Starting phenix.real_space_refine on Sun Sep 13 12:24:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6u8e_20687/09_2026/6u8e_20687.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u8e_20687/09_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6u8e_20687/09_2026/6u8e_20687.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u8e_20687/09_2026/6u8e_20687.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6u8e_20687/09_2026/6u8e_20687.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6u8e_20687/09_2026/6u8e_20687.cif" model { file = "/net/cci-nas-00/data/ceres_data/6u8e_20687/09_2026/6u8e_20687.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u8e_20687/09_2026/6u8e_20687.cif" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNAv2': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 5.04, per 1000 atoms: 0.22 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: 1.89 Conformation dependent library (CDL) restraints added in 1.1 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: 0.73 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: 4.72 Time building geometry restraints manager: 2.53 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: 30845 3.33 - 6.65: 651 6.65 - 9.98: 104 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: 13396 28.40 - 56.81: 384 56.81 - 85.21: 16 85.21 - 113.62: 0 113.62 - 142.02: 4 Dihedral angle restraints: 13800 sinusoidal: 5328 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 13797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 2643 0.065 - 0.130: 856 0.130 - 0.195: 109 0.195 - 0.260: 16 0.260 - 0.326: 24 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.180 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 : 1.273 16.626 31640 Z= 0.631 Chirality : 0.065 0.326 3648 Planarity : 0.006 0.046 3976 Dihedral : 12.080 142.020 8424 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/Z covalent geometry : bond 0.01395 / 0.65 (23376) covalent geometry : angle 1.27347 / 0.63 (31640) hydrogen bonds : bond 0.22392 / 14.58 ( 881) hydrogen bonds : angle 8.58230 / 5.94 ( 2547) Misc. bond : bond 0.26927 / 13.50 ( 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 : 0.821 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: 0.1577 time to fit residues: 201.2312 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 : 0.853 ------------------------------------------------------------------------------- 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... 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 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** 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: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.104807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.086362 restraints weight = 33138.165| |-----------------------------------------------------------------------------| r_work (start): 0.2921 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: 0.7832 moved from start: 0.2090 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= 0.147 Angle : 0.590 6.657 31640 Z= 0.305 Chirality : 0.044 0.151 3648 Planarity : 0.004 0.041 3976 Dihedral : 7.843 66.686 3330 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.32 % Allowed : 10.06 % 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: -1.17 (0.14), residues: 1144 sheet: -2.77 (0.18), residues: 544 loop : -1.46 (0.15), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 105 TYR 0.019 0.002 TYR G 12 PHE 0.013 0.001 PHE D 401 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 (23376) covalent geometry : angle 0.59049 / 0.30 (31640) hydrogen bonds : bond 0.03421 / 2.28 ( 881) hydrogen bonds : angle 5.48399 / 3.77 ( 2547) Misc. bond : bond 0.00073 / 0.04 ( 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 678 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 599 time to evaluate : 0.791 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 84 LEU cc_start: 0.6876 (OUTLIER) cc_final: 0.6489 (mt) REVERT: A 269 ASP cc_start: 0.8739 (m-30) cc_final: 0.8353 (m-30) REVERT: A 271 VAL cc_start: 0.8949 (m) cc_final: 0.8719 (p) REVERT: A 329 SER cc_start: 0.9590 (p) cc_final: 0.9304 (p) REVERT: A 399 GLU cc_start: 0.8691 (pm20) cc_final: 0.8317 (pm20) REVERT: A 483 MET cc_start: 0.9308 (tmm) cc_final: 0.8363 (tmm) REVERT: A 487 GLU cc_start: 0.9137 (tt0) cc_final: 0.8797 (tt0) REVERT: A 512 ARG cc_start: 0.8937 (mtp-110) cc_final: 0.8532 (ttp-110) REVERT: B 16 ASP cc_start: 0.8933 (t0) cc_final: 0.8648 (t0) REVERT: B 28 ASP cc_start: 0.8873 (m-30) cc_final: 0.8533 (m-30) REVERT: B 84 LEU cc_start: 0.6838 (OUTLIER) cc_final: 0.6405 (mt) REVERT: B 269 ASP cc_start: 0.8838 (m-30) cc_final: 0.8319 (m-30) REVERT: B 277 GLN cc_start: 0.8649 (tp40) cc_final: 0.8281 (tp40) REVERT: B 300 ILE cc_start: 0.8380 (mm) cc_final: 0.8133 (mm) REVERT: B 399 GLU cc_start: 0.8682 (pm20) cc_final: 0.8313 (pm20) REVERT: B 417 LEU cc_start: 0.8582 (pt) cc_final: 0.8267 (pt) REVERT: B 487 GLU cc_start: 0.9028 (tt0) cc_final: 0.8765 (tt0) REVERT: C 28 ASP cc_start: 0.8959 (m-30) cc_final: 0.8535 (m-30) REVERT: C 84 LEU cc_start: 0.7032 (OUTLIER) cc_final: 0.6650 (mt) REVERT: C 254 GLU cc_start: 0.9172 (tp30) cc_final: 0.8950 (tp30) REVERT: C 269 ASP cc_start: 0.8811 (m-30) cc_final: 0.8385 (m-30) REVERT: C 329 SER cc_start: 0.9603 (p) cc_final: 0.9351 (p) REVERT: C 399 GLU cc_start: 0.8753 (pm20) cc_final: 0.8365 (pm20) REVERT: C 483 MET cc_start: 0.9318 (tmm) cc_final: 0.8354 (tmm) REVERT: C 487 GLU cc_start: 0.9112 (tt0) cc_final: 0.8803 (tt0) REVERT: C 512 ARG cc_start: 0.8934 (mtp-110) cc_final: 0.8499 (ttp-110) REVERT: D 16 ASP cc_start: 0.8920 (t0) cc_final: 0.8578 (t0) REVERT: D 28 ASP cc_start: 0.8902 (m-30) cc_final: 0.8523 (m-30) REVERT: D 84 LEU cc_start: 0.6835 (OUTLIER) cc_final: 0.6405 (mt) REVERT: D 269 ASP cc_start: 0.8842 (m-30) cc_final: 0.8184 (m-30) REVERT: D 399 GLU cc_start: 0.8691 (pm20) cc_final: 0.8287 (pm20) REVERT: D 417 LEU cc_start: 0.8630 (pt) cc_final: 0.8288 (pt) REVERT: D 483 MET cc_start: 0.9343 (tmm) cc_final: 0.8237 (tmm) REVERT: D 487 GLU cc_start: 0.9065 (tt0) cc_final: 0.8789 (tt0) REVERT: E 16 ASP cc_start: 0.8881 (t0) cc_final: 0.8605 (t0) REVERT: E 28 ASP cc_start: 0.8957 (m-30) cc_final: 0.8536 (m-30) REVERT: E 62 LYS cc_start: 0.8186 (mmtp) cc_final: 0.7807 (mmmt) REVERT: E 84 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6550 (mt) REVERT: E 269 ASP cc_start: 0.8775 (m-30) cc_final: 0.8392 (m-30) REVERT: E 300 ILE cc_start: 0.8545 (mm) cc_final: 0.8322 (mm) REVERT: E 399 GLU cc_start: 0.8688 (pm20) cc_final: 0.8321 (pm20) REVERT: E 483 MET cc_start: 0.9385 (tmm) cc_final: 0.8433 (tmm) REVERT: E 487 GLU cc_start: 0.9093 (tt0) cc_final: 0.8830 (tt0) REVERT: E 512 ARG cc_start: 0.8959 (mtp-110) cc_final: 0.8603 (ttp-110) REVERT: F 16 ASP cc_start: 0.8783 (t0) cc_final: 0.8519 (t0) REVERT: F 28 ASP cc_start: 0.8951 (m-30) cc_final: 0.8518 (m-30) REVERT: F 84 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6383 (mt) REVERT: F 254 GLU cc_start: 0.9214 (tp30) cc_final: 0.8987 (tp30) REVERT: F 269 ASP cc_start: 0.8923 (m-30) cc_final: 0.8261 (m-30) REVERT: F 300 ILE cc_start: 0.8435 (mm) cc_final: 0.8216 (mm) REVERT: F 399 GLU cc_start: 0.8683 (pm20) cc_final: 0.8305 (pm20) REVERT: F 417 LEU cc_start: 0.8561 (pt) cc_final: 0.8240 (pt) REVERT: F 487 GLU cc_start: 0.9090 (tt0) cc_final: 0.8819 (tt0) REVERT: G 16 ASP cc_start: 0.8923 (t0) cc_final: 0.8662 (t0) REVERT: G 84 LEU cc_start: 0.6549 (OUTLIER) cc_final: 0.6151 (mt) REVERT: G 254 GLU cc_start: 0.9071 (tp30) cc_final: 0.8714 (tp30) REVERT: G 269 ASP cc_start: 0.8766 (m-30) cc_final: 0.8381 (m-30) REVERT: G 300 ILE cc_start: 0.8594 (mm) cc_final: 0.8376 (mm) REVERT: G 399 GLU cc_start: 0.8700 (pm20) cc_final: 0.8333 (pm20) REVERT: G 483 MET cc_start: 0.9324 (tmm) cc_final: 0.8327 (tmm) REVERT: G 487 GLU cc_start: 0.9111 (tt0) cc_final: 0.8835 (tt0) REVERT: G 512 ARG cc_start: 0.8884 (mtp-110) cc_final: 0.8440 (ttp-110) REVERT: H 16 ASP cc_start: 0.8916 (t0) cc_final: 0.8545 (t0) REVERT: H 28 ASP