t0) REVERT: H 28 ASP cc_start: 0.8885 (m-30) cc_final: 0.8412 (m-30) REVERT: H 84 LEU cc_start: 0.6452 (OUTLIER) cc_final: 0.6026 (mt) REVERT: H 277 GLN cc_start: 0.8602 (tp40) cc_final: 0.8346 (tp40) REVERT: H 399 GLU cc_start: 0.8662 (pm20) cc_final: 0.8268 (pm20) REVERT: H 483 MET cc_start: 0.9405 (tmm) cc_final: 0.8372 (tmm) REVERT: H 487 GLU cc_start: 0.9059 (tt0) cc_final: 0.8782 (tt0) outliers start: 80 outliers final: 17 residues processed: 640 average time/residue: 0.1329 time to fit residues: 140.2817 Evaluate side-chains 540 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 515 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 276 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 290 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 281 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 192 optimal weight: 0.0980 chunk 121 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN B 243 GLN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 265 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.104720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.086093 restraints weight = 33526.919| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 3.22 r_work: 0.2747 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23384 Z= 0.145 Angle : 0.533 7.378 31640 Z= 0.275 Chirality : 0.043 0.153 3648 Planarity : 0.004 0.039 3976 Dihedral : 9.362 62.577 3726 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.20 % Allowed : 12.25 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.53 (0.14), residues: 2952 helix: -0.06 (0.15), residues: 1112 sheet: -2.42 (0.19), residues: 544 loop : -1.07 (0.15), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 105 TYR 0.013 0.001 TYR F 12 PHE 0.012 0.001 PHE D 401 HIS 0.002 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00342 (23376) covalent geometry : angle 0.53263 (31640) hydrogen bonds : bond 0.02835 ( 881) hydrogen bonds : angle 5.09742 ( 2547) Misc. bond : bond 0.00088 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 556 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8805 (t0) cc_final: 0.8373 (t0) REVERT: A 75 GLU cc_start: 0.8049 (mm-30) cc_final: 0.7488 (mm-30) REVERT: A 84 LEU cc_start: 0.6498 (OUTLIER) cc_final: 0.6104 (mt) REVERT: A 269 ASP cc_start: 0.8748 (m-30) cc_final: 0.8246 (m-30) REVERT: A 399 GLU cc_start: 0.8724 (pm20) cc_final: 0.8311 (pm20) REVERT: A 420 MET cc_start: 0.5914 (ttm) cc_final: 0.5707 (ttm) REVERT: A 483 MET cc_start: 0.9344 (tmm) cc_final: 0.8350 (tmm) REVERT: A 487 GLU cc_start: 0.9138 (tt0) cc_final: 0.8832 (tt0) REVERT: A 512 ARG cc_start: 0.8898 (mtp-110) cc_final: 0.8482 (ttp-110) REVERT: B 16 ASP cc_start: 0.8930 (t0) cc_final: 0.8604 (t0) REVERT: B 28 ASP cc_start: 0.8880 (m-30) cc_final: 0.8540 (m-30) REVERT: B 75 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7677 (mm-30) REVERT: B 84 LEU cc_start: 0.6458 (OUTLIER) cc_final: 0.6056 (mt) REVERT: B 269 ASP cc_start: 0.8725 (m-30) cc_final: 0.8263 (m-30) REVERT: B 271 VAL cc_start: 0.8950 (m) cc_final: 0.8738 (p) REVERT: B 277 GLN cc_start: 0.8562 (tp40) cc_final: 0.8251 (tp40) REVERT: B 300 ILE cc_start: 0.8380 (mm) cc_final: 0.8153 (mm) REVERT: B 385 MET cc_start: 0.8726 (ttm) cc_final: 0.8350 (ttp) REVERT: B 399 GLU cc_start: 0.8699 (pm20) cc_final: 0.8316 (pm20) REVERT: B 417 LEU cc_start: 0.8583 (pt) cc_final: 0.8306 (pt) REVERT: B 420 MET cc_start: 0.5846 (ttm) cc_final: 0.5589 (ttm) REVERT: B 483 MET cc_start: 0.9418 (tmm) cc_final: 0.8420 (tmm) REVERT: B 487 GLU cc_start: 0.9035 (tt0) cc_final: 0.8760 (tt0) REVERT: C 16 ASP cc_start: 0.8850 (t0) cc_final: 0.8483 (t0) REVERT: C 28 ASP cc_start: 0.8977 (m-30) cc_final: 0.8661 (m-30) REVERT: C 34 ASP cc_start: 0.8815 (t0) cc_final: 0.8443 (t0) REVERT: C 75 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7536 (mm-30) REVERT: C 84 LEU cc_start: 0.6299 (OUTLIER) cc_final: 0.5906 (mt) REVERT: C 254 GLU cc_start: 0.9099 (tp30) cc_final: 0.8892 (tp30) REVERT: C 269 ASP cc_start: 0.8753 (m-30) cc_final: 0.8269 (m-30) REVERT: C 271 VAL cc_start: 0.9073 (m) cc_final: 0.8850 (p) REVERT: C 399 GLU cc_start: 0.8787 (pm20) cc_final: 0.8390 (pm20) REVERT: C 420 MET cc_start: 0.5925 (ttm) cc_final: 0.5686 (ttm) REVERT: C 483 MET cc_start: 0.9352 (tmm) cc_final: 0.8345 (tmm) REVERT: C 487 GLU cc_start: 0.9140 (tt0) cc_final: 0.8848 (tt0) REVERT: C 512 ARG cc_start: 0.8922 (mtp-110) cc_final: 0.8439 (ttp-110) REVERT: D 16 ASP cc_start: 0.8925 (t0) cc_final: 0.8502 (t0) REVERT: D 28 ASP cc_start: 0.8907 (m-30) cc_final: 0.8568 (m-30) REVERT: D 75 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7712 (mm-30) REVERT: D 84 LEU cc_start: 0.6426 (OUTLIER) cc_final: 0.5988 (mt) REVERT: D 269 ASP cc_start: 0.8793 (m-30) cc_final: 0.8222 (m-30) REVERT: D 271 VAL cc_start: 0.8979 (m) cc_final: 0.8758 (p) REVERT: D 300 ILE cc_start: 0.8536 (mm) cc_final: 0.8287 (mm) REVERT: D 399 GLU cc_start: 0.8710 (pm20) cc_final: 0.8335 (pm20) REVERT: D 417 LEU cc_start: 0.8620 (pt) cc_final: 0.8301 (pt) REVERT: D 487 GLU cc_start: 0.9106 (tt0) cc_final: 0.8832 (tt0) REVERT: D 512 ARG cc_start: 0.9109 (ttp80) cc_final: 0.8726 (ttp-110) REVERT: E 16 ASP cc_start: 0.8864 (t0) cc_final: 0.8539 (t0) REVERT: E 28 ASP cc_start: 0.8976 (m-30) cc_final: 0.8591 (m-30) REVERT: E 62 LYS cc_start: 0.8292 (mmtp) cc_final: 0.8008 (mmmt) REVERT: E 75 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7427 (mm-30) REVERT: E 84 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6246 (mt) REVERT: E 269 ASP cc_start: 0.8767 (m-30) cc_final: 0.8281 (m-30) REVERT: E 271 VAL cc_start: 0.9006 (m) cc_final: 0.8802 (p) REVERT: E 277 GLN cc_start: 0.8550 (tp40) cc_final: 0.8296 (tp40) REVERT: E 300 ILE cc_start: 0.8557 (mm) cc_final: 0.8328 (mm) REVERT: E 385 MET cc_start: 0.8720 (ttm) cc_final: 0.8347 (ttp) REVERT: E 399 GLU cc_start: 0.8720 (pm20) cc_final: 0.8334 (pm20) REVERT: E 483 MET cc_start: 0.9411 (tmm) cc_final: 0.8428 (tmm) REVERT: E 487 GLU cc_start: 0.9137 (tt0) cc_final: 0.8869 (tt0) REVERT: E 512 ARG cc_start: 0.8889 (mtp-110) cc_final: 0.8469 (ttp-110) REVERT: F 16 ASP cc_start: 0.8824 (t0) cc_final: 0.8579 (t0) REVERT: F 28 ASP cc_start: 0.8987 (m-30) cc_final: 0.8580 (m-30) REVERT: F 75 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7545 (mm-30) REVERT: F 84 LEU cc_start: 0.6499 (OUTLIER) cc_final: 0.6101 (mt) REVERT: F 105 ARG cc_start: 0.8483 (ttp80) cc_final: 0.8280 (ttp80) REVERT: F 254 GLU cc_start: 0.9161 (tp30) cc_final: 0.8949 (tp30) REVERT: F 269 ASP cc_start: 0.8818 (m-30) cc_final: 0.8248 (m-30) REVERT: F 300 ILE cc_start: 0.8421 (mm) cc_final: 0.8183 (mm) REVERT: F 385 MET cc_start: 0.8722 (ttm) cc_final: 0.8359 (ttp) REVERT: F 399 GLU cc_start: 0.8702 (pm20) cc_final: 0.8303 (pm20) REVERT: F 417 LEU cc_start: 0.8544 (pt) cc_final: 0.8264 (pt) REVERT: F 420 MET cc_start: 0.5574 (ttm) cc_final: 0.5347 (ttm) REVERT: F 483 MET cc_start: 0.9397 (tmm) cc_final: 0.8418 (tmm) REVERT: F 487 GLU cc_start: 0.9124 (tt0) cc_final: 0.8846 (tt0) REVERT: G 16 ASP cc_start: 0.8897 (t0) cc_final: 0.8565 (t0) REVERT: G 28 ASP cc_start: 0.8727 (m-30) cc_final: 0.8373 (m-30) REVERT: G 75 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7511 (mm-30) REVERT: G 84 LEU cc_start: 0.6546 (OUTLIER) cc_final: 0.6171 (mt) REVERT: G 102 ASN cc_start: 0.8832 (t0) cc_final: 0.8538 (t0) REVERT: G 105 ARG cc_start: 0.8540 (tmm160) cc_final: 0.8309 (ttp80) REVERT: G 254 GLU cc_start: 0.9056 (tp30) cc_final: 0.8715 (tp30) REVERT: G 269 ASP cc_start: 0.8787 (m-30) cc_final: 0.8312 (m-30) REVERT: G 277 GLN cc_start: 0.8567 (tp40) cc_final: 0.8340 (tp40) REVERT: G 300 ILE cc_start: 0.8563 (mm) cc_final: 0.8333 (mm) REVERT: G 385 MET cc_start: 0.8659 (ttm) cc_final: 0.8334 (ttp) REVERT: G 399 GLU cc_start: 0.8719 (pm20) cc_final: 0.8303 (pm20) REVERT: G 483 MET cc_start: 0.9376 (tmm) cc_final: 0.8361 (tmm) REVERT: G 487 GLU cc_start: 0.9157 (tt0) cc_final: 0.8882 (tt0) REVERT: G 512 ARG cc_start: 0.8861 (mtp-110) cc_final: 0.8395 (ttp-110) REVERT: H 16 ASP cc_start: 0.8912 (t0) cc_final: 0.8509 (t0) REVERT: H 28 ASP cc_start: 0.8884 (m-30) cc_final: 0.8604 (m-30) REVERT: H 75 GLU cc_start: 