cc_start: 0.8882 (m-30) cc_final: 0.8413 (m-30) REVERT: H 84 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6366 (mt) REVERT: H 277 GLN cc_start: 0.8608 (tp40) cc_final: 0.8348 (tp40) REVERT: H 399 GLU cc_start: 0.8664 (pm20) cc_final: 0.8271 (pm20) REVERT: H 483 MET cc_start: 0.9404 (tmm) cc_final: 0.8376 (tmm) REVERT: H 487 GLU cc_start: 0.9057 (tt0) cc_final: 0.8780 (tt0) outliers start: 79 outliers final: 18 residues processed: 637 average time/residue: 0.1382 time to fit residues: 145.7645 Evaluate side-chains 534 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 508 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 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 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: 0.0770 chunk 194 optimal weight: 0.6980 chunk 103 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 281 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 192 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 112 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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** 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 = 0.3191 r_free = 0.3191 target = 0.104901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.086531 restraints weight = 33365.957| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.19 r_work: 0.2775 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23384 Z= 0.128 Angle : 0.539 7.735 31640 Z= 0.273 Chirality : 0.043 0.152 3648 Planarity : 0.004 0.039 3976 Dihedral : 7.382 65.222 3326 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.90 % Allowed : 12.71 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.52 (0.14), residues: 2952 helix: -0.06 (0.15), residues: 1112 sheet: -2.45 (0.19), residues: 544 loop : -1.04 (0.15), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 105 TYR 0.012 0.001 TYR F 12 PHE 0.011 0.001 PHE F 401 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 (23376) covalent geometry : angle 0.53868 / 0.27 (31640) hydrogen bonds : bond 0.02742 / 1.83 ( 881) hydrogen bonds : angle 5.02840 / 3.46 ( 2547) Misc. bond : bond 0.00071 / 0.04 ( 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 644 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 575 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8814 (t0) cc_final: 0.8386 (t0) REVERT: A 36 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7574 (pp) REVERT: A 75 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7556 (mm-30) REVERT: A 84 LEU cc_start: 0.6240 (OUTLIER) cc_final: 0.5840 (mt) REVERT: A 269 ASP cc_start: 0.8721 (m-30) cc_final: 0.8297 (m-30) REVERT: A 399 GLU cc_start: 0.8711 (pm20) cc_final: 0.8330 (pm20) REVERT: A 487 GLU cc_start: 0.9142 (tt0) cc_final: 0.8841 (tt0) REVERT: A 512 ARG cc_start: 0.8897 (mtp-110) cc_final: 0.8488 (ttp-110) REVERT: B 16 ASP cc_start: 0.8933 (t0) cc_final: 0.8613 (t0) REVERT: B 28 ASP cc_start: 0.8863 (m-30) cc_final: 0.8524 (m-30) REVERT: B 75 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7816 (mm-30) REVERT: B 84 LEU cc_start: 0.6187 (OUTLIER) cc_final: 0.5764 (mt) REVERT: B 269 ASP cc_start: 0.8671 (m-30) cc_final: 0.8217 (m-30) REVERT: B 271 VAL cc_start: 0.8964 (m) cc_final: 0.8756 (p) REVERT: B 274 ASP cc_start: 0.9326 (t0) cc_final: 0.9035 (t0) REVERT: B 277 GLN cc_start: 0.8543 (tp40) cc_final: 0.8203 (tp40) REVERT: B 300 ILE cc_start: 0.8321 (mm) cc_final: 0.8102 (mm) REVERT: B 399 GLU cc_start: 0.8691 (pm20) cc_final: 0.8315 (pm20) REVERT: B 417 LEU cc_start: 0.8559 (pt) cc_final: 0.8300 (pt) REVERT: B 420 MET cc_start: 0.5650 (ttm) cc_final: 0.5438 (ttm) REVERT: B 483 MET cc_start: 0.9427 (tmm) cc_final: 0.8360 (tmm) REVERT: B 487 GLU cc_start: 0.9064 (tt0) cc_final: 0.8795 (tt0) REVERT: C 16 ASP cc_start: 0.8855 (t0) cc_final: 0.8502 (t0) REVERT: C 28 ASP cc_start: 0.8992 (m-30) cc_final: 0.8705 (m-30) REVERT: C 34 ASP cc_start: 0.8730 (t0) cc_final: 0.8365 (t0) REVERT: C 36 LEU cc_start: 0.7972 (OUTLIER) cc_final: 0.7631 (pp) REVERT: C 75 GLU cc_start: 0.8056 (mm-30) cc_final: 0.7679 (mm-30) REVERT: C 84 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.5954 (mt) REVERT: C 254 GLU cc_start: 0.9121 (tp30) cc_final: 0.8917 (tp30) REVERT: C 269 ASP cc_start: 0.8748 (m-30) cc_final: 0.8273 (m-30) REVERT: C 271 VAL cc_start: 0.9065 (m) cc_final: 0.8857 (p) REVERT: C 399 GLU cc_start: 0.8809 (pm20) cc_final: 0.8440 (pm20) REVERT: C 420 MET cc_start: 0.5854 (ttm) cc_final: 0.5630 (ttm) REVERT: C 487 GLU cc_start: 0.9150 (tt0) cc_final: 0.8860 (tt0) REVERT: C 512 ARG cc_start: 0.8924 (mtp-110) cc_final: 0.8462 (ttp-110) REVERT: D 16 ASP cc_start: 0.8916 (t0) cc_final: 0.8487 (t0) REVERT: D 28 ASP cc_start: 0.8889 (m-30) cc_final: 0.8549 (m-30) REVERT: D 36 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7583 (pp) REVERT: D 75 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7742 (mm-30) REVERT: D 84 LEU cc_start: 0.6419 (OUTLIER) cc_final: 0.5971 (mt) REVERT: D 269 ASP cc_start: 0.8720 (m-30) cc_final: 0.8156 (m-30) REVERT: D 271 VAL cc_start: 0.8978 (m) cc_final: 0.8771 (p) REVERT: D 300 ILE cc_start: 0.8544 (mm) cc_final: 0.8293 (mm) REVERT: D 399 GLU cc_start: 0.8698 (pm20) cc_final: 0.8332 (pm20) REVERT: D 417 LEU cc_start: 0.8622 (pt) cc_final: 0.8323 (pt) REVERT: D 487 GLU cc_start: 0.9115 (tt0) cc_final: 0.8838 (tt0) REVERT: D 512 ARG cc_start: 0.9122 (ttp80) cc_final: 0.8775 (ttp-110) REVERT: E 28 ASP cc_start: 0.8957 (m-30) cc_final: 0.8588 (m-30) REVERT: E 36 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7658 (pp) REVERT: E 62 LYS cc_start: 0.8343 (mmtp) cc_final: 0.8047 (mmmt) REVERT: E 75 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7593 (mm-30) REVERT: E 84 LEU cc_start: 0.6612 (OUTLIER) cc_final: 0.6234 (mt) REVERT: E 269 ASP cc_start: 0.8745 (m-30) cc_final: 0.8247 (m-30) REVERT: E 300 ILE cc_start: 0.8532 (mm) cc_final: 0.8305 (mm) REVERT: E 399 GLU cc_start: 0.8716 (pm20) cc_final: 0.8333 (pm20) REVERT: E 483 MET cc_start: 0.9416 (tmm) cc_final: 0.8428 (tmm) REVERT: E 487 GLU cc_start: 0.9145 (tt0) cc_final: 0.8872 (tt0) REVERT: E 512 ARG cc_start: 0.8895 (mtp-110) cc_final: 0.8484 (ttp-110) REVERT: F 16 ASP cc_start: 0.8825 (t0) cc_final: 0.8565 (t0) REVERT: F 28 ASP cc_start: 0.8961 (m-30) cc_final: 0.8569 (m-30) REVERT: F 75 GLU cc_start: 0.8168 (mm-30) cc_final: 0.7720 (mm-30) REVERT: F 84 LEU cc_start: 0.6460 (OUTLIER) cc_final: 0.6046 (mt) REVERT: F 254 GLU cc_start: 0.9172 (tp30) cc_final: 0.8965 (tp30) REVERT: F 269 ASP cc_start: 0.8800 (m-30) cc_final: 0.8218 (m-30) REVERT: F 274 ASP cc_start: 0.9319 (t0) cc_final: 0.9046 (t0) REVERT: F 300 ILE cc_start: 0.8408 (mm) cc_final: 0.8166 (mm) REVERT: F 399 GLU cc_start: 0.8694 (pm20) cc_final: 0.8296 (pm20) REVERT: F 417 LEU cc_start: 0.8544 (pt) cc_final: 0.8287 (pt) REVERT: F 420 MET cc_start: 0.5521 (ttm) cc_final: 0.5303 (ttm) REVERT: F 483 MET cc_start: 0.9407 (tmm) cc_final: 0.8345 (tmm) REVERT: F 487 GLU cc_start: 0.9135 (tt0) cc_final: 0.8855 (tt0) REVERT: G 16 ASP cc_start: 0.8886 (t0) cc_final: 0.8547 (t0) REVERT: G 28 ASP cc_start: 0.8737 (m-30) cc_final: 0.8404 (m-30) REVERT: G 75 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7548 (mm-30) REVERT: G 84 LEU cc_start: 0.6219 (OUTLIER) cc_final: 0.5821 (mt) REVERT: G 102 ASN cc_start: 0.8829 (t0) cc_final: 0.8345 (t0) REVERT: G 105 ARG cc_start: 0.8499 (tmm160) cc_final: 0.8200 (ttp80) REVERT: G 254 GLU cc_start: 0.9055 (tp30) cc_final: 0.8713 (tp30) REVERT: G 269 ASP cc_start: 0.8791 (m-30) cc_final: 0.8328 (m-30) REVERT: G 277 GLN cc_start: 0.8556 (tp40) cc_final: 0.8263 (tp40) REVERT: G 300 ILE cc_start: 0.8538 (mm) cc_final: 0.8309 (mm) REVERT: G 399 GLU cc_start: 0.8712 (pm20) cc_final: 0.8328 (pm20) REVERT: G 483 MET cc_start: 0.9364 (tmm) cc_final: 0.8347 (tmm) REVERT: G 487 GLU cc_start: 0.9168 (tt0) cc_final: 0.8887 (tt0) REVERT: G 512 ARG cc_start: 0.8870 (mtp-110) cc_final: 0.8407 (ttp-110) REVERT: H 16 ASP cc_start: 0.8910 (t0) cc_final: 0.8471 (t0) REVERT: H 28 ASP cc_start: 0.8861 (m-30) cc_final: 0.8581 (m-30) REVERT: H 75 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7715 (mm-30) REVERT: H 84 LEU cc_start: 0.6371 (OUTLIER) cc_final: 0.5925 (mt) REVERT: H 271 VAL cc_start: 0.8968 (m) cc_final: 0.8716 (p) REVERT: H 274 ASP cc_start: 0.9341 (t0) cc_final: 0.9052 (t0) REVERT: H 277 GLN cc_start: 0.8528 (tp40) cc_final: 0.8167 (tp40) REVERT: H 399 GLU cc_start: 0.8675 (pm20) cc_final: 0.8304 (pm20) REVERT: H 483 MET cc_start: 0.9423 (tmm) cc_final: 0.8382 (tmm) REVERT: H 487 GLU cc_start: 0.9113 (tt0) cc_final: 0.8829 (tt0) REVERT: H 512 ARG cc_start: 0.9142 (ttp80) cc_final: 0.8614 (ttp80) outliers start: 69 outliers final: 29 residues processed: 609 average time/residue: 0.1354 time to fit residues: 135.8505 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 : 0.818 ------------------------------------------------------------------------------- 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 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 453 ILE Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 500 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 109 LYS Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 500 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 453 ILE 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 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 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 325 MET 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 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: 0.8980 chunk 14 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 259 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 235 optimal weight: 1.9990 chunk 148 optimal weight: 3.9990 chunk 181 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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** ** 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 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 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 = 0.3125 r_free = 0.3125 target = 0.100137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.081376 restraints weight = 34020.563| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 3.21 r_work: 0.2666 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 23384 Z= 0.223 Angle : 0.595 6.961 31640 Z= 0.302 Chirality : 0.046 0.209 3648 Planarity : 0.004 0.036 3976 Dihedral : 7.559 68.255 3324 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.50 % Allowed : 13.26 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.10 (0.15), residues: 2952 helix: 0.50 (0.16), residues: 1112 sheet: -2.30 (0.19), residues: 544 loop : -0.98 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 105 TYR 0.013 0.002 TYR D 348 PHE 0.011 0.001 PHE G 401 HIS 0.004 0.001 HIS A 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.22 (23376) covalent geometry : angle 0.59491 / 0.30 (31640) hydrogen bonds : bond 0.03079 / 2.05 ( 881) hydrogen bonds : angle 5.12624 / 3.53 ( 2547) Misc. bond : bond 0.00175 / 0.09 ( 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 665 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 558 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7741 (mm-30) REVERT: A 84 LEU cc_start: 0.6818 (OUTLIER) cc_final: 0.6472 (mt) REVERT: A 269 ASP cc_start: 0.8695 (m-30) cc_final: 0.8202 (m-30) REVERT: A 319 ASP cc_start: 0.8370 (m-30) cc_final: 0.7981 (m-30) REVERT: A 329 SER cc_start: 0.9587 (p) cc_final: 0.9368 (p) REVERT: A 352 GLU cc_start: 0.8650 (tp30) cc_final: 0.8379 (tp30) REVERT: A 399 GLU cc_start: 0.8804 (pm20) cc_final: 0.8429 (pm20) REVERT: A 483 MET cc_start: 0.9329 (tmm) cc_final: 0.8364 (tmm) REVERT: A 487 GLU cc_start: 0.9113 (tt0) cc_final: 0.8828 (tt0) REVERT: A 512 ARG cc_start: 0.8808 (mtp-110) cc_final: 0.8380 (ttp-110) REVERT: B 16 ASP cc_start: 0.8898 (t0) cc_final: 0.8564 (t0) REVERT: B 28 ASP cc_start: 0.8948 (m-30) cc_final: 0.8640 (m-30) REVERT: B 75 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7820 (mm-30) REVERT: B 84 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6477 (mt) REVERT: B 269 ASP cc_start: 0.8570 (m-30) cc_final: 0.8007 (m-30) REVERT: B 271 VAL cc_start: 0.9037 (m) cc_final: 0.8831 (p) REVERT: B 274 ASP cc_start: 0.9353 (t0) cc_final: 0.9112 (t0) REVERT: B 277 GLN cc_start: 0.8625 (tp40) cc_final: 0.8310 (tp40) REVERT: B 300 ILE cc_start: 0.8509 (mm) cc_final: 0.8265 (mm) REVERT: B 319 ASP cc_start: 0.8272 (m-30) cc_final: 0.7805 (m-30) REVERT: B 385 MET cc_start: 0.8754 (ttm) cc_final: 0.8396 (ttp) REVERT: B 399 GLU cc_start: 0.8755 (pm20) cc_final: 0.8357 (pm20) REVERT: B 417 LEU cc_start: 0.8619 (pt) cc_final: 0.8273 (pt) REVERT: B 483 MET cc_start: 0.9440 (tmm) cc_final: 0.8498 (tmm) REVERT: C 28 ASP cc_start: 0.9037 (m-30) cc_final: 0.8738 (m-30) REVERT: C 33 ASN cc_start: 0.8177 (p0) cc_final: 0.7952 (p0) REVERT: C 75 GLU cc_start: 0.8160 (mm-30) cc_final: 0.7804 (mm-30) REVERT: C 84 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6606 (mt) REVERT: C 102 ASN cc_start: 0.8884 (t0) cc_final: 0.8660 (t0) REVERT: C 269 ASP cc_start: 0.8666 (m-30) cc_final: 0.8137 (m-30) REVERT: C 271 VAL cc_start: 0.9073 (m) cc_final: 0.8807 (p) REVERT: C 329 SER cc_start: 0.9590 (p) cc_final: 0.9361 (p) REVERT: C 399 GLU cc_start: 0.8835 (pm20) cc_final: 0.8459 (pm20) REVERT: C 483 MET cc_start: 0.9342 (tmm) cc_final: 0.8389 (tmm) REVERT: C 512 ARG cc_start: 0.8819 (mtp-110) cc_final: 0.8349 (ttp-110) REVERT: D 16 ASP cc_start: 0.8894 (t0) cc_final: 0.8494 (t0) REVERT: D 28 ASP cc_start: 0.8974 (m-30) cc_final: 0.8684 (m-30) REVERT: D 75 GLU cc_start: 0.8208 (mm-30) cc_final: 0.7811 (mm-30) REVERT: D 84 LEU cc_start: 0.6490 (OUTLIER) cc_final: 0.6156 (mt) REVERT: D 269 ASP cc_start: 0.8654 (m-30) cc_final: 0.8216 (m-30) REVERT: D 271 VAL cc_start: 0.9023 (m) cc_final: 0.8791 (p) REVERT: D 399 GLU cc_start: 0.8789 (pm20) cc_final: 0.8399 (pm20) REVERT: D 483 MET cc_start: 0.9374 (tmm) cc_final: 0.8411 (tmm) REVERT: D 512 ARG cc_start: 0.9083 (ttp80) cc_final: 0.8554 (ttp80) REVERT: E 28 ASP cc_start: 0.9030 (m-30) cc_final: 0.8681 (m-30) REVERT: E 62 LYS cc_start: 0.8355 (mmtp) cc_final: 0.8094 (mmmt) REVERT: E 75 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7771 (mm-30) REVERT: E 84 LEU cc_start: 0.6856 (OUTLIER) cc_final: 0.6606 (mt) REVERT: E 269 ASP cc_start: 0.8678 (m-30) cc_final: 0.8187 (m-30) REVERT: E 300 ILE cc_start: 0.8633 (mm) cc_final: 0.8391 (mm) REVERT: E 329 SER cc_start: 0.9592 (p) cc_final: 0.9265 (p) REVERT: E 399 GLU cc_start: 0.8779 (pm20) cc_final: 0.8406 (pm20) REVERT: E 483 MET cc_start: 0.9413 (tmm) cc_final: 0.8480 (tmm) REVERT: E 487 GLU cc_start: 0.9051 (tt0) cc_final: 0.8772 (tt0) REVERT: E 512 ARG cc_start: 0.8841 (mtp-110) cc_final: 0.8420 (ttp-110) REVERT: F 16 ASP cc_start: 0.8887 (t0) cc_final: 0.8604 (t0) REVERT: F 28 ASP cc_start: 0.9032 (m-30) cc_final: 0.8649 (m-30) REVERT: F 75 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7790 (mm-30) REVERT: F 84 LEU cc_start: 0.6848 (OUTLIER) cc_final: 0.6463 (mt) REVERT: F 254 GLU cc_start: 0.9123 (tp30) cc_final: 0.8886 (tp30) REVERT: F 269 ASP cc_start: 0.8732 (m-30) cc_final: 0.8304 (m-30) REVERT: F 274 ASP cc_start: 0.9320 (t0) cc_final: 0.9112 (t0) REVERT: F 300 ILE cc_start: 0.8512 (mm) cc_final: 0.8265 (mm) REVERT: F 319 ASP cc_start: 0.8271 (m-30) cc_final: 0.7812 (m-30) REVERT: F 329 SER cc_start: 0.9574 (p) cc_final: 0.9276 (p) REVERT: F 385 MET cc_start: 0.8800 (ttm) cc_final: 0.8432 (ttp) REVERT: F 399 GLU cc_start: 0.8757 (pm20) cc_final: 0.8347 (pm20) REVERT: F 417 LEU cc_start: 0.8611 (pt) cc_final: 0.8262 (pt) REVERT: F 483 MET cc_start: 0.9416 (tmm) cc_final: 0.8450 (tmm) REVERT: G 28 ASP cc_start: 0.8753 (m-30) cc_final: 0.8394 (m-30) REVERT: G 70 MET cc_start: 0.8445 (mtm) cc_final: 0.8060 (mtp) REVERT: G 75 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7792 (mm-30) REVERT: G 84 LEU cc_start: 0.6878 (OUTLIER) cc_final: 0.6531 (mt) REVERT: G 102 ASN cc_start: 0.8832 (t0) cc_final: 0.8518 (t0) REVERT: G 105 ARG cc_start: 0.8585 (tmm160) cc_final: 0.8320 (ttp80) REVERT: G 254 GLU cc_start: 0.9024 (tp30) cc_final: 0.8642 (tp30) REVERT: G 269 ASP cc_start: 0.8744 (m-30) cc_final: 0.8227 (m-30) REVERT: G 319 ASP cc_start: 0.8311 (m-30) cc_final: 0.7928 (m-30) REVERT: G 329 SER cc_start: 0.9556 (p) cc_final: 0.9229 (p) REVERT: G 399 GLU cc_start: 0.8790 (pm20) cc_final: 0.8387 (pm20) REVERT: G 483 MET cc_start: 0.9374 (tmm) cc_final: 0.8368 (tmm) REVERT: G 487 GLU cc_start: 0.9073 (tt0) cc_final: 0.8812 (tt0) REVERT: G 512 ARG cc_start: 0.8734 (mtp-110) cc_final: 0.8299 (ttp-110) REVERT: H 16 ASP cc_start: 0.8890 (t0) cc_final: 0.8670 (t0) REVERT: H 28 ASP cc_start: 0.8940 (m-30) cc_final: 0.8547 (m-30) REVERT: H 75 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7767 (mm-30) REVERT: H 84 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.6108 (mt) REVERT: H 102 ASN cc_start: 0.8837 (t0) cc_final: 0.8466 (t0) REVERT: H 105 ARG cc_start: 0.8613 (tmm160) cc_final: 0.8354 (ttp80) REVERT: H 271 VAL cc_start: 0.9023 (m) cc_final: 0.8773 (p) REVERT: H 274 ASP cc_start: 0.9351 (t0) cc_final: 0.9126 (t0) REVERT: H 277 GLN cc_start: 0.8626 (tp40) cc_final: 0.8318 (tp40) REVERT: H 329 SER cc_start: 0.9577 (p) cc_final: 0.9292 (p) REVERT: H 399 GLU cc_start: 0.8747 (pm20) cc_final: 0.8361 (pm20) REVERT: H 483 MET cc_start: 0.9420 (tmm) cc_final: 0.8495 (tmm) REVERT: H 487 GLU cc_start: 0.9009 (tt0) cc_final: 0.8708 (tt0) REVERT: H 512 ARG cc_start: 0.9097 (ttp80) cc_final: 0.8561 (ttp80) outliers start: 107 outliers final: 60 residues processed: 628 average time/residue: 0.1355 time to fit residues: 140.3217 Evaluate side-chains 593 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 525 time to evaluate : 0.836 ------------------------------------------------------------------------------- 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 109 LYS Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 280 SER 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 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 361 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 471 ILE 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 109 LYS Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 453 ILE 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 276 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 510 GLU 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 361 VAL Chi-restraints excluded: chain E residue 370 VAL 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 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 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 361 VAL Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 500 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 276 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 370 VAL 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: 0.6980 chunk 75 optimal weight: 0.2980 chunk 72 optimal weight: 0.8980 chunk 255 optimal weight: 0.9990 chunk 226 optimal weight: 2.9990 chunk 183 optimal weight: 1.9990 chunk 275 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 282 optimal weight: 0.6980 chunk 290 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 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** ** B 504 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 285 ASN ** 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 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 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 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 504 HIS ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.101909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.083667 restraints weight = 33541.477| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 3.16 r_work: 0.2728 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2943 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= 0.135 Angle : 0.539 6.459 31640 Z= 0.273 Chirality : 0.043 0.157 3648 Planarity : 0.003 0.038 3976 Dihedral : 7.425 71.304 3324 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.07 % Allowed : 15.53 % Favored : 81.40 % 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: -0.76 (0.15), residues: 2952 helix: 0.88 (0.16), residues: 1096 sheet: -2.09 (0.20), residues: 544 loop : -0.88 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 105 TYR 0.009 0.001 TYR A 348 PHE 0.011 0.001 PHE G 401 HIS 0.003 0.001 HIS E 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (23376) covalent geometry : angle 0.53888 / 0.27 (31640) hydrogen bonds : bond 0.02510 / 1.67 ( 881) hydrogen bonds : angle 4.83180 / 3.33 ( 2547) Misc. bond : bond 0.00088 / 0.04 ( 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 617 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 544 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8103 (mm-30) cc_final: 0.7829 (mm-30) REVERT: A 269 ASP cc_start: 0.8688 (m-30) cc_final: 0.7969 (m-30) REVERT: A 319 ASP cc_start: 0.8390 (m-30) cc_final: 0.8010 (m-30) REVERT: A 399 GLU cc_start: 0.8803 (pm20) cc_final: 0.8448 (pm20) REVERT: A 483 MET cc_start: 0.9345 (tmm) cc_final: 0.8377 (tmm) REVERT: A 487 GLU cc_start: 0.9136 (tt0) cc_final: 0.8869 (tt0) REVERT: A 512 ARG cc_start: 0.8826 (mtp-110) cc_final: 0.8425 (ttp-110) REVERT: B 16 ASP cc_start: 0.8934 (t0) cc_final: 0.8589 (t0) REVERT: B 28 ASP cc_start: 0.8919 (m-30) cc_final: 0.8586 (m-30) REVERT: B 75 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7933 (mm-30) REVERT: B 84 LEU cc_start: 0.6765 (OUTLIER) cc_final: 0.6375 (mt) REVERT: B 269 ASP cc_start: 0.8544 (m-30) cc_final: 0.7867 (m-30) REVERT: B 274 ASP cc_start: 0.9345 (t0) cc_final: 0.9085 (t0) REVERT: B 300 ILE cc_start: 0.8490 (mm) cc_final: 0.8249 (mm) REVERT: B 327 SER cc_start: 0.9306 (t) cc_final: 0.8927 (p) REVERT: B 399 GLU cc_start: 0.8768 (pm20) cc_final: 0.8424 (pm20) REVERT: B 410 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8166 (ttmm) REVERT: B 417 LEU cc_start: 0.8603 (pt) cc_final: 0.8273 (pt) REVERT: C 16 ASP cc_start: 0.8682 (t0) cc_final: 0.8282 (t0) REVERT: C 28 ASP cc_start: 0.9001 (m-30) cc_final: 0.8687 (m-30) REVERT: C 75 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7832 (mm-30) REVERT: C 84 LEU cc_start: 0.6780 (OUTLIER) cc_final: 0.6431 (mt) REVERT: C 269 ASP cc_start: 0.8752 (m-30) cc_final: 0.8205 (m-30) REVERT: C 399 GLU cc_start: 0.8816 (pm20) cc_final: 0.8459 (pm20) REVERT: C 410 LYS cc_start: 0.8602 (ptpp) cc_final: 0.8221 (ttmm) REVERT: C 483 MET cc_start: 0.9353 (tmm) cc_final: 0.8378 (tmm) REVERT: C 512 ARG cc_start: 0.8836 (mtp-110) cc_final: 0.8370 (ttp-110) REVERT: D 16 ASP cc_start: 0.8915 (t0) cc_final: 0.8495 (t0) REVERT: D 28 ASP cc_start: 0.8963 (m-30) cc_final: 0.8670 (m-30) REVERT: D 75 GLU cc_start: 0.8179 (mm-30) cc_final: 0.7888 (mm-30) REVERT: D 84 LEU cc_start: 0.6424 (OUTLIER) cc_final: 0.5993 (mt) REVERT: D 269 ASP cc_start: 0.8607 (m-30) cc_final: 0.8106 (m-30) REVERT: D 300 ILE cc_start: 0.8463 (mm) cc_final: 0.8153 (mm) REVERT: D 399 GLU cc_start: 0.8796 (pm20) cc_final: 0.8431 (pm20) REVERT: D 410 LYS cc_start: 0.8606 (ptpp) cc_final: 0.8286 (ttmm) REVERT: E 28 ASP cc_start: 0.8950 (m-30) cc_final: 0.8607 (m-30) REVERT: E 62 LYS cc_start: 0.8355 (mmtp) cc_final: 0.8082 (mmmt) REVERT: E 75 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7824 (mm-30) REVERT: E 84 LEU cc_start: 0.6804 (OUTLIER) cc_final: 0.6464 (mt) REVERT: E 98 GLU cc_start: 0.8957 (pm20) cc_final: 0.8750 (mp0) REVERT: E 252 THR cc_start: 0.9343 (OUTLIER) cc_final: 0.9116 (m) REVERT: E 254 GLU cc_start: 0.9203 (tp30) cc_final: 0.8904 (tp30) REVERT: E 256 ASP cc_start: 0.9005 (m-30) cc_final: 0.8794 (t0) REVERT: E 269 ASP cc_start: 0.8731 (m-30) cc_final: 0.8091 (m-30) REVERT: E 277 GLN cc_start: 0.8541 (tp40) cc_final: 0.8339 (tp40) REVERT: E 399 GLU cc_start: 0.8772 (pm20) cc_final: 0.8397 (pm20) REVERT: E 487 GLU cc_start: 0.9144 (tt0) cc_final: 0.8888 (tt0) REVERT: E 512 ARG cc_start: 0.8810 (mtp-110) cc_final: 0.8411 (ttp-110) REVERT: F 16 ASP cc_start: 0.8877 (t0) cc_final: 0.8550 (t0) REVERT: F 28 ASP cc_start: 0.8992 (m-30) cc_final: 0.8676 (m-30) REVERT: F 75 