0.8159 (mm-30) cc_final: 0.7683 (mm-30) REVERT: H 84 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.5956 (mt) REVERT: H 271 VAL cc_start: 0.8997 (m) cc_final: 0.8741 (p) REVERT: H 274 ASP cc_start: 0.9333 (t0) cc_final: 0.9072 (t0) REVERT: H 277 GLN cc_start: 0.8544 (tp40) cc_final: 0.8233 (tp40) REVERT: H 399 GLU cc_start: 0.8692 (pm20) cc_final: 0.8325 (pm20) REVERT: H 483 MET cc_start: 0.9425 (tmm) cc_final: 0.8399 (tmm) REVERT: H 487 GLU cc_start: 0.9096 (tt0) cc_final: 0.8816 (tt0) REVERT: H 512 ARG cc_start: 0.9120 (ttp80) cc_final: 0.8543 (ttp80) outliers start: 76 outliers final: 33 residues processed: 598 average time/residue: 0.1385 time to fit residues: 136.0746 Evaluate side-chains 567 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 526 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 109 LYS Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 37 optimal weight: 5.9990 chunk 217 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 157 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 259 optimal weight: 0.0870 chunk 130 optimal weight: 1.9990 chunk 235 optimal weight: 3.9990 chunk 148 optimal weight: 0.0060 chunk 181 optimal weight: 3.9990 overall best weight: 0.7176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 498 GLN B 102 ASN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 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 = 0.3184 r_free = 0.3184 target = 0.104289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.085680 restraints weight = 33744.927| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 3.22 r_work: 0.2742 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23384 Z= 0.130 Angle : 0.505 6.822 31640 Z= 0.262 Chirality : 0.042 0.194 3648 Planarity : 0.003 0.038 3976 Dihedral : 8.866 61.039 3724 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.07 % Allowed : 14.39 % Favored : 82.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.03 (0.15), residues: 2952 helix: 0.56 (0.16), residues: 1112 sheet: -2.21 (0.19), residues: 544 loop : -0.98 (0.15), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 105 TYR 0.010 0.001 TYR G 348 PHE 0.011 0.001 PHE G 401 HIS 0.002 0.001 HIS E 92 Details of bonding type rmsd covalent geometry : bond 0.00311 (23376) covalent geometry : angle 0.50534 (31640) hydrogen bonds : bond 0.02585 ( 881) hydrogen bonds : angle 4.88339 ( 2547) Misc. bond : bond 0.00077 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 539 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8118 (mm-30) cc_final: 0.7775 (mm-30) REVERT: A 269 ASP cc_start: 0.8700 (m-30) cc_final: 0.8167 (m-30) REVERT: A 399 GLU cc_start: 0.8744 (pm20) cc_final: 0.8340 (pm20) REVERT: A 483 MET cc_start: 0.9343 (tmm) cc_final: 0.8367 (tmm) REVERT: A 487 GLU cc_start: 0.9162 (tt0) cc_final: 0.8862 (tt0) REVERT: A 512 ARG cc_start: 0.8833 (mtp-110) cc_final: 0.8401 (ttp-110) REVERT: B 16 ASP cc_start: 0.8949 (t0) cc_final: 0.8607 (t0) REVERT: B 28 ASP cc_start: 0.8896 (m-30) cc_final: 0.8563 (m-30) REVERT: B 75 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7768 (mm-30) REVERT: B 84 LEU cc_start: 0.6237 (OUTLIER) cc_final: 0.5822 (mt) REVERT: B 102 ASN cc_start: 0.8806 (t0) cc_final: 0.8515 (t0) REVERT: B 105 ARG cc_start: 0.8429 (ttp80) cc_final: 0.8199 (ttp80) REVERT: B 269 ASP cc_start: 0.8657 (m-30) cc_final: 0.8145 (m-30) REVERT: B 277 GLN cc_start: 0.8467 (tp40) cc_final: 0.8234 (tp40) REVERT: B 300 ILE cc_start: 0.8493 (mm) cc_final: 0.8233 (mm) REVERT: B 385 MET cc_start: 0.8757 (ttm) cc_final: 0.8387 (ttp) REVERT: B 399 GLU cc_start: 0.8702 (pm20) cc_final: 0.8329 (pm20) REVERT: B 417 LEU cc_start: 0.8579 (pt) cc_final: 0.8279 (pt) REVERT: B 483 MET cc_start: 0.9437 (tmm) cc_final: 0.8426 (tmm) REVERT: B 487 GLU cc_start: 0.9053 (tt0) cc_final: 0.8770 (tt0) REVERT: C 16 ASP cc_start: 0.8807 (t0) cc_final: 0.8379 (t0) REVERT: C 28 ASP cc_start: 0.8984 (m-30) cc_final: 0.8682 (m-30) REVERT: C 75 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7758 (mm-30) REVERT: C 84 LEU cc_start: 0.6519 (OUTLIER) cc_final: 0.6172 (mt) REVERT: C 254 GLU cc_start: 0.9105 (tp30) cc_final: 0.8867 (tp30) REVERT: C 269 ASP cc_start: 0.8724 (m-30) cc_final: 0.8195 (m-30) REVERT: C 274 ASP cc_start: 0.9197 (t0) cc_final: 0.8969 (t0) REVERT: C 399 GLU cc_start: 0.8794 (pm20) cc_final: 0.8411 (pm20) REVERT: C 420 MET cc_start: 0.5949 (ttm) cc_final: 0.5730 (ttm) REVERT: C 487 GLU cc_start: 0.9168 (tt0) cc_final: 0.8879 (tt0) REVERT: C 512 ARG cc_start: 0.8859 (mtp-110) cc_final: 0.8475 (ttp-110) REVERT: D 16 ASP cc_start: 0.8919 (t0) cc_final: 0.8467 (t0) REVERT: D 28 ASP cc_start: 0.8898 (m-30) cc_final: 0.8558 (m-30) REVERT: D 75 GLU cc_start: 0.8248 (mm-30) cc_final: 0.7907 (mm-30) REVERT: D 84 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.6026 (mt) REVERT: D 269 ASP cc_start: 0.8687 (m-30) cc_final: 0.8201 (m-30) REVERT: D 300 ILE cc_start: 0.8480 (mm) cc_final: 0.8212 (mm) REVERT: D 399 GLU cc_start: 0.8751 (pm20) cc_final: 0.8384 (pm20) REVERT: D 417 LEU cc_start: 0.8645 (pt) cc_final: 0.8348 (pt) REVERT: D 483 MET cc_start: 0.9364 (tmm) cc_final: 0.8302 (tmm) REVERT: D 487 GLU cc_start: 0.9104 (tt0) cc_final: 0.8830 (tt0) REVERT: D 512 ARG cc_start: 0.9112 (ttp80) cc_final: 0.8572 (ttp80) REVERT: E 16 ASP cc_start: 0.8834 (t0) cc_final: 0.8464 (t0) REVERT: E 28 ASP cc_start: 0.8973 (m-30) cc_final: 0.8639 (m-30) REVERT: E 75 GLU cc_start: 0.8053 (mm-30) cc_final: 0.7719 (mm-30) REVERT: E 84 LEU cc_start: 0.6884 (OUTLIER) cc_final: 0.6529 (mt) REVERT: E 256 ASP cc_start: 0.9041 (m-30) cc_final: 0.8805 (t0) REVERT: E 269 ASP cc_start: 0.8695 (m-30) cc_final: 0.8005 (m-30) REVERT: E 300 ILE cc_start: 0.8581 (mm) cc_final: 0.8341 (mm) REVERT: E 385 MET cc_start: 0.8716 (ttm) cc_final: 0.8408 (ttp) REVERT: E 399 GLU cc_start: 0.8726 (pm20) cc_final: 0.8342 (pm20) REVERT: E 483 MET cc_start: 0.9412 (tmm) cc_final: 0.8452 (tmm) REVERT: E 487 GLU cc_start: 0.9142 (tt0) cc_final: 0.8854 (tt0) REVERT: E 512 ARG cc_start: 0.8848 (mtp-110) cc_final: 0.8429 (ttp-110) REVERT: F 16 ASP cc_start: 0.8812 (t0) cc_final: 0.8551 (t0) REVERT: F 28 ASP cc_start: 0.8994 (m-30) cc_final: 0.8659 (m-30) REVERT: F 70 MET cc_start: 0.8412 (mtm) cc_final: 0.8142 (mtp) REVERT: F 75 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7814 (mm-30) REVERT: F 84 LEU cc_start: 0.6388 (OUTLIER) cc_final: 0.5988 (mt) REVERT: F 254 GLU cc_start: 0.9142 (tp30) cc_final: 0.8912 (tp30) REVERT: F 269 ASP cc_start: 0.8769 (m-30) cc_final: 0.8311 (m-30) REVERT: F 300 ILE cc_start: 0.8528 (mm) cc_final: 0.8280 (mm) REVERT: F 399 GLU cc_start: 0.8698 (pm20) cc_final: 0.8322 (pm20) REVERT: F 417 LEU cc_start: 0.8573 (pt) cc_final: 0.8264 (pt) REVERT: F 483 MET cc_start: 0.9413 (tmm) cc_final: 0.8363 (tmm) REVERT: F 487 GLU cc_start: 0.9115 (tt0) cc_final: 0.8838 (tt0) REVERT: G 16 ASP cc_start: 0.8854 (t0) cc_final: 0.8488 (t0) REVERT: G 75 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7740 (mm-30) REVERT: G 84 LEU cc_start: 0.6196 (OUTLIER) cc_final: 0.5833 (mt) REVERT: G 105 ARG cc_start: 0.8480 (tmm160) cc_final: 0.8244 (ttp-110) REVERT: G 254 GLU cc_start: 0.9042 (tp30) cc_final: 0.8699 (tp30) REVERT: G 269 ASP cc_start: 0.8770 (m-30) cc_final: 0.8269 (m-30) REVERT: G 300 ILE cc_start: 0.8602 (mm) cc_final: 0.8372 (mm) REVERT: G 385 MET cc_start: 0.8633 (ttm) cc_final: 0.8294 (ttp) REVERT: G 399 GLU cc_start: 0.8736 (pm20) cc_final: 0.8355 (pm20) REVERT: G 483 MET cc_start: 0.9374 (tmm) cc_final: 0.8332 (tmm) REVERT: G 487 GLU cc_start: 0.9168 (tt0) cc_final: 0.8891 (tt0) REVERT: G 512 ARG cc_start: 0.8812 (mtp-110) cc_final: 0.8377 (ttp-110) REVERT: H 16 ASP cc_start: 0.8912 (t0) cc_final: 0.8477 (t0) REVERT: H 28 ASP cc_start: 0.8881 (m-30) cc_final: 0.8474 (m-30) REVERT: H 75 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7872 (mm-30) REVERT: H 84 LEU cc_start: 0.6375 (OUTLIER) cc_final: 0.5938 (mt) REVERT: H 274 ASP cc_start: 0.9272 (t0) cc_final: 0.8956 (t0) REVERT: H 277 GLN cc_start: 0.8472 (tp40) cc_final: 0.8188 (tp40) REVERT: H 300 ILE cc_start: 0.8480 (mm) cc_final: 0.8234 (mm) REVERT: H 399 GLU cc_start: 0.8692 (pm20) cc_final: 0.8323 (pm20) REVERT: H 483 MET cc_start: 0.9414 (tmm) cc_final: 0.8392 (tmm) REVERT: H 487 GLU cc_start: 0.9091 (tt0) cc_final: 0.8810 (tt0) REVERT: H 512 ARG cc_start: 0.9119 (ttp80) cc_final: 0.8596 (ttp80) outliers start: 73 outliers final: 28 residues processed: 582 average time/residue: 0.1357 time to fit residues: 130.6625 Evaluate side-chains 554 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 519 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 109 LYS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 109 LYS Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 109 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 4.9990 chunk 206 optimal weight: 0.7980 chunk 75 optimal weight: 0.0060 chunk 72 optimal weight: 2.9990 chunk 255 optimal weight: 0.0670 chunk 226 optimal weight: 0.5980 chunk 183 optimal weight: 0.7980 chunk 275 optimal weight: 0.8980 chunk 11 optimal weight: 0.0770 chunk 282 optimal weight: 0.3980 chunk 290 optimal weight: 3.9990 overall best weight: 0.2292 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 498 GLN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 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 = 0.3244 r_free = 0.3244 target = 0.108847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.090645 restraints weight = 33145.023| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 3.20 r_work: 0.2815 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 23384 Z= 0.092 Angle : 0.481 6.644 31640 Z= 0.249 Chirality : 0.041 0.178 3648 Planarity : 0.003 0.038 3976 Dihedral : 8.396 61.209 3724 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.86 % Allowed : 15.87 % Favored : 81.27 % 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: -0.67 (0.15), residues: 2952 helix: 0.94 (0.16), residues: 1104 sheet: -2.14 (0.21), residues: 528 loop : -0.80 (0.15), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 105 TYR 0.008 0.001 TYR D 353 PHE 0.010 0.001 PHE E 401 HIS 0.003 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00214 (23376) covalent geometry : angle 0.48133 (31640) hydrogen bonds : bond 0.02217 ( 881) hydrogen bonds : angle 4.64158 ( 2547) Misc. bond : bond 0.00022 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 612 time to evaluate : 0.877 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: A 16 ASP cc_start: 0.8800 (t0) cc_final: 0.8378 (t0) REVERT: A 36 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7458 (pp) REVERT: A 75 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7869 (mm-30) REVERT: A 84 LEU cc_start: 0.6056 (OUTLIER) cc_final: 0.5629 (mt) REVERT: A 269 ASP cc_start: 0.8695 (m-30) cc_final: 0.7949 (m-30) REVERT: A 274 ASP cc_start: 0.9035 (t0) cc_final: 0.8821 (t0) REVERT: A 399 GLU cc_start: 0.8756 (pm20) cc_final: 0.8419 (pm20) REVERT: A 407 ARG cc_start: 0.8582 (ttt180) cc_final: 0.7805 (ttt90) REVERT: A 483 MET cc_start: 0.9347 (tmm) cc_final: 0.8311 (tmm) REVERT: A 487 GLU cc_start: 0.9130 (tt0) cc_final: 0.8822 (tt0) REVERT: A 512 ARG cc_start: 0.8814 (mtp-110) cc_final: 0.8379 (ttp-110) REVERT: B 16 ASP cc_start: 0.8769 (t0) cc_final: 0.8465 (t0) REVERT: B 28 ASP cc_start: 0.8843 (m-30) cc_final: 0.8459 (m-30) REVERT: B 36 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7391 (pp) REVERT: B 75 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7872 (mm-30) REVERT: B 84 LEU cc_start: 0.6017 (OUTLIER) cc_final: 0.5582 (mt) REVERT: B 269 ASP cc_start: 0.8638 (m-30) cc_final: 0.7995 (m-30) REVERT: B 300 ILE cc_start: 0.8397 (mm) cc_final: 0.8176 (mm) REVERT: B 399 GLU cc_start: 0.8714 (pm20) cc_final: 0.8355 (pm20) REVERT: B 417 LEU cc_start: 0.8495 (pt) cc_final: 0.8206 (pt) REVERT: C 16 ASP cc_start: 0.8773 (t0) cc_final: 0.8326 (t0) REVERT: C 28 ASP cc_start: 0.8960 (m-30) cc_final: 0.8648 (m-30) REVERT: C 31 THR cc_start: 0.8753 (p) cc_final: 0.8535 (p) REVERT: C 36 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7305 (pp) REVERT: C 75 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7878 (mm-30) REVERT: C 84 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6481 (mt) REVERT: C 254 GLU cc_start: 0.9106 (tp30) cc_final: 0.8837 (tp30) REVERT: C 269 ASP cc_start: 0.8707 (m-30) cc_final: 0.8061 (m-30) REVERT: C 274 ASP cc_start: 0.9113 (t0) cc_final: 0.8813 (t0) REVERT: C 393 THR cc_start: 0.8532 (p) cc_final: 0.8294 (p) REVERT: C 399 GLU cc_start: 0.8782 (pm20) cc_final: 0.8453 (pm20) REVERT: C 407 ARG cc_start: 0.8588 (ttt180) cc_final: 0.7834 (ttt90) REVERT: C 410 LYS cc_start: 0.8712 (ptpp) cc_final: 0.8304 (ttmm) REVERT: C 412 ARG cc_start: 0.8335 (ptp-170) cc_final: 0.8046 (ptp-170) REVERT: C 483 MET cc_start: 0.9331 (tmm) cc_final: 0.8345 (tmm) REVERT: C 487 GLU cc_start: 0.9143 (tt0) cc_final: 0.8801 (tt0) REVERT: C 512 ARG cc_start: 0.8808 (mtp-110) cc_final: 0.8411 (ttp-110) REVERT: D 12 TYR cc_start: 0.8735 (t80) cc_final: 0.8435 (t80) REVERT: D 16 ASP cc_start: 0.8875 (t0) cc_final: 0.8404 (t0) REVERT: D 28 ASP cc_start: 0.8855 (m-30) cc_final: 0.8552 (m-30) REVERT: D 36 LEU cc_start: 0.7667 (OUTLIER) cc_final: 0.7329 (pp) REVERT: D 75 GLU cc_start: 0.8230 (mm-30) cc_final: 0.7966 (mm-30) REVERT: D 84 LEU cc_start: 0.6522 (OUTLIER) cc_final: 0.6082 (mt) REVERT: D 254 GLU cc_start: 0.9121 (tp30) cc_final: 0.8723 (tp30) REVERT: D 269 ASP cc_start: 0.8662 (m-30) cc_final: 0.8049 (m-30) REVERT: D 300 ILE cc_start: 0.8453 (mm) cc_final: 0.8183 (mm) REVERT: D 399 GLU cc_start: 0.8734 (pm20) cc_final: 0.8382 (pm20) REVERT: D 417 LEU cc_start: 0.8557 (pt) cc_final: 0.8273 (pt) REVERT: D 487 GLU cc_start: 0.9108 (tt0) cc_final: 0.8839 (tt0) REVERT: D 512 ARG cc_start: 0.9140 (ttp80) cc_final: 0.8658 (ttp80) REVERT: E 28 ASP cc_start: 0.8943 (m-30) cc_final: 0.8644 (m-30) REVERT: E 36 LEU cc_start: 0.7774 (OUTLIER) cc_final: 0.7421 (pp) REVERT: E 84 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.6106 (mt) REVERT: E 256 ASP cc_start: 0.8981 (m-30) cc_final: 0.8678 (t0) REVERT: E 269 ASP cc_start: 0.8577 (m-30) cc_final: 0.7785 (m-30) REVERT: E 300 ILE cc_start: 0.8488 (mm) cc_final: 0.8278 (mm) REVERT: E 385 MET cc_start: 0.8681 (ttm) cc_final: 0.8338 (ttp) REVERT: E 393 THR cc_start: 0.8590 (p) cc_final: 0.8352 (p) REVERT: E 399 GLU cc_start: 0.8734 (pm20) cc_final: 0.8373 (pm20) REVERT: E 412 ARG cc_start: 0.8344 (ptp-170) cc_final: 0.8075 (ptp-170) REVERT: E 483 MET cc_start: 0.9418 (tmm) cc_final: 0.8412 (tmm) REVERT: E 487 GLU cc_start: 0.9158 (tt0) cc_final: 0.8862 (tt0) REVERT: E 512 ARG cc_start: 0.8822 (mtp-110) cc_final: 0.8380 (ttp-110) REVERT: F 16 ASP cc_start: 0.8721 (t0) cc_final: 0.8431 (t0) REVERT: F 28 ASP cc_start: 0.8951 (m-30) cc_final: 0.8643 (m-30) REVERT: F 36 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7400 (pp) REVERT: F 75 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7920 (mm-30) REVERT: F 84 LEU cc_start: 0.5941 (OUTLIER) cc_final: 0.5508 (mt) REVERT: F 254 GLU cc_start: 0.9117 (tp30) cc_final: 0.8863 (tp30) REVERT: F 269 ASP cc_start: 0.8678 (m-30) cc_final: 0.8057 (m-30) REVERT: F 300 ILE cc_start: 0.8436 (mm) cc_final: 0.8212 (mm) REVERT: F 393 THR cc_start: 0.8538 (p) cc_final: 0.8281 (p) REVERT: F 399 GLU cc_start: 0.8725 (pm20) cc_final: 0.8365 (pm20) REVERT: F 417 LEU cc_start: 0.8480 (pt) cc_final: 0.8185 (pt) REVERT: F 487 GLU cc_start: 0.9143 (tt0) cc_final: 0.8849 (tt0) REVERT: G 16 ASP cc_start: 0.8682 (t0) cc_final: 0.8325 (t0) REVERT: G 36 LEU cc_start: 0.7702 (OUTLIER) cc_final: 0.7358 (pp) REVERT: G 75 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7917 (mm-30) REVERT: G 84 LEU cc_start: 0.6023 (OUTLIER) cc_final: 0.5647 (mt) REVERT: G 254 GLU cc_start: 0.8976 (tp30) cc_final: 0.8646 (tp30) REVERT: G 269 ASP cc_start: 0.8742 (m-30) cc_final: 0.8076 (m-30) REVERT: G 399 GLU cc_start: 0.8775 (pm20) cc_final: 0.8420 (pm20) REVERT: G 412 ARG cc_start: 0.8399 (ptp-170) cc_final: 0.8086 (ptp-170) REVERT: G 483 MET cc_start: 0.9373 (tmm) cc_final: 0.8298 (tmm) REVERT: G 487 GLU cc_start: 0.9154 (tt0) cc_final: 0.8869 (tt0) REVERT: G 512 ARG cc_start: 0.8822 (mtp-110) cc_final: 0.8371 (ttp-110) REVERT: H 16 ASP cc_start: 0.8866 (t0) cc_final: 0.8390 (t0) REVERT: H 28 ASP cc_start: 0.8810 (m-30) cc_final: 0.8444 (m-30) REVERT: H 36 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7378 (pp) REVERT: H 75 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7958 (mm-30) REVERT: H 84 LEU cc_start: 0.6472 (OUTLIER) cc_final: 0.6041 (mt) REVERT: H 274 ASP cc_start: 0.9160 (t0) cc_final: 0.8824 (t0) REVERT: H 393 THR cc_start: 0.8370 (p) cc_final: 0.8124 (p) REVERT: H 399 GLU cc_start: 0.8716 (pm20) cc_final: 0.8364 (pm20) REVERT: H 483 MET cc_start: 0.9415 (tmm) cc_final: 0.8374 (tmm) REVERT: H 487 GLU cc_start: 0.9128 (tt0) cc_final: 0.8860 (tt0) REVERT: H 512 ARG cc_start: 0.9141 (ttp80) cc_final: 0.8678 (ttp80) outliers start: 68 outliers final: 23 residues processed: 644 average time/residue: 0.1455 time to fit residues: 150.8508 Evaluate side-chains 573 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 534 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 325 MET Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 98 GLU Chi-restraints excluded: chain H residue 325 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 66 optimal weight: 0.0060 chunk 49 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 249 optimal weight: 0.9980 chunk 234 optimal weight: 0.5980 chunk 152 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 overall best weight: 1.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 GLN ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 498 GLN ** C 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 25 ASN D 102 ASN D 265 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 283 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 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.098436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.079815 restraints weight = 34211.553| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.20 r_work: 0.2654 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 23384 Z= 0.249 Angle : 0.605 6.849 31640 Z= 0.309 Chirality : 0.046 0.175 3648 Planarity : 0.003 0.035 3976 Dihedral : 8.885 59.008 3724 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 4.08 % Allowed : 15.45 % Favored : 80.47 % 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: -0.57 (0.15), residues: 2952 helix: 0.87 (0.16), residues: 1112 sheet: -1.70 (0.22), residues: 504 loop : -0.81 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 407 TYR 0.013 0.002 TYR C 353 PHE 0.009 0.001 PHE D 401 HIS 0.005 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00593 (23376) covalent geometry : angle 0.60529 (31640) hydrogen bonds : bond 0.03069 ( 881) hydrogen bonds : angle 5.11497 ( 2547) Misc. bond : bond 0.00182 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 545 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7784 (mm-30) REVERT: A 245 LEU cc_start: 0.8514 (mt) cc_final: 0.8298 (mm) REVERT: A 269 ASP cc_start: 0.8530 (m-30) cc_final: 0.8030 (m-30) REVERT: A 319 ASP cc_start: 0.8343 (m-30) cc_final: 0.7931 (m-30) REVERT: A 352 GLU cc_start: 0.8639 (tp30) cc_final: 0.8355 (tp30) REVERT: A 399 GLU cc_start: 0.8802 (pm20) cc_final: 0.8458 (pm20) REVERT: A 487 GLU cc_start: 0.9092 (tt0) cc_final: 0.8838 (tt0) REVERT: A 512 ARG cc_start: 0.8840 (mtp-110) cc_final: 0.8331 (ttp-110) REVERT: B 16 ASP cc_start: 0.8851 (t0) cc_final: 0.8526 (t0) REVERT: B 28 ASP cc_start: 0.8941 (m-30) cc_final: 0.8622 (m-30) REVERT: B 75 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7689 (mm-30) REVERT: B 269 ASP cc_start: 0.8480 (m-30) cc_final: 0.8043 (m-30) REVERT: B 300 ILE cc_start: 0.8538 (mm) cc_final: 0.8289 (mm) REVERT: B 319 ASP cc_start: 0.8268 (m-30) cc_final: 0.7799 (m-30) REVERT: B 399 GLU cc_start: 0.8773 (pm20) cc_final: 0.8413 (pm20) REVERT: B 410 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8247 (ttmm) REVERT: B 417 LEU cc_start: 0.8642 (pt) cc_final: 0.8269 (pt) REVERT: B 483 MET cc_start: 0.9405 (tmm) cc_final: 0.8499 (tmm) REVERT: C 16 ASP cc_start: 0.8778 (t0) cc_final: 0.8350 (t0) REVERT: C 28 ASP cc_start: 0.9038 (m-30) cc_final: 0.8748 (m-30) REVERT: C 33 ASN cc_start: 0.8471 (p0) cc_final: 0.8209 (p0) REVERT: C 75 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7735 (mm-30) REVERT: C 84 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6603 (mt) REVERT: C 254 GLU cc_start: 0.9085 (tp30) cc_final: 0.8818 (tp30) REVERT: C 256 ASP cc_start: 0.9029 (m-30) cc_final: 0.8710 (m-30) REVERT: C 269 ASP cc_start: 0.8554 (m-30) cc_final: 0.8049 (m-30) REVERT: C 274 ASP cc_start: 0.9249 (t0) cc_final: 0.9033 (t0) REVERT: C 352 GLU cc_start: 0.8686 (tp30) cc_final: 0.8481 (tp30) REVERT: C 399 GLU cc_start: 0.8909 (pm20) cc_final: 0.8589 (pm20) REVERT: C 410 LYS cc_start: 0.8586 (ptpp) cc_final: 0.8220 (ttmm) REVERT: C 483 MET cc_start: 0.9349 (tmm) cc_final: 0.8428 (tmm) REVERT: C 512 ARG cc_start: 0.8812 (mtp-110) cc_final: 0.8387 (ttp-110) REVERT: D 16 ASP cc_start: 0.8860 (t0) cc_final: 0.8584 (t0) REVERT: D 28 ASP cc_start: 0.8982 (m-30) cc_final: 0.8702 (m-30) REVERT: D 75 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7860 (mm-30) REVERT: D 84 LEU cc_start: 0.6457 (OUTLIER) cc_final: 0.6055 (mt) REVERT: D 254 GLU cc_start: 0.9073 (tp30) cc_final: 0.8661 (tp30) REVERT: D 269 ASP cc_start: 0.8469 (m-30) cc_final: 0.7859 (m-30) REVERT: D 274 ASP cc_start: 0.9332 (t70) cc_final: 0.9100 (t0) REVERT: D 399 GLU cc_start: 0.8783 (pm20) cc_final: 0.8427 (pm20) REVERT: D 410 LYS cc_start: 0.8689 (OUTLIER) cc_final: 0.8318 (ttmm) REVERT: D 483 MET cc_start: 0.9357 (tmm) cc_final: 0.8405 (tmm) REVERT: E 16 ASP cc_start: 0.8797 (t0) cc_final: 0.8461 (t0) REVERT: E 28 ASP cc_start: 0.8970 (m-30) cc_final: 0.8675 (m-30) REVERT: E 84 LEU cc_start: 0.6820 (OUTLIER) cc_final: 0.6545 (mt) REVERT: E 269 ASP cc_start: 0.8521 (m-30) cc_final: 0.8083 (m-30) REVERT: E 319 ASP cc_start: 0.8267 (m-30) cc_final: 0.7893 (m-30) REVERT: E 329 SER cc_start: 0.9573 (p) cc_final: 0.9260 (p) REVERT: E 399 GLU cc_start: 0.8836 (pm20) cc_final: 0.8474 (pm20) REVERT: E 412 ARG cc_start: 0.8246 (ptp-170) cc_final: 0.7983 (ptp-170) REVERT: E 483 MET cc_start: 0.9413 (tmm) cc_final: 0.8434 (tmm) REVERT: E 487 GLU cc_start: 0.9114 (tt0) cc_final: 0.8876 (tt0) REVERT: E 512 ARG cc_start: 0.8768 (mtp-110) cc_final: 0.8273 (ttp-110) REVERT: F 16 ASP cc_start: 0.8850 (t0) cc_final: 0.8555 (t0) REVERT: F 28 ASP cc_start: 0.9029 (m-30) cc_final: 0.8707 (m-30) REVERT: F 75 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7914 (mm-30) REVERT: F 84 LEU cc_start: 0.6721 (OUTLIER) cc_final: 0.6399 (mt) REVERT: F 254 GLU cc_start: 0.9118 (tp30) cc_final: 0.8873 (tp30) REVERT: F 269 ASP cc_start: 0.8471 (m-30) cc_final: 0.8066 (m-30) REVERT: F 300 ILE cc_start: 0.8572 (mm) cc_final: 0.8346 (mm) REVERT: F 319 ASP cc_start: 0.8270 (m-30) cc_final: 0.7814 (m-30) REVERT: F 329 SER cc_start: 0.9565 (p) cc_final: 0.9255 (p) REVERT: F 399 GLU cc_start: 0.8764 (pm20) cc_final: 0.8352 (pm20) REVERT: F 417 LEU cc_start: 0.8634 (pt) cc_final: 0.8260 (pt) REVERT: F 483 MET cc_start: 0.9400 (tmm) cc_final: 0.8469 (tmm) REVERT: G 28 ASP cc_start: 0.8760 (m-30) cc_final: 0.8524 (m-30) REVERT: G 75 GLU cc_start: 0.8093 (mm-30) cc_final: 0.7661 (mm-30) REVERT: G 84 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6548 (mt) REVERT: G 254 GLU cc_start: 0.9014 (tp30) cc_final: 0.8631 (tp30) REVERT: G 269 ASP cc_start: 0.8572 (m-30) cc_final: 0.8058 (m-30) REVERT: G 319 ASP cc_start: 0.8290 (m-30) cc_final: 0.7912 (m-30) REVERT: G 329 SER cc_start: 0.9540 (p) cc_final: 0.9222 (p) REVERT: G 399 GLU cc_start: 0.8823 (pm20) cc_final: 0.8469 (pm20) REVERT: G 410 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8256 (ttmm) REVERT: G 483 MET cc_start: 0.9395 (tmm) cc_final: 0.8375 (tmm) REVERT: G 487 GLU cc_start: 0.9130 (tt0) cc_final: 0.8896 (tt0) REVERT: G 512 ARG cc_start: 0.8772 (mtp-110) cc_final: 0.8475 (ttp80) REVERT: H 16 ASP cc_start: 0.8856 (t0) cc_final: 0.8587 (t0) REVERT: H 28 ASP cc_start: 0.8961 (m-30) cc_final: 0.8633 (m-30) REVERT: H 75 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7835 (mm-30) REVERT: H 84 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6380 (mt) REVERT: H 105 ARG cc_start: 