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7893 (mm-30) REVERT: F 84 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.6123 (mt) REVERT: F 254 GLU cc_start: 0.9129 (tp30) cc_final: 0.8886 (tp30) REVERT: F 269 ASP cc_start: 0.8670 (m-30) cc_final: 0.8087 (m-30) REVERT: F 274 ASP cc_start: 0.9332 (t0) cc_final: 0.9101 (t0) REVERT: F 300 ILE cc_start: 0.8421 (mm) cc_final: 0.8196 (mm) REVERT: F 399 GLU cc_start: 0.8747 (pm20) cc_final: 0.8380 (pm20) REVERT: F 417 LEU cc_start: 0.8577 (pt) cc_final: 0.8244 (pt) REVERT: G 75 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7879 (mm-30) REVERT: G 84 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6429 (mt) REVERT: G 102 ASN cc_start: 0.8841 (t0) cc_final: 0.8532 (t0) REVERT: G 105 ARG cc_start: 0.8439 (tmm160) cc_final: 0.8235 (ttp80) REVERT: G 254 GLU cc_start: 0.9028 (tp30) cc_final: 0.8681 (tp30) REVERT: G 269 ASP cc_start: 0.8746 (m-30) cc_final: 0.8100 (m-30) REVERT: G 399 GLU cc_start: 0.8783 (pm20) cc_final: 0.8403 (pm20) REVERT: G 483 MET cc_start: 0.9362 (tmm) cc_final: 0.8389 (tmm) REVERT: G 487 GLU cc_start: 0.9163 (tt0) cc_final: 0.8915 (tt0) REVERT: G 512 ARG cc_start: 0.8788 (mtp-110) cc_final: 0.8303 (ttp-110) REVERT: H 16 ASP cc_start: 0.8917 (t0) cc_final: 0.8505 (t0) REVERT: H 28 ASP cc_start: 0.8916 (m-30) cc_final: 0.8658 (m-30) REVERT: H 70 MET cc_start: 0.8756 (mtp) cc_final: 0.8417 (mtp) REVERT: H 84 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.6037 (mt) REVERT: H 102 ASN cc_start: 0.8867 (t0) cc_final: 0.8506 (t0) REVERT: H 105 ARG cc_start: 0.8507 (tmm160) cc_final: 0.8261 (ttp80) REVERT: H 271 VAL cc_start: 0.9017 (m) cc_final: 0.8810 (p) REVERT: H 274 ASP cc_start: 0.9340 (t0) cc_final: 0.9047 (t0) REVERT: H 300 ILE cc_start: 0.8391 (mm) cc_final: 0.8164 (mm) REVERT: H 399 GLU cc_start: 0.8734 (pm20) cc_final: 0.8370 (pm20) REVERT: H 483 MET cc_start: 0.9426 (tmm) cc_final: 0.8432 (tmm) REVERT: H 487 GLU cc_start: 0.9109 (tt0) cc_final: 0.8837 (tt0) outliers start: 73 outliers final: 35 residues processed: 589 average time/residue: 0.1345 time to fit residues: 130.5222 Evaluate side-chains 562 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 518 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 276 SER 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 109 LYS Chi-restraints excluded: chain B residue 410 LYS 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 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 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 386 MET 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 252 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 109 LYS Chi-restraints excluded: chain F residue 276 SER 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 276 SER Chi-restraints excluded: chain G residue 500 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 276 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 66 optimal weight: 0.0970 chunk 49 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 249 optimal weight: 0.9980 chunk 234 optimal weight: 0.8980 chunk 152 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 184 optimal weight: 3.9990 chunk 74 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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 504 HIS ** 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** ** 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 504 HIS ** 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** ** 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 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 ** G 504 HIS ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.100341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.082061 restraints weight = 33865.069| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.17 r_work: 0.2702 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.3028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23384 Z= 0.160 Angle : 0.554 7.825 31640 Z= 0.278 Chirality : 0.044 0.211 3648 Planarity : 0.003 0.037 3976 Dihedral : 7.436 71.707 3324 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.58 % Allowed : 14.98 % Favored : 81.44 % 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: -0.66 (0.15), residues: 2952 helix: 1.00 (0.16), residues: 1096 sheet: -2.14 (0.22), residues: 496 loop : -0.88 (0.15), residues: 1360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 105 TYR 0.021 0.001 TYR C 12 PHE 0.010 0.001 PHE H 401 HIS 0.003 0.001 HIS C 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.16 (23376) covalent geometry : angle 0.55399 / 0.28 (31640) hydrogen bonds : bond 0.02573 / 1.72 ( 881) hydrogen bonds : angle 4.84317 / 3.33 ( 2547) Misc. bond : bond 0.00107 / 0.05 ( 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 629 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 544 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7779 (mm-30) REVERT: A 269 ASP cc_start: 0.8712 (m-30) cc_final: 0.8072 (m-30) REVERT: A 319 ASP cc_start: 0.8363 (m-30) cc_final: 0.8002 (m-30) REVERT: A 352 GLU cc_start: 0.8587 (tp30) cc_final: 0.8258 (tp30) REVERT: A 399 GLU cc_start: 0.8834 (pm20) cc_final: 0.8493 (pm20) REVERT: A 483 MET cc_start: 0.9360 (tmm) cc_final: 0.8369 (tmm) REVERT: A 487 GLU cc_start: 0.9129 (tt0) cc_final: 0.8885 (tt0) REVERT: A 512 ARG cc_start: 0.8855 (mtp-110) cc_final: 0.8404 (ttp-110) REVERT: B 16 ASP cc_start: 0.8891 (t0) cc_final: 0.8544 (t0) REVERT: B 28 ASP cc_start: 0.8948 (m-30) cc_final: 0.8645 (m-30) REVERT: B 75 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7875 (mm-30) REVERT: B 84 LEU cc_start: 0.6526 (OUTLIER) cc_final: 0.6288 (mm) REVERT: B 269 ASP cc_start: 0.8516 (m-30) cc_final: 0.8040 (m-30) REVERT: B 274 ASP cc_start: 0.9343 (t0) cc_final: 0.9096 (t0) REVERT: B 300 ILE cc_start: 0.8481 (mm) cc_final: 0.8258 (mm) REVERT: B 327 SER cc_start: 0.9261 (t) cc_final: 0.8946 (p) REVERT: B 385 MET cc_start: 0.8769 (ttm) cc_final: 0.8391 (ttp) REVERT: B 399 GLU cc_start: 0.8805 (pm20) cc_final: 0.8442 (pm20) REVERT: B 410 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8198 (ttmm) REVERT: B 417 LEU cc_start: 0.8629 (pt) cc_final: 0.8285 (pt) REVERT: B 483 MET cc_start: 0.9405 (tmm) cc_final: 0.8462 (tmm) REVERT: C 16 ASP cc_start: 0.8639 (t0) cc_final: 0.8171 (t0) REVERT: C 28 ASP cc_start: 0.9000 (m-30) cc_final: 0.8698 (m-30) REVERT: C 75 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7816 (mm-30) REVERT: C 269 ASP cc_start: 0.8705 (m-30) cc_final: 0.8239 (m-30) REVERT: C 399 GLU cc_start: 0.8856 (pm20) cc_final: 0.8521 (pm20) REVERT: C 410 LYS cc_start: 0.8561 (ptpp) cc_final: 0.8201 (ttmm) REVERT: C 483 MET cc_start: 0.9353 (tmm) cc_final: 0.8366 (tmm) REVERT: C 512 ARG cc_start: 0.8809 (mtp-110) cc_final: 0.8403 (mtp-110) REVERT: D 16 ASP cc_start: 0.8878 (t0) cc_final: 0.8439 (t0) REVERT: D 28 ASP cc_start: 0.8956 (m-30) cc_final: 0.8667 (m-30) REVERT: D 75 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7856 (mm-30) REVERT: D 84 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.6040 (mt) REVERT: D 269 ASP cc_start: 0.8591 (m-30) cc_final: 0.8069 (m-30) REVERT: D 399 GLU cc_start: 0.8804 (pm20) cc_final: 0.8451 (pm20) REVERT: D 410 LYS cc_start: 0.8594 (ptpp) cc_final: 0.8312 (ttmm) REVERT: D 483 MET cc_start: 0.9364 (tmm) cc_final: 0.8391 (tmm) REVERT: D 512 ARG cc_start: 0.9115 (ttp80) cc_final: 0.8744 (ttp-110) REVERT: E 28 ASP cc_start: 0.8952 (m-30) cc_final: 0.8621 (m-30) REVERT: E 62 LYS cc_start: 0.8382 (mmtp) cc_final: 0.8107 (mmmt) REVERT: E 75 GLU cc_start: 0.8012 (mm-30) cc_final: 0.7769 (mm-30) REVERT: E 84 LEU cc_start: 0.6588 (OUTLIER) cc_final: 0.6260 (mt) REVERT: E 252 THR cc_start: 0.9343 (OUTLIER) cc_final: 0.9130 (m) REVERT: E 269 ASP cc_start: 0.8590 (m-30) cc_final: 0.8139 (m-30) REVERT: E 399 GLU cc_start: 0.8825 (pm20) cc_final: 0.8465 (pm20) REVERT: E 483 MET cc_start: 0.9453 (tmm) cc_final: 0.8493 (tmm) REVERT: E 487 GLU cc_start: 0.9144 (tt0) cc_final: 0.8911 (tt0) REVERT: E 512 ARG cc_start: 0.8815 (mtp-110) cc_final: 0.8376 (ttp-110) REVERT: F 16 ASP cc_start: 0.8886 (t0) cc_final: 0.8567 (t0) REVERT: F 28 ASP cc_start: 0.9025 (m-30) cc_final: 0.8709 (m-30) REVERT: F 75 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7836 (mm-30) REVERT: F 84 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6378 (mt) REVERT: F 254 GLU cc_start: 0.9112 (tp30) cc_final: 0.8634 (tp30) REVERT: F 269 ASP cc_start: 0.8531 (m-30) cc_final: 0.8087 (m-30) REVERT: F 274 ASP cc_start: 0.9307 (t0) cc_final: 0.9057 (t0) REVERT: F 300 ILE cc_start: 0.8511 (mm) cc_final: 0.8271 (mm) REVERT: F 399 GLU cc_start: 0.8795 (pm20) cc_final: 0.8412 (pm20) REVERT: F 417 LEU cc_start: 0.8606 (pt) cc_final: 0.8249 (pt) REVERT: F 483 MET cc_start: 0.9395 (tmm) cc_final: 0.8441 (tmm) REVERT: G 75 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7819 (mm-30) REVERT: G 102 ASN cc_start: 0.8808 (t0) cc_final: 0.8495 (t0) REVERT: G 105 ARG cc_start: 0.8438 (tmm160) cc_final: 0.8227 (ttp80) REVERT: G 254 GLU cc_start: 0.9024 (tp30) cc_final: 0.8575 (tp30) REVERT: G 269 ASP cc_start: 0.8660 (m-30) cc_final: 0.8214 (m-30) REVERT: G 399 GLU cc_start: 0.8839 (pm20) cc_final: 0.8475 (pm20) REVERT: G 410 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8246 (ttmm) REVERT: G 483 MET cc_start: 0.9368 (tmm) cc_final: 0.8367 (tmm) REVERT: G 487 GLU cc_start: 0.9148 (tt0) cc_final: 0.8924 (tt0) REVERT: G 512 ARG cc_start: 0.8807 (mtp-110) cc_final: 0.8542 (ttp80) REVERT: H 16 ASP cc_start: 0.8873 (t0) cc_final: 0.8462 (t0) REVERT: H 28 ASP cc_start: 0.8906 (m-30) cc_final: 0.8606 (m-30) REVERT: H 70 MET cc_start: 0.8939 (mtp) cc_final: 0.8720 (mtp) REVERT: H 84 LEU cc_start: 0.6416 (OUTLIER) cc_final: 0.6016 (mt) REVERT: H 98 GLU cc_start: 0.8974 (pm20) cc_final: 0.8691 (mp0) REVERT: H 102 ASN cc_start: 0.8871 (t0) cc_final: 0.8505 (t0) REVERT: H 105 ARG cc_start: 0.8583 (tmm160) cc_final: 0.8308 (ttp80) REVERT: H 271 VAL cc_start: 0.9019 (m) cc_final: 0.8799 (p) REVERT: H 274 ASP cc_start: 0.9335 (t0) cc_final: 0.9052 (t0) REVERT: H 300 ILE cc_start: 0.8417 (mm) cc_final: 0.8194 (mm) REVERT: H 399 GLU cc_start: 0.8778 (pm20) cc_final: 0.8407 (pm20) REVERT: H 483 MET cc_start: 0.9420 (tmm) cc_final: 0.8468 (tmm) REVERT: H 487 GLU cc_start: 0.9112 (tt0) cc_final: 0.8881 (tt0) REVERT: H 512 ARG cc_start: 0.9040 (ttp80) cc_final: 0.8435 (ttp80) outliers start: 85 outliers final: 51 residues processed: 593 average time/residue: 0.1381 time to fit residues: 135.3148 Evaluate side-chains 594 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 535 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 66 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 453 ILE 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 276 SER Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 410 LYS 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 B residue 510 GLU Chi-restraints excluded: chain C residue 66 VAL 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 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 276 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 510 GLU 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 252 THR 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 36 LEU 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 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 36 LEU 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 325 MET 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 276 SER 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: 4.9990 chunk 203 optimal weight: 0.0010 chunk 279 optimal weight: 0.5980 chunk 252 optimal weight: 0.9990 chunk 11 optimal weight: 0.0470 chunk 295 optimal weight: 3.9990 chunk 229 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 293 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 overall best weight: 0.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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 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 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 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 498 GLN ** 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 277 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.104122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.085895 restraints weight = 33576.150| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.19 r_work: 0.2759 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23384 Z= 0.107 Angle : 0.524 7.609 31640 Z= 0.263 Chirality : 0.042 0.178 3648 Planarity : 0.003 0.037 3976 Dihedral : 7.304 73.632 3322 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.37 % Allowed : 15.61 % Favored : 81.02 % 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: -0.49 (0.15), residues: 2952 helix: 1.15 (0.16), residues: 1096 sheet: -2.20 (0.23), residues: 480 loop : -0.76 (0.15), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 512 TYR 0.013 0.001 TYR C 12 PHE 0.010 0.001 PHE H 401 HIS 0.002 0.000 HIS E 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (23376) covalent geometry : angle 0.52418 / 0.26 (31640) hydrogen bonds : bond 0.02300 / 1.53 ( 881) hydrogen bonds : angle 4.62317 / 3.19 ( 2547) Misc. bond : bond 0.00034 / 0.02 ( 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 659 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 579 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASP cc_start: 0.8677 (t0) cc_final: 0.8140 (t0) REVERT: A 75 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7740 (mm-30) REVERT: A 269 ASP cc_start: 0.8640 (m-30) cc_final: 0.8159 (m-30) REVERT: A 319 ASP cc_start: 0.8367 (m-30) cc_final: 0.8009 (m-30) REVERT: A 399 GLU cc_start: 0.8843 (pm20) cc_final: 0.8529 (pm20) REVERT: A 410 LYS cc_start: 0.8628 (ptpp) cc_final: 0.8233 (ttmm) REVERT: A 483 MET cc_start: 0.9352 (tmm) cc_final: 0.8305 (tmm) REVERT: A 487 GLU cc_start: 0.9136 (tt0) cc_final: 0.8906 (tt0) REVERT: A 512 ARG cc_start: 0.8849 (mtp-110) cc_final: 0.8403 (ttp-110) REVERT: B 15 ASP cc_start: 0.8931 (p0) cc_final: 0.8712 (p0) REVERT: B 16 ASP cc_start: 0.8701 (t0) cc_final: 0.8456 (t0) REVERT: B 28 ASP cc_start: 0.8884 (m-30) cc_final: 0.8584 (m-30) REVERT: B 75 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7885 (mm-30) REVERT: B 84 LEU cc_start: 0.6331 (OUTLIER) cc_final: 0.5949 (mt) REVERT: B 269 ASP cc_start: 0.8493 (m-30) cc_final: 0.7834 (m-30) REVERT: B 274 ASP cc_start: 0.9351 (t0) cc_final: 0.9062 (t0) REVERT: B 300 ILE cc_start: 0.8437 (mm) cc_final: 0.8203 (mm) REVERT: B 327 SER cc_start: 0.9253 (t) cc_final: 0.8875 (p) REVERT: B 385 MET cc_start: 0.8757 (ttm) cc_final: 0.8371 (ttp) REVERT: B 399 GLU cc_start: 0.8785 (pm20) cc_final: 0.8446 (pm20) REVERT: B 417 LEU cc_start: 0.8544 (pt) cc_final: 0.8197 (pt) REVERT: B 483 MET cc_start: 0.9425 (tmm) cc_final: 0.8372 (tmm) REVERT: C 15 ASP cc_start: 0.8795 (p0) cc_final: 0.8587 (p0) REVERT: C 16 ASP cc_start: 0.8644 (t0) cc_final: 0.8181 (t0) REVERT: C 28 ASP cc_start: 0.8940 (m-30) cc_final: 0.8640 (m-30) REVERT: C 75 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7692 (mm-30) REVERT: C 78 MET cc_start: 0.9127 (tpp) cc_final: 0.8904 (tpp) REVERT: C 254 GLU cc_start: 0.9256 (tp30) cc_final: 0.8999 (tp30) REVERT: C 269 ASP cc_start: 0.8592 (m-30) cc_final: 0.8200 (m-30) REVERT: C 399 GLU cc_start: 0.8879 (pm20) cc_final: 0.8534 (pm20) REVERT: C 410 LYS cc_start: 0.8663 (ptpp) cc_final: 0.8281 (ttmm) REVERT: C 483 MET cc_start: 0.9357 (tmm) cc_final: 0.8348 (tmm) REVERT: C 512 ARG cc_start: 0.8798 (mtp-110) cc_final: 0.8408 (mtp-110) REVERT: D 16 ASP cc_start: 0.8871 (t0) cc_final: 0.8452 (t0) REVERT: D 28 ASP cc_start: 0.8896 (m-30) cc_final: 0.8608 (m-30) REVERT: D 75 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7842 (mm-30) REVERT: D 78 MET cc_start: 0.9223 (tpp) cc_final: 0.8965 (tpp) REVERT: D 84 LEU cc_start: 0.6440 (OUTLIER) cc_final: 0.6030 (mt) REVERT: D 269 ASP cc_start: 0.8575 (m-30) cc_final: 0.8088 (m-30) REVERT: D 399 GLU cc_start: 0.8814 (pm20) cc_final: 0.8500 (pm20) REVERT: D 410 LYS cc_start: 0.8639 (ptpp) cc_final: 