0.8616 (tmm160) cc_final: 0.8343 (ttp80) REVERT: H 274 ASP cc_start: 0.9293 (t0) cc_final: 0.9015 (t0) REVERT: H 277 GLN cc_start: 0.8577 (tp40) cc_final: 0.8346 (tp40) REVERT: H 352 GLU cc_start: 0.8624 (tp30) cc_final: 0.8309 (tp30) REVERT: H 399 GLU cc_start: 0.8740 (pm20) cc_final: 0.8370 (pm20) REVERT: H 483 MET cc_start: 0.9420 (tmm) cc_final: 0.8456 (tmm) REVERT: H 487 GLU cc_start: 0.9113 (tt0) cc_final: 0.8903 (tt0) outliers start: 97 outliers final: 54 residues processed: 601 average time/residue: 0.1359 time to fit residues: 133.4983 Evaluate side-chains 588 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 525 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 109 LYS Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 109 LYS Chi-restraints excluded: chain E residue 276 SER Chi-restraints excluded: chain E residue 510 GLU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 276 SER Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 109 LYS Chi-restraints excluded: chain G residue 276 SER Chi-restraints excluded: chain G residue 367 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 410 LYS Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 109 LYS Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 41 optimal weight: 3.9990 chunk 203 optimal weight: 0.7980 chunk 279 optimal weight: 1.9990 chunk 252 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 295 optimal weight: 1.9990 chunk 229 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 293 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 96 optimal weight: 0.7980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN D 265 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN ** G 283 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 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.102063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.083321 restraints weight = 33911.272| |-----------------------------------------------------------------------------| r_work (start): 0.2858 rms_B_bonded: 3.22 r_work: 0.2705 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23384 Z= 0.149 Angle : 0.537 7.900 31640 Z= 0.276 Chirality : 0.043 0.171 3648 Planarity : 0.003 0.036 3976 Dihedral : 8.529 60.598 3724 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.28 % Allowed : 16.84 % Favored : 79.88 % 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: -0.48 (0.15), residues: 2952 helix: 0.94 (0.16), residues: 1112 sheet: -1.62 (0.22), residues: 504 loop : -0.76 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 407 TYR 0.010 0.001 TYR C 348 PHE 0.010 0.001 PHE D 401 HIS 0.003 0.001 HIS H 454 Details of bonding type rmsd covalent geometry : bond 0.00358 (23376) covalent geometry : angle 0.53689 (31640) hydrogen bonds : bond 0.02609 ( 881) hydrogen bonds : angle 4.90032 ( 2547) Misc. bond : bond 0.00098 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 548 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8694 (t0) cc_final: 0.8281 (t0) REVERT: A 75 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7696 (mm-30) REVERT: A 84 LEU cc_start: 0.6698 (OUTLIER) cc_final: 0.6370 (mt) REVERT: A 269 ASP cc_start: 0.8624 (m-30) cc_final: 0.8142 (m-30) REVERT: A 319 ASP cc_start: 0.8357 (m-30) cc_final: 0.8016 (m-30) REVERT: A 352 GLU cc_start: 0.8563 (tp30) cc_final: 0.8258 (tp30) REVERT: A 399 GLU cc_start: 0.8887 (pm20) cc_final: 0.8551 (pm20) REVERT: A 483 MET cc_start: 0.9334 (tmm) cc_final: 0.8275 (tmm) REVERT: A 487 GLU cc_start: 0.9127 (tt0) cc_final: 0.8895 (tt0) REVERT: A 512 ARG cc_start: 0.8835 (mtp-110) cc_final: 0.8377 (ttp-110) REVERT: B 16 ASP cc_start: 0.8868 (t0) cc_final: 0.8531 (t0) REVERT: B 28 ASP cc_start: 0.8910 (m-30) cc_final: 0.8620 (m-30) REVERT: B 75 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7774 (mm-30) REVERT: B 84 LEU cc_start: 0.6497 (OUTLIER) cc_final: 0.6203 (mt) REVERT: B 269 ASP cc_start: 0.8496 (m-30) cc_final: 0.8174 (m-30) REVERT: B 300 ILE cc_start: 0.8464 (mm) cc_final: 0.8208 (mm) REVERT: B 327 SER cc_start: 0.9313 (t) cc_final: 0.8773 (t) REVERT: B 399 GLU cc_start: 0.8791 (pm20) cc_final: 0.8460 (pm20) REVERT: B 417 LEU cc_start: 0.8574 (pt) cc_final: 0.8208 (pt) REVERT: B 483 MET cc_start: 0.9415 (tmm) cc_final: 0.8444 (tmm) REVERT: C 28 ASP cc_start: 0.9011 (m-30) cc_final: 0.8701 (m-30) REVERT: C 75 GLU cc_start: 0.8041 (mm-30) cc_final: 0.7740 (mm-30) REVERT: C 84 LEU cc_start: 0.6953 (OUTLIER) cc_final: 0.6599 (mt) REVERT: C 254 GLU cc_start: 0.9078 (tp30) cc_final: 0.8732 (tp30) REVERT: C 269 ASP cc_start: 0.8605 (m-30) cc_final: 0.8243 (m-30) REVERT: C 274 ASP cc_start: 0.9239 (t0) cc_final: 0.9013 (t0) REVERT: C 352 GLU cc_start: 0.8568 (tp30) cc_final: 0.8352 (tp30) REVERT: C 399 GLU cc_start: 0.8918 (pm20) cc_final: 0.8600 (pm20) REVERT: C 410 LYS cc_start: 0.8535 (ptpp) cc_final: 0.8226 (ttmm) REVERT: C 483 MET cc_start: 0.9332 (tmm) cc_final: 0.8382 (tmm) REVERT: C 512 ARG cc_start: 0.8764 (mtp-110) cc_final: 0.8392 (mtp-110) REVERT: D 16 ASP cc_start: 0.8878 (t0) cc_final: 0.8476 (t0) REVERT: D 28 ASP cc_start: 0.8938 (m-30) cc_final: 0.8640 (m-30) REVERT: D 75 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7881 (mm-30) REVERT: D 84 LEU cc_start: 0.6706 (OUTLIER) cc_final: 0.6275 (mt) REVERT: D 254 GLU cc_start: 0.9090 (tp30) cc_final: 0.8562 (tp30) REVERT: D 269 ASP cc_start: 0.8604 (m-30) cc_final: 0.7927 (m-30) REVERT: D 300 ILE cc_start: 0.8520 (mm) cc_final: 0.8261 (mm) REVERT: D 399 GLU cc_start: 0.8809 (pm20) cc_final: 0.8474 (pm20) REVERT: D 483 MET cc_start: 0.9364 (tmm) cc_final: 0.8357 (tmm) REVERT: D 512 ARG cc_start: 0.9068 (ttp80) cc_final: 0.8463 (ttp80) REVERT: E 28 ASP cc_start: 0.8954 (m-30) cc_final: 0.8667 (m-30) REVERT: E 84 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.6395 (mt) REVERT: E 269 ASP cc_start: 0.8556 (m-30) cc_final: 0.8083 (m-30) REVERT: E 399 GLU cc_start: 0.8896 (pm20) cc_final: 0.8568 (pm20) REVERT: E 412 ARG cc_start: 0.8289 (ptp-170) cc_final: 0.8043 (ptp-170) REVERT: E 487 GLU cc_start: 0.9159 (tt0) cc_final: 0.8951 (tt0) REVERT: E 512 ARG cc_start: 0.8770 (mtp-110) cc_final: 0.8325 (ttp-110) REVERT: F 16 ASP cc_start: 0.8859 (t0) cc_final: 0.8563 (t0) REVERT: F 28 ASP cc_start: 0.9011 (m-30) cc_final: 0.8708 (m-30) REVERT: F 75 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7846 (mm-30) REVERT: F 84 LEU cc_start: 0.6684 (OUTLIER) cc_final: 0.6276 (mt) REVERT: F 254 GLU cc_start: 0.9115 (tp30) cc_final: 0.8637 (tp30) REVERT: F 269 ASP cc_start: 0.8542 (m-30) cc_final: 0.8252 (m-30) REVERT: F 300 ILE cc_start: 0.8511 (mm) cc_final: 0.8276 (mm) REVERT: F 399 GLU cc_start: 0.8780 (pm20) cc_final: 0.8403 (pm20) REVERT: F 417 LEU cc_start: 0.8567 (pt) cc_final: 0.8212 (pt) REVERT: F 483 MET cc_start: 0.9400 (tmm) cc_final: 0.8421 (tmm) REVERT: G 75 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7793 (mm-30) REVERT: G 84 LEU cc_start: 0.6814 (OUTLIER) cc_final: 0.6465 (mt) REVERT: G 254 GLU cc_start: 0.8995 (tp30) cc_final: 0.8617 (tp30) REVERT: G 269 ASP cc_start: 0.8571 (m-30) cc_final: 0.7861 (m-30) REVERT: G 399 GLU cc_start: 0.8887 (pm20) cc_final: 0.8572 (pm20) REVERT: G 483 MET cc_start: 0.9388 (tmm) cc_final: 0.8325 (tmm) REVERT: G 487 GLU cc_start: 0.9161 (tt0) cc_final: 0.8956 (tt0) REVERT: G 512 ARG cc_start: 0.8817 (mtp-110) cc_final: 0.8332 (mtp-110) REVERT: H 15 ASP cc_start: 0.8917 (p0) cc_final: 0.8715 (p0) REVERT: H 16 ASP cc_start: 0.8894 (t0) cc_final: 0.8682 (t0) REVERT: H 28 ASP cc_start: 0.8908 (m-30) cc_final: 0.8591 (m-30) REVERT: H 75 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7836 (mm-30) REVERT: H 84 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6265 (mt) REVERT: H 105 ARG cc_start: 0.8517 (tmm160) cc_final: 0.8282 (ttp80) REVERT: H 274 ASP cc_start: 0.9280 (t0) cc_final: 0.8967 (t0) REVERT: H 352 GLU cc_start: 0.8537 (tp30) cc_final: 0.8165 (tp30) REVERT: H 399 GLU cc_start: 0.8761 (pm20) cc_final: 0.8403 (pm20) REVERT: H 483 MET cc_start: 0.9424 (tmm) cc_final: 0.8441 (tmm) REVERT: H 512 ARG cc_start: 0.9094 (ttp80) cc_final: 0.8758 (ttp-110) outliers start: 78 outliers final: 40 residues processed: 589 average time/residue: 0.1366 time to fit residues: 132.6958 Evaluate side-chains 581 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 533 time to evaluate : 0.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 109 LYS Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 109 LYS Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 33 optimal weight: 0.3980 chunk 95 optimal weight: 0.4980 chunk 115 optimal weight: 0.2980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN ** G 283 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 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.104569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.086177 restraints weight = 33629.043| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 3.20 r_work: 0.2748 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.3286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23384 Z= 0.120 Angle : 0.519 7.811 31640 Z= 0.268 Chirality : 0.042 0.154 3648 Planarity : 0.003 0.037 3976 Dihedral : 8.229 59.415 3724 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.41 % Allowed : 17.00 % Favored : 79.59 % 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: -0.34 (0.15), residues: 2952 helix: 1.18 (0.16), residues: 1096 sheet: -1.74 (0.25), residues: 424 loop : -0.80 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 407 TYR 0.010 0.001 TYR C 348 PHE 0.010 0.001 PHE D 401 HIS 0.002 0.001 HIS E 92 Details of bonding type rmsd covalent geometry : bond 0.00287 (23376) covalent geometry : angle 0.51923 (31640) hydrogen bonds : bond 0.02424 ( 881) hydrogen bonds : angle 4.75666 ( 2547) Misc. bond : bond 0.00054 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 551 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8701 (t0) cc_final: 0.8238 (t0) REVERT: A 75 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7770 (mm-30) REVERT: A 269 ASP cc_start: 0.8620 (m-30) cc_final: 0.8187 (m-30) REVERT: A 319 ASP cc_start: 0.8365 (m-30) cc_final: 0.8009 (m-30) REVERT: A 335 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7711 (tt0) REVERT: A 399 GLU cc_start: 0.8891 (pm20) cc_final: 0.8586 (pm20) REVERT: A 410 LYS cc_start: 0.8645 (ptpp) cc_final: 0.8286 (ttmm) REVERT: A 483 MET cc_start: 0.9345 (tmm) cc_final: 0.8242 (tmm) REVERT: A 487 GLU cc_start: 0.9131 (tt0) cc_final: 0.8911 (tt0) REVERT: A 512 ARG cc_start: 0.8822 (mtp-110) cc_final: 0.8349 (ttp-110) REVERT: B 16 ASP cc_start: 0.8850 (t0) cc_final: 0.8510 (t0) REVERT: B 28 ASP cc_start: 0.8896 (m-30) cc_final: 0.8601 (m-30) REVERT: B 75 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7789 (mm-30) REVERT: B 84 LEU cc_start: 0.6462 (OUTLIER) cc_final: 0.6096 (mt) REVERT: B 269 ASP cc_start: 0.8504 (m-30) cc_final: 0.8165 (m-30) REVERT: B 300 ILE cc_start: 0.8462 (mm) cc_final: 0.8228 (mm) REVERT: B 327 SER cc_start: 0.9259 (t) cc_final: 0.8833 (p) REVERT: B 399 GLU cc_start: 0.8858 (pm20) cc_final: 0.8551 (pm20) REVERT: B 410 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8371 (ttmm) REVERT: B 417 LEU cc_start: 0.8501 (pt) cc_final: 0.8189 (pt) REVERT: C 16 ASP cc_start: 0.8781 (t0) cc_final: 0.8310 (t0) REVERT: C 28 ASP cc_start: 0.8924 (m-30) cc_final: 0.8612 (m-30) REVERT: C 75 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7791 (mm-30) REVERT: C 84 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6512 (mt) REVERT: C 239 ASP cc_start: 0.8203 (p0) cc_final: 0.7927 (p0) REVERT: C 254 GLU cc_start: 0.9089 (tp30) cc_final: 0.8800 (tp30) REVERT: C 269 ASP cc_start: 0.8634 (m-30) cc_final: 0.8180 (m-30) REVERT: C 274 ASP cc_start: 0.9213 (t0) cc_final: 0.8964 (t0) REVERT: C 399 GLU cc_start: 0.8905 (pm20) cc_final: 0.8592 (pm20) REVERT: C 410 LYS cc_start: 0.8653 (ptpp) cc_final: 0.8284 (ttmm) REVERT: C 483 MET cc_start: 0.9336 (tmm) cc_final: 0.8382 (tmm) REVERT: C 512 ARG cc_start: 0.8766 (mtp-110) cc_final: 0.8398 (mtp-110) REVERT: D 16 ASP cc_start: 0.8835 (t0) cc_final: 0.8405 (t0) REVERT: D 28 ASP cc_start: 0.8882 (m-30) cc_final: 0.8595 (m-30) REVERT: D 75 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7911 (mm-30) REVERT: D 84 LEU cc_start: 0.6681 (OUTLIER) cc_final: 0.6238 (mt) REVERT: D 254 GLU cc_start: 0.9025 (tp30) cc_final: 0.8592 (tp30) REVERT: D 269 ASP cc_start: 0.8523 (m-30) cc_final: 0.8051 (m-30) REVERT: D 300 ILE cc_start: 0.8499 (mm) cc_final: 0.8229 (mm) REVERT: D 399 GLU cc_start: 0.8832 (pm20) cc_final: 0.8522 (pm20) REVERT: D 512 ARG cc_start: 0.9041 (ttp80) cc_final: 0.8489 (ttp80) REVERT: E 28 ASP cc_start: 0.8940 (m-30) cc_final: 0.8680 (m-30) REVERT: E 84 LEU cc_start: 0.6633 (OUTLIER) cc_final: 0.6331 (mt) REVERT: E 98 GLU cc_start: 0.8976 (mp0) cc_final: 0.8755 (pm20) REVERT: E 105 ARG cc_start: 0.8355 (ttp80) cc_final: 0.8143 (ttp80) REVERT: E 269 ASP cc_start: 0.8535 (m-30) cc_final: 0.8075 (m-30) REVERT: E 393 THR cc_start: 0.8739 (p) cc_final: 0.8476 (p) REVERT: E 399 GLU cc_start: 0.8882 (pm20) cc_final: 0.8567 (pm20) REVERT: E 412 ARG cc_start: 0.8333 (ptp-170) cc_final: 0.8117 (ptp-170) REVERT: E 512 ARG cc_start: 0.8792 (mtp-110) cc_final: 0.8344 (ttp-110) REVERT: F 16 ASP cc_start: 0.8664 (t0) cc_final: 0.8426 (t0) REVERT: F 28 ASP cc_start: 0.8947 (m-30) cc_final: 0.8690 (m-30) REVERT: F 75 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7822 (mm-30) REVERT: F 84 LEU cc_start: 0.6685 (OUTLIER) cc_final: 0.6245 (mt) REVERT: F 254 GLU cc_start: 0.9103 (tp30) cc_final: 0.8618 (tp30) REVERT: F 269 ASP cc_start: 0.8534 (m-30) cc_final: 0.8201 (m-30) REVERT: F 300 ILE cc_start: 0.8492 (mm) cc_final: 0.8278 (mm) REVERT: F 393 THR cc_start: 0.8687 (p) cc_final: 0.8473 (p) REVERT: F 399 GLU cc_start: 0.8798 (pm20) cc_final: 0.8457 (pm20) REVERT: F 417 LEU cc_start: 0.8523 (pt) cc_final: 0.8173 (pt) REVERT: G 28 ASP cc_start: 0.8678 (m-30) cc_final: 0.8322 (m-30) REVERT: G 75 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7876 (mm-30) REVERT: G 84 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.6250 (mt) REVERT: G 254 GLU cc_start: 0.9023 (tp30) cc_final: 0.8651 (tp30) REVERT: G 269 ASP cc_start: 0.8567 (m-30) cc_final: 0.8120 (m-30) REVERT: G 399 GLU cc_start: 0.8892 (pm20) cc_final: 0.8581 (pm20) REVERT: G 512 ARG cc_start: 0.8811 (mtp-110) cc_final: 0.8523 (ttp80) REVERT: H 15 ASP cc_start: 0.8900 (p0) cc_final: 0.8699 (p0) REVERT: H 16 ASP cc_start: 0.8868 (t0) cc_final: 0.8457 (t0) REVERT: H 28 ASP cc_start: 0.8834 (m-30) cc_final: 0.8565 (m-30) REVERT: H 75 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7851 (mm-30) REVERT: H 78 MET cc_start: 0.9172 (tpp) cc_final: 0.8910 (tpp) REVERT: H 105 ARG cc_start: 0.8503 (tmm160) cc_final: 0.8274 (ttp80) REVERT: H 274 ASP cc_start: 0.9179 (t0) cc_final: 0.8855 (t0) REVERT: H 393 THR cc_start: 0.8607 (p) cc_final: 0.8390 (p) REVERT: H 399 GLU cc_start: 0.8822 (pm20) cc_final: 0.8508 (pm20) REVERT: H 483 MET cc_start: 0.9423 (tmm) cc_final: 0.8433 (tmm) REVERT: H 512 ARG cc_start: 0.9153 (ttp80) cc_final: 0.8860 (ttp-110) outliers start: 81 outliers final: 40 residues processed: 592 average time/residue: 0.1354 time to fit residues: 131.9055 Evaluate side-chains 605 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 558 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 2 optimal weight: 0.6980 chunk 141 optimal weight: 0.1980 chunk 251 optimal weight: 1.9990 chunk 241 optimal weight: 3.9990 chunk 265 optimal weight: 4.9990 chunk 138 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 149 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.104206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.085724 restraints weight = 33706.226| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 3.20 r_work: 0.2740 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23384 Z= 0.131 Angle : 0.534 7.726 31640 Z= 0.274 Chirality : 0.043 0.153 3648 Planarity : 0.003 0.037 3976 Dihedral : 8.113 59.989 3724 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.82 % Allowed : 17.47 % Favored : 79.71 % 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: -0.31 (0.15), residues: 2952 helix: 1.23 (0.16), residues: 1096 sheet: -1.66 (0.24), residues: 456 loop : -0.80 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 407 TYR 0.010 0.001 TYR C 348 PHE 0.010 0.001 PHE D 401 HIS 0.003 0.001 HIS D 454 Details of bonding type rmsd covalent geometry : bond 0.00315 (23376) covalent geometry : angle 0.53415 (31640) hydrogen bonds : bond 0.02458 ( 881) hydrogen bonds : angle 4.75258 ( 2547) Misc. bond : bond 0.00064 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 632 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 565 time to evaluate : 0.