0.8366 (ttmm) REVERT: D 512 ARG cc_start: 0.9068 (ttp80) cc_final: 0.8496 (ttp-110) REVERT: E 28 ASP cc_start: 0.8927 (m-30) cc_final: 0.8629 (m-30) REVERT: E 75 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7777 (mm-30) REVERT: E 78 MET cc_start: 0.9141 (tpp) cc_final: 0.8940 (tpp) REVERT: E 84 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.6255 (mt) REVERT: E 102 ASN cc_start: 0.8781 (t0) cc_final: 0.8371 (t0) REVERT: E 105 ARG cc_start: 0.8429 (ttp-110) cc_final: 0.7894 (ttp80) REVERT: E 269 ASP cc_start: 0.8502 (m-30) cc_final: 0.8150 (m-30) REVERT: E 393 THR cc_start: 0.8728 (p) cc_final: 0.8463 (p) REVERT: E 399 GLU cc_start: 0.8803 (pm20) cc_final: 0.8460 (pm20) REVERT: E 412 ARG cc_start: 0.8426 (ptp-170) cc_final: 0.8221 (ptp-170) REVERT: E 487 GLU cc_start: 0.9142 (tt0) cc_final: 0.8931 (tt0) REVERT: E 512 ARG cc_start: 0.8825 (mtp-110) cc_final: 0.8391 (ttp-110) REVERT: F 16 ASP cc_start: 0.8738 (t0) cc_final: 0.8468 (t0) REVERT: F 28 ASP cc_start: 0.8962 (m-30) cc_final: 0.8693 (m-30) REVERT: F 75 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7909 (mm-30) REVERT: F 84 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.6014 (mt) REVERT: F 254 GLU cc_start: 0.9107 (tp30) cc_final: 0.8621 (tp30) REVERT: F 269 ASP cc_start: 0.8494 (m-30) cc_final: 0.7954 (m-30) REVERT: F 274 ASP cc_start: 0.9301 (t0) cc_final: 0.9034 (t0) REVERT: F 300 ILE cc_start: 0.8469 (mm) cc_final: 0.8244 (mm) REVERT: F 393 THR cc_start: 0.8645 (p) cc_final: 0.8416 (p) REVERT: F 399 GLU cc_start: 0.8794 (pm20) cc_final: 0.8428 (pm20) REVERT: F 417 LEU cc_start: 0.8513 (pt) cc_final: 0.8154 (pt) REVERT: F 483 MET cc_start: 0.9395 (tmm) cc_final: 0.8352 (tmm) REVERT: G 16 ASP cc_start: 0.8686 (t0) cc_final: 0.8228 (t0) REVERT: G 28 ASP cc_start: 0.8683 (m-30) cc_final: 0.8340 (m-30) REVERT: G 75 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7795 (mm-30) REVERT: G 78 MET cc_start: 0.9126 (tpp) cc_final: 0.8910 (tpp) REVERT: G 254 GLU cc_start: 0.8939 (tp30) cc_final: 0.8584 (tp30) REVERT: G 256 ASP cc_start: 0.9033 (m-30) cc_final: 0.8766 (m-30) REVERT: G 269 ASP cc_start: 0.8626 (m-30) cc_final: 0.8229 (m-30) REVERT: G 399 GLU cc_start: 0.8828 (pm20) cc_final: 0.8486 (pm20) REVERT: G 483 MET cc_start: 0.9353 (tmm) cc_final: 0.8327 (tmm) REVERT: G 487 GLU cc_start: 0.9163 (tt0) cc_final: 0.8945 (tt0) REVERT: G 512 ARG cc_start: 0.8786 (mtp-110) cc_final: 0.8344 (ttp-110) REVERT: H 16 ASP cc_start: 0.8835 (t0) cc_final: 0.8444 (t0) REVERT: H 28 ASP cc_start: 0.8873 (m-30) cc_final: 0.8607 (m-30) REVERT: H 70 MET cc_start: 0.8795 (mtp) cc_final: 0.8547 (mtp) REVERT: H 75 GLU cc_start: 0.8077 (mm-30) cc_final: 0.7733 (mm-30) REVERT: H 84 LEU cc_start: 0.6347 (OUTLIER) cc_final: 0.5938 (mt) REVERT: H 102 ASN cc_start: 0.8816 (t0) cc_final: 0.8469 (t0) REVERT: H 105 ARG cc_start: 0.8535 (tmm160) cc_final: 0.8298 (ttp80) REVERT: H 274 ASP cc_start: 0.9353 (t0) cc_final: 0.9054 (t0) REVERT: H 393 THR cc_start: 0.8536 (p) cc_final: 0.8296 (p) REVERT: H 399 GLU cc_start: 0.8824 (pm20) cc_final: 0.8484 (pm20) REVERT: H 487 GLU cc_start: 0.9121 (tt0) cc_final: 0.8911 (tt0) REVERT: H 512 ARG cc_start: 0.9011 (ttp80) cc_final: 0.8669 (ttp-110) outliers start: 80 outliers final: 39 residues processed: 620 average time/residue: 0.1426 time to fit residues: 143.7594 Evaluate side-chains 613 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 569 time to evaluate : 0.695 ------------------------------------------------------------------------------- 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 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 109 LYS Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 510 GLU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 333 THR 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 66 VAL Chi-restraints excluded: chain E residue 84 LEU Chi-restraints excluded: chain E residue 333 THR 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 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 66 VAL Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 276 SER 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 66 VAL Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 510 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 228 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 43 optimal weight: 0.1980 chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** C 498 GLN 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 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 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 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 = 0.3157 r_free = 0.3157 target = 0.103326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.085347 restraints weight = 33640.149| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 3.22 r_work: 0.2719 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3281 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= 0.131 Angle : 0.544 7.435 31640 Z= 0.271 Chirality : 0.043 0.172 3648 Planarity : 0.003 0.037 3976 Dihedral : 7.305 71.885 3322 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.16 % Allowed : 16.41 % Favored : 80.43 % 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: -0.28 (0.15), residues: 2952 helix: 1.23 (0.16), residues: 1096 sheet: -1.78 (0.24), residues: 440 loop : -0.72 (0.15), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 105 TYR 0.024 0.001 TYR C 12 PHE 0.010 0.001 PHE B 401 HIS 0.002 0.001 HIS E 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 (23376) covalent geometry : angle 0.54351 / 0.27 (31640) hydrogen bonds : bond 0.02383 / 1.59 ( 881) hydrogen bonds : angle 4.64215 / 3.20 ( 2547) Misc. bond : bond 0.00058 / 0.03 ( 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 649 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 574 time to evaluate : 0.857 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.8004 (mm-30) cc_final: 0.7702 (mm-30) REVERT: A 269 ASP cc_start: 0.8545 (m-30) cc_final: 0.8002 (m-30) REVERT: A 319 ASP cc_start: 0.8359 (m-30) cc_final: 0.8011 (m-30) REVERT: A 399 GLU cc_start: 0.8924 (pm20) cc_final: 0.8624 (pm20) REVERT: A 410 LYS cc_start: 0.8615 (ptpp) cc_final: 0.8265 (ttmm) REVERT: A 487 GLU cc_start: 0.9095 (tt0) cc_final: 0.8864 (tt0) REVERT: A 512 ARG cc_start: 0.8804 (mtp-110) cc_final: 0.8326 (ttp-110) REVERT: B 16 ASP cc_start: 0.8847 (t0) cc_final: 0.8523 (t0) REVERT: B 28 ASP cc_start: 0.8919 (m-30) cc_final: 0.8632 (m-30) REVERT: B 36 LEU cc_start: 0.7866 (OUTLIER) cc_final: 0.7637 (pp) REVERT: B 75 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7825 (mm-30) REVERT: B 84 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6318 (mm) REVERT: B 269 ASP cc_start: 0.8428 (m-30) cc_final: 0.7894 (m-30) REVERT: B 274 ASP cc_start: 0.9302 (t0) cc_final: 0.9010 (t0) REVERT: B 300 ILE cc_start: 0.8441 (mm) cc_final: 0.8197 (mm) REVERT: B 327 SER cc_start: 0.9226 (t) cc_final: 0.8888 (p) REVERT: B 385 MET cc_start: 0.8765 (ttm) cc_final: 0.8371 (ttp) REVERT: B 399 GLU cc_start: 0.8893 (pm20) cc_final: 0.8552 (pm20) REVERT: B 417 LEU cc_start: 0.8527 (pt) cc_final: 0.8188 (pt) REVERT: B 483 MET cc_start: 0.9391 (tmm) cc_final: 0.8388 (tmm) REVERT: C 16 ASP cc_start: 0.8717 (t0) cc_final: 0.8287 (t0) REVERT: C 28 ASP cc_start: 0.8949 (m-30) cc_final: 0.8653 (m-30) REVERT: C 75 GLU cc_start: 0.8034 (mm-30) cc_final: 0.7705 (mm-30) REVERT: C 84 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7336 (mm) REVERT: C 254 GLU cc_start: 0.9206 (tp30) cc_final: 0.8950 (tp30) REVERT: C 269 ASP cc_start: 0.8614 (m-30) cc_final: 0.8236 (m-30) REVERT: C 399 GLU cc_start: 0.8936 (pm20) cc_final: 0.8609 (pm20) REVERT: C 410 LYS cc_start: 0.8629 (ptpp) cc_final: 0.8259 (ttmm) REVERT: C 483 MET cc_start: 0.9341 (tmm) cc_final: 0.8386 (tmm) REVERT: C 512 ARG cc_start: 0.8775 (mtp-110) cc_final: 0.8394 (mtp-110) REVERT: D 16 ASP cc_start: 0.8801 (t0) cc_final: 0.8321 (t0) REVERT: D 28 ASP cc_start: 0.8932 (m-30) cc_final: 0.8662 (m-30) REVERT: D 36 