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8831 (p0) cc_final: 0.8625 (p0) REVERT: A 16 ASP cc_start: 0.8704 (t0) cc_final: 0.8278 (t0) REVERT: A 36 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7515 (pp) REVERT: A 75 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7739 (mm-30) REVERT: A 269 ASP cc_start: 0.8563 (m-30) cc_final: 0.8160 (m-30) REVERT: A 319 ASP cc_start: 0.8330 (m-30) cc_final: 0.7990 (m-30) REVERT: A 335 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7723 (tt0) REVERT: A 399 GLU cc_start: 0.8898 (pm20) cc_final: 0.8607 (pm20) REVERT: A 410 LYS cc_start: 0.8647 (ptpp) cc_final: 0.8343 (ttmm) REVERT: A 483 MET cc_start: 0.9342 (tmm) cc_final: 0.8263 (tmm) REVERT: A 487 GLU cc_start: 0.9103 (tt0) cc_final: 0.8900 (tt0) REVERT: A 512 ARG cc_start: 0.8815 (mtp-110) cc_final: 0.8340 (ttp-110) REVERT: B 15 ASP cc_start: 0.8918 (p0) cc_final: 0.8706 (p0) REVERT: B 16 ASP cc_start: 0.8835 (t0) cc_final: 0.8531 (t0) REVERT: B 28 ASP cc_start: 0.8886 (m-30) cc_final: 0.8605 (m-30) REVERT: B 36 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7581 (pp) REVERT: B 75 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7818 (mm-30) REVERT: B 84 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6281 (mm) REVERT: B 269 ASP cc_start: 0.8550 (m-30) cc_final: 0.8054 (m-30) REVERT: B 300 ILE cc_start: 0.8492 (mm) cc_final: 0.8256 (mm) REVERT: B 327 SER cc_start: 0.9290 (t) cc_final: 0.8837 (p) REVERT: B 399 GLU cc_start: 0.8863 (pm20) cc_final: 0.8553 (pm20) REVERT: B 410 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8417 (ttmm) REVERT: B 417 LEU cc_start: 0.8437 (pt) cc_final: 0.8124 (pt) REVERT: B 483 MET cc_start: 0.9393 (tmm) cc_final: 0.8475 (tmm) REVERT: C 16 ASP cc_start: 0.8778 (t0) cc_final: 0.8359 (t0) REVERT: C 28 ASP cc_start: 0.8938 (m-30) cc_final: 0.8639 (m-30) REVERT: C 75 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7804 (mm-30) REVERT: C 84 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6536 (mt) REVERT: C 239 ASP cc_start: 0.8137 (p0) cc_final: 0.7874 (p0) REVERT: C 254 GLU cc_start: 0.9091 (tp30) cc_final: 0.8715 (tp30) REVERT: C 269 ASP cc_start: 0.8581 (m-30) cc_final: 0.8203 (m-30) REVERT: C 274 ASP cc_start: 0.9191 (t0) cc_final: 0.8945 (t0) REVERT: C 399 GLU cc_start: 0.8918 (pm20) cc_final: 0.8641 (pm20) REVERT: C 410 LYS cc_start: 0.8627 (ptpp) cc_final: 0.8263 (ttmm) REVERT: C 483 MET cc_start: 0.9338 (tmm) cc_final: 0.8418 (tmm) REVERT: C 512 ARG cc_start: 0.8765 (mtp-110) cc_final: 0.8396 (mtp-110) REVERT: D 16 ASP cc_start: 0.8877 (t0) cc_final: 0.8440 (t0) REVERT: D 28 ASP cc_start: 0.8857 (m-30) cc_final: 0.8598 (m-30) REVERT: D 75 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7892 (mm-30) REVERT: D 84 LEU cc_start: 0.6767 (OUTLIER) cc_final: 0.6299 (mt) REVERT: D 254 GLU cc_start: 0.9042 (tp30) cc_final: 0.8644 (tp30) REVERT: D 269 ASP cc_start: 0.8481 (m-30) cc_final: 0.7961 (m-30) REVERT: D 300 ILE cc_start: 0.8495 (mm) cc_final: 0.8252 (mm) REVERT: D 399 GLU cc_start: 0.8884 (pm20) cc_final: 0.8578 (pm20) REVERT: D 410 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8429 (ttmm) REVERT: D 483 MET cc_start: 0.9341 (tmm) cc_final: 0.8391 (tmm) REVERT: D 512 ARG cc_start: 0.9020 (ttp80) cc_final: 0.8455 (ttp80) REVERT: E 28 ASP cc_start: 0.8942 (m-30) cc_final: 0.8689 (m-30) REVERT: E 78 MET cc_start: 0.9068 (tpp) cc_final: 0.8840 (tpp) REVERT: E 84 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6309 (mt) REVERT: E 98 GLU cc_start: 0.8964 (mp0) cc_final: 0.8738 (pm20) REVERT: E 269 ASP cc_start: 0.8499 (m-30) cc_final: 0.8028 (m-30) REVERT: E 393 THR cc_start: 0.8776 (p) cc_final: 0.8542 (p) REVERT: E 399 GLU cc_start: 0.8901 (pm20) cc_final: 0.8596 (pm20) REVERT: E 483 MET cc_start: 0.9436 (tmm) cc_final: 0.8541 (tmm) REVERT: E 512 ARG cc_start: 0.8773 (mtp-110) cc_final: 0.8321 (ttp-110) REVERT: F 15 ASP cc_start: 0.8915 (p0) cc_final: 0.8695 (p0) REVERT: F 16 ASP cc_start: 0.8659 (t0) cc_final: 0.8455 (t0) REVERT: F 28 ASP cc_start: 0.8955 (m-30) cc_final: 0.8717 (m-30) REVERT: F 36 LEU cc_start: 0.7844 (OUTLIER) cc_final: 0.7601 (pp) REVERT: F 75 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7849 (mm-30) REVERT: F 84 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6281 (mt) REVERT: F 254 GLU cc_start: 0.9103 (tp30) cc_final: 0.8616 (tp30) REVERT: F 269 ASP cc_start: 0.8583 (m-30) cc_final: 0.8259 (m-30) REVERT: F 300 ILE cc_start: 0.8533 (mm) cc_final: 0.8332 (mm) REVERT: F 393 THR cc_start: 0.8748 (p) cc_final: 0.8546 (p) REVERT: F 399 GLU cc_start: 0.8831 (pm20) cc_final: 0.8497 (pm20) REVERT: F 410 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8360 (ttmm) REVERT: F 417 LEU cc_start: 0.8462 (pt) cc_final: 0.8155 (pt) REVERT: F 483 MET cc_start: 0.9377 (tmm) cc_final: 0.8443 (tmm) REVERT: G 16 ASP cc_start: 0.8691 (t0) cc_final: 0.8192 (t0) REVERT: G 28 ASP cc_start: 0.8676 (m-30) cc_final: 0.8332 (m-30) REVERT: G 75 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7820 (mm-30) REVERT: G 84 LEU cc_start: 0.6567 (OUTLIER) cc_final: 0.6195 (mt) REVERT: G 254 GLU cc_start: 0.9036 (tp30) cc_final: 0.8619 (tp30) REVERT: G 269 ASP cc_start: 0.8566 (m-30) cc_final: 0.8044 (m-30) REVERT: G 399 GLU cc_start: 0.8921 (pm20) cc_final: 0.8604 (pm20) REVERT: G 512 ARG cc_start: 0.8793 (mtp-110) cc_final: 0.8478 (ttp80) REVERT: H 16 ASP cc_start: 0.8851 (t0) cc_final: 0.8612 (t0) REVERT: H 28 ASP cc_start: 0.8857 (m-30) cc_final: 0.8601 (m-30) REVERT: H 78 MET cc_start: 0.9176 (tpp) cc_final: 0.8923 (tpp) REVERT: H 84 LEU cc_start: 0.6757 (OUTLIER) cc_final: 0.6308 (mt) REVERT: H 105 ARG cc_start: 0.8512 (tmm160) cc_final: 0.8275 (ttp80) REVERT: H 274 ASP cc_start: 0.9204 (t0) cc_final: 0.8866 (t0) REVERT: H 393 THR cc_start: 0.8606 (p) cc_final: 0.8398 (p) REVERT: H 399 GLU cc_start: 0.8841 (pm20) cc_final: 0.8515 (pm20) REVERT: H 483 MET cc_start: 0.9430 (tmm) cc_final: 0.8417 (tmm) REVERT: H 487 GLU cc_start: 0.9036 (tt0) cc_final: 0.8832 (tt0) REVERT: H 512 ARG cc_start: 0.9070 (ttp80) cc_final: 0.8591 (ttp80) outliers start: 67 outliers final: 39 residues processed: 602 average time/residue: 0.1366 time to fit residues: 134.8031 Evaluate side-chains 589 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 537 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 410 LYS Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 510 GLU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 74 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 185 optimal weight: 0.0060 chunk 70 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 chunk 11 optimal weight: 5.9990 chunk 246 optimal weight: 1.9990 chunk 217 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 102 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.103969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.085309 restraints weight = 33778.652| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.22 r_work: 0.2736 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23384 Z= 0.141 Angle : 0.555 8.086 31640 Z= 0.284 Chirality : 0.044 0.283 3648 Planarity : 0.003 0.037 3976 Dihedral : 8.086 58.650 3724 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.48 % Allowed : 18.31 % Favored : 79.21 % 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: -0.27 (0.15), residues: 2952 helix: 1.26 (0.16), residues: 1096 sheet: -1.61 (0.24), residues: 456 loop : -0.78 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 105 TYR 0.010 0.001 TYR F 348 PHE 0.010 0.001 PHE B 401 HIS 0.003 0.001 HIS B 454 Details of bonding type rmsd covalent geometry : bond 0.00339 (23376) covalent geometry : angle 0.55466 (31640) hydrogen bonds : bond 0.02476 ( 881) hydrogen bonds : angle 4.77805 ( 2547) Misc. bond : bond 0.00075 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 619 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 560 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8721 (t0) cc_final: 0.8299 (t0) REVERT: A 36 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7554 (pp) REVERT: A 75 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7730 (mm-30) REVERT: A 102 ASN cc_start: 0.8816 (t0) cc_final: 0.8235 (t0) REVERT: A 105 ARG cc_start: 0.8159 (ttp80) cc_final: 0.7758 (ttp-110) REVERT: A 269 ASP cc_start: 0.8643 (m-30) cc_final: 0.8241 (m-30) REVERT: A 319 ASP cc_start: 0.8326 (m-30) cc_final: 0.7964 (m-30) REVERT: A 399 GLU cc_start: 0.8919 (pm20) cc_final: 0.8630 (pm20) REVERT: A 410 LYS cc_start: 0.8670 (ptpp) cc_final: 0.8406 (ttmm) REVERT: A 483 MET cc_start: 0.9357 (tmm) cc_final: 0.8304 (tmm) REVERT: A 512 ARG cc_start: 0.8799 (mtp-110) cc_final: 0.8352 (ttp-110) REVERT: B 15 ASP cc_start: 0.8906 (p0) cc_final: 0.8691 (p0) REVERT: B 16 ASP cc_start: 0.8845 (t0) cc_final: 0.8542 (t0) REVERT: B 28 ASP cc_start: 0.8890 (m-30) cc_final: 0.8613 (m-30) REVERT: B 36 LEU cc_start: 0.7800 (OUTLIER) cc_final: 0.7559 (pp) REVERT: B 75 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7778 (mm-30) REVERT: B 84 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6275 (mm) REVERT: B 269 ASP cc_start: 0.8538 (m-30) cc_final: 0.8123 (m-30) REVERT: B 300 ILE cc_start: 0.8506 (mm) cc_final: 0.8273 (mm) REVERT: B 327 SER cc_start: 0.9278 (t) cc_final: 0.8860 (p) REVERT: B 399 GLU cc_start: 0.8888 (pm20) cc_final: 0.8588 (pm20) REVERT: B 410 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8428 (ttmm) REVERT: B 417 LEU cc_start: 0.8405 (pt) cc_final: 0.8114 (pt) REVERT: B 483 MET cc_start: 0.9400 (tmm) cc_final: 0.8389 (tmm) REVERT: C 28 ASP cc_start: 0.8948 (m-30) cc_final: 0.8664 (m-30) REVERT: C 75 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7799 (mm-30) REVERT: C 84 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6581 (mt) REVERT: C 239 ASP cc_start: 0.8049 (p0) cc_final: 0.7797 (p0) REVERT: C 254 GLU cc_start: 0.9090 (tp30) cc_final: 0.8691 (tp30) REVERT: C 269 ASP cc_start: 0.8585 (m-30) cc_final: 0.8206 (m-30) REVERT: C 274 ASP cc_start: 0.9209 (t0) cc_final: 0.8954 (t0) REVERT: C 399 GLU cc_start: 0.8931 (pm20) cc_final: 0.8665 (pm20) REVERT: C 410 LYS cc_start: 0.8614 (ptpp) cc_final: 0.8259 (ttmm) REVERT: C 483 MET cc_start: 0.9337 (tmm) cc_final: 0.8422 (tmm) REVERT: C 512 ARG cc_start: 0.8757 (mtp-110) cc_final: 0.8379 (mtp-110) REVERT: D 16 ASP cc_start: 0.8862 (t0) cc_final: 0.8421 (t0) REVERT: D 28 ASP cc_start: 0.8867 (m-30) cc_final: 0.8610 (m-30) REVERT: D 75 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7893 (mm-30) REVERT: D 84 LEU cc_start: 0.6680 (OUTLIER) cc_final: 0.6224 (mt) REVERT: D 239 ASP cc_start: 0.7931 (p0) cc_final: 0.7583 (p0) REVERT: D 254 GLU cc_start: 0.9032 (tp30) cc_final: 0.8600 (tp30) REVERT: D 269 ASP cc_start: 0.8432 (m-30) cc_final: 0.7907 (m-30) REVERT: D 300 ILE cc_start: 0.8522 (mm) cc_final: 0.8272 (mm) REVERT: D 399 GLU cc_start: 0.8890 (pm20) cc_final: 0.8590 (pm20) REVERT: D 410 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8448 (ttmm) REVERT: D 483 MET cc_start: 0.9349 (tmm) cc_final: 0.8353 (tmm) REVERT: D 512 ARG cc_start: 0.9010 (ttp80) cc_final: 0.8471 (ttp80) REVERT: E 28 ASP cc_start: 0.8951 (m-30) cc_final: 0.8700 (m-30) REVERT: E 78 MET cc_start: 0.9039 (tpp) cc_final: 0.8756 (tpp) REVERT: E 84 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6317 (mt) REVERT: E 105 ARG cc_start: 0.8507 (ttp80) cc_final: 0.8262 (ttp80) REVERT: E 269 ASP cc_start: 0.8510 (m-30) cc_final: 0.8005 (m-30) REVERT: E 399 GLU cc_start: 0.8901 (pm20) cc_final: 0.8594 (pm20) REVERT: E 483 MET cc_start: 0.9418 (tmm) cc_final: 0.8548 (tmm) REVERT: E 487 GLU cc_start: 0.9083 (tt0) cc_final: 0.8861 (tt0) REVERT: E 512 ARG cc_start: 0.8740 (mtp-110) cc_final: 0.8326 (ttp-110) REVERT: F 15 ASP cc_start: 0.8938 (p0) cc_final: 0.8730 (p0) REVERT: F 28 ASP cc_start: 0.8952 (m-30) cc_final: 0.8712 (m-30) REVERT: F 36 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7589 (pp) REVERT: F 75 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7888 (mm-30) REVERT: F 84 LEU cc_start: 0.6725 (OUTLIER) cc_final: 0.6288 (mt) REVERT: F 254 GLU cc_start: 0.9104 (tp30) cc_final: 0.8879 (tp30) REVERT: F 269 ASP cc_start: 0.8608 (m-30) cc_final: 0.8214 (m-30) REVERT: F 300 ILE cc_start: 0.8519 (mm) cc_final: 0.8302 (mm) REVERT: F 393 THR cc_start: 0.8782 (p) cc_final: 0.8566 (p) REVERT: F 399 GLU cc_start: 0.8892 (pm20) cc_final: 0.8569 (pm20) REVERT: F 417 LEU cc_start: 0.8412 (pt) cc_final: 0.8142 (pt) REVERT: F 483 MET cc_start: 0.9390 (tmm) cc_final: 0.8408 (tmm) REVERT: G 28 ASP cc_start: 0.8690 (m-30) cc_final: 0.8355 (m-30) REVERT: G 75 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7845 (mm-30) REVERT: G 254 GLU cc_start: 0.9064 (tp30) cc_final: 0.8676 (tp30) REVERT: G 269 ASP cc_start: 0.8545 (m-30) cc_final: 0.8016 (m-30) REVERT: G 399 GLU cc_start: 0.8915 (pm20) cc_final: 0.8603 (pm20) REVERT: G 483 MET cc_start: 0.9417 (tmm) cc_final: 0.8429 (tmm) REVERT: G 487 GLU cc_start: 0.9118 (tt0) cc_final: 0.8856 (tt0) REVERT: G 512 ARG cc_start: 0.8809 (mtp-110) cc_final: 0.8319 (mtp-110) REVERT: H 16 ASP cc_start: 0.8820 (t0) cc_final: 0.8557 (t0) REVERT: H 28 ASP cc_start: 0.8875 (m-30) cc_final: 0.8607 (m-30) REVERT: H 75 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7724 (mm-30) REVERT: H 84 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6279 (mt) REVERT: H 274 ASP cc_start: 0.9225 (t0) cc_final: 0.8884 (t0) REVERT: H 393 THR cc_start: 0.8621 (p) cc_final: 0.8396 (p) REVERT: H 399 GLU cc_start: 0.8866 (pm20) cc_final: 0.8538 (pm20) REVERT: H 483 MET cc_start: 0.9438 (tmm) cc_final: 0.8414 (tmm) REVERT: H 512 ARG cc_start: 0.9063 (ttp80) cc_final: 0.8577 (ttp80) outliers start: 59 outliers final: 45 residues processed: 594 average time/residue: 0.1382 time to fit residues: 135.2692 Evaluate side-chains 600 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 544 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 510 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 410 LYS Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 329 SER Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 410 LYS Chi-restraints excluded: chain D residue 510 GLU Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 244 LEU Chi-restraints excluded: chain E residue 280 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 510 GLU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 280 SER Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 191 optimal weight: 0.9980 chunk 129 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 192 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 102 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 102 ASN ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 372 HIS F 102 ASN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.100498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.081709 restraints weight = 33838.409| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.21 r_work: 0.2676 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 23384 Z= 0.201 Angle : 0.609 9.153 31640 Z= 0.310 Chirality : 0.045 0.158 3648 Planarity : 0.003 0.037 3976 Dihedral : 8.259 59.301 3724 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.78 % Allowed : 18.43 % Favored : 78.79 % 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: -0.22 (0.15), residues: 2952 helix: 1.10 (0.16), residues: 1112 sheet: -1.44 (0.23), residues: 488 loop : -0.61 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 105 TYR 0.012 0.001 TYR F 348 PHE 0.009 0.001 PHE D 401 HIS 0.005 0.001 HIS A 454 Details of bonding type rmsd covalent geometry : bond 0.00484 (23376) covalent geometry : angle 0.60916 (31640) hydrogen bonds : bond 0.02747 ( 881) hydrogen bonds : angle 4.94403 ( 2547) Misc. bond : bond 0.00143 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4634.00 seconds wall clock time: 80 minutes 32.63 seconds (4832.63 seconds total)