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7393 (pp) REVERT: D 75 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7816 (mm-30) REVERT: D 84 LEU cc_start: 0.6352 (OUTLIER) cc_final: 0.5946 (mt) REVERT: D 269 ASP cc_start: 0.8537 (m-30) cc_final: 0.7758 (m-30) REVERT: D 399 GLU cc_start: 0.8833 (pm20) cc_final: 0.8521 (pm20) REVERT: D 410 LYS cc_start: 0.8640 (ptpp) cc_final: 0.8389 (ttmm) REVERT: D 483 MET cc_start: 0.9331 (tmm) cc_final: 0.8354 (tmm) REVERT: D 512 ARG cc_start: 0.9062 (ttp80) cc_final: 0.8505 (ttp-110) REVERT: E 28 ASP cc_start: 0.8946 (m-30) cc_final: 0.8651 (m-30) REVERT: E 75 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7702 (mm-30) REVERT: E 84 LEU cc_start: 0.6552 (OUTLIER) cc_final: 0.6245 (mt) REVERT: E 269 ASP cc_start: 0.8547 (m-30) cc_final: 0.8154 (m-30) REVERT: E 399 GLU cc_start: 0.8917 (pm20) cc_final: 0.8596 (pm20) REVERT: E 512 ARG cc_start: 0.8792 (mtp-110) cc_final: 0.8339 (ttp-110) REVERT: F 15 ASP cc_start: 0.8884 (p0) cc_final: 0.8647 (p0) REVERT: F 16 ASP cc_start: 0.8709 (t0) cc_final: 0.8467 (t0) REVERT: F 28 ASP cc_start: 0.8995 (m-30) cc_final: 0.8723 (m-30) REVERT: F 36 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7567 (pp) REVERT: F 75 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7868 (mm-30) REVERT: F 84 LEU cc_start: 0.6785 (OUTLIER) cc_final: 0.6369 (mt) REVERT: F 254 GLU cc_start: 0.9082 (tp30) cc_final: 0.8596 (tp30) REVERT: F 269 ASP cc_start: 0.8495 (m-30) cc_final: 0.8024 (m-30) REVERT: F 274 ASP cc_start: 0.9263 (t0) cc_final: 0.8987 (t0) REVERT: F 300 ILE cc_start: 0.8457 (mm) cc_final: 0.8233 (mm) REVERT: F 393 THR cc_start: 0.8692 (p) cc_final: 0.8475 (p) REVERT: F 399 GLU cc_start: 0.8833 (pm20) cc_final: 0.8480 (pm20) REVERT: F 417 LEU cc_start: 0.8517 (pt) cc_final: 0.8179 (pt) REVERT: F 483 MET cc_start: 0.9391 (tmm) cc_final: 0.8381 (tmm) REVERT: G 16 ASP cc_start: 0.8719 (t0) cc_final: 0.8291 (t0) REVERT: G 28 ASP cc_start: 0.8723 (m-30) cc_final: 0.8467 (m-30) REVERT: G 36 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7428 (pp) REVERT: G 75 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7751 (mm-30) REVERT: G 254 GLU cc_start: 0.8973 (tp30) cc_final: 0.8589 (tp30) REVERT: G 269 ASP cc_start: 0.8547 (m-30) cc_final: 0.8227 (m-30) REVERT: G 399 GLU cc_start: 0.8893 (pm20) cc_final: 0.8570 (pm20) REVERT: G 483 MET cc_start: 0.9340 (tmm) cc_final: 0.8358 (tmm) REVERT: G 487 GLU cc_start: 0.9132 (tt0) cc_final: 0.8926 (tt0) REVERT: G 512 ARG cc_start: 0.8764 (mtp-110) cc_final: 0.8482 (ttp80) REVERT: H 16 ASP cc_start: 0.8809 (t0) cc_final: 0.8354 (t0) REVERT: H 28 ASP cc_start: 0.8908 (m-30) cc_final: 0.8682 (m-30) REVERT: H 36 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7402 (pp) REVERT: H 70 MET cc_start: 0.8802 (mtp) cc_final: 0.8500 (mtp) REVERT: H 75 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7772 (mm-30) REVERT: H 84 LEU cc_start: 0.6319 (OUTLIER) cc_final: 0.5914 (mt) REVERT: H 102 ASN cc_start: 0.8824 (t0) cc_final: 0.8490 (t0) REVERT: H 105 ARG cc_start: 0.8552 (tmm160) cc_final: 0.8311 (ttp80) REVERT: H 274 ASP cc_start: 0.9302 (t0) cc_final: 0.8992 (t0) REVERT: H 399 GLU cc_start: 0.8800 (pm20) cc_final: 0.8451 (pm20) REVERT: H 483 MET cc_start: 0.9449 (tmm) cc_final: 0.8473 (tmm) REVERT: H 512 ARG cc_start: 0.9021 (ttp80) cc_final: 0.8474 (ttp80) outliers start: 75 outliers final: 46 residues processed: 609 average time/residue: 0.1378 time to fit residues: 137.9734 Evaluate side-chains 600 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 543 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 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 98 GLU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 471 ILE Chi-restraints excluded: chain B residue 500 GLU 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 333 THR Chi-restraints excluded: chain C residue 500 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 333 THR Chi-restraints excluded: chain D residue 370 VAL 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 333 THR 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 244 LEU 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 36 LEU 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 325 MET Chi-restraints excluded: chain G residue 370 VAL 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 276 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 510 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: 0.8980 chunk 251 optimal weight: 0.0770 chunk 241 optimal weight: 1.9990 chunk 265 optimal weight: 1.9990 chunk 138 optimal weight: 0.0770 chunk 20 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 35 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 277 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** ** 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 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 = 0.3192 r_free = 0.3192 target = 0.105811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.087850 restraints weight = 33584.997| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 3.24 r_work: 0.2760 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.3409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23384 Z= 0.115 Angle : 0.547 7.706 31640 Z= 0.274 Chirality : 0.043 0.173 3648 Planarity : 0.003 0.037 3976 Dihedral : 7.276 72.121 3322 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.86 % Allowed : 17.30 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.21 (0.15), residues: 2952 helix: 1.29 (0.16), residues: 1096 sheet: -1.61 (0.25), residues: 424 loop : -0.75 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 105 TYR 0.017 0.001 TYR C 12 PHE 0.010 0.001 PHE B 401 HIS 0.002 0.000 HIS E 372 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.11 (23376) covalent geometry : angle 0.54731 / 0.27 (31640) hydrogen bonds : bond 0.02302 / 1.53 ( 881) hydrogen bonds : angle 4.59157 / 3.16 ( 2547) Misc. bond : bond 0.00025 / 0.01 ( 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 635 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 567 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 ASP cc_start: 0.8784 (p0) cc_final: 0.8581 (p0) REVERT: A 16 ASP cc_start: 0.8711 (t0) cc_final: 0.8301 (t0) REVERT: A 36 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7488 (pp) REVERT: A 75 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7663 (mm-30) REVERT: A 269 ASP cc_start: 0.8487 (m-30) cc_final: 0.7996 (m-30) REVERT: A 399 GLU cc_start: 0.8913 (pm20) cc_final: 0.8625 (pm20) REVERT: A 410 LYS cc_start: 0.8628 (ptpp) cc_final: 0.8314 (ttmm) REVERT: A 483 MET cc_start: 0.9302 (tmm) cc_final: 0.8192 (tmm) REVERT: A 487 GLU cc_start: 0.9087 (tt0) cc_final: 0.8882 (tt0) REVERT: A 512 ARG cc_start: 0.8790 (mtp-110) cc_final: 0.8316 (ttp-110) REVERT: B 15 ASP cc_start: 0.8843 (p0) cc_final: 0.8619 (p0) REVERT: B 16 ASP cc_start: 0.8819 (t0) cc_final: 0.8518 (t0) REVERT: B 28 ASP cc_start: 0.8900 (m-30) cc_final: 0.8608 (m-30) REVERT: B 36 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7395 (pp) REVERT: B 75 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7861 (mm-30) REVERT: B 78 MET cc_start: 0.9186 (tpp) cc_final: 0.8919 (tpp) REVERT: B 102 ASN cc_start: 0.8917 (t0) cc_final: 0.8557 (t0) REVERT: B 105 ARG cc_start: 0.8376 (ttp-110) cc_final: 0.8013 (ttp80) REVERT: B 269 ASP cc_start: 0.8363 (m-30) cc_final: 0.7847 (m-30) REVERT: B 274 ASP cc_start: 0.9311 (t0) cc_final: 0.9014 (t0) REVERT: B 300 ILE cc_start: 0.8396 (mm) cc_final: 0.8172 (mm) REVERT: B 327 SER cc_start: 0.9252 (t) cc_final: 0.8867 (p) REVERT: B 385 MET cc_start: 0.8704 (ttm) cc_final: 0.8297 (ttp) REVERT: B 399 GLU cc_start: 0.8902 (pm20) cc_final: 0.8572 (pm20) REVERT: B 417 LEU cc_start: 0.8421 (pt) cc_final: 0.8090 (pt) REVERT: C 16 ASP cc_start: 0.8702 (t0) cc_final: 0.8264 (t0) REVERT: C 28 ASP cc_start: 0.8905 (m-30) cc_final: 0.8619 (m-30) REVERT: C 36 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7402 (pp) REVERT: C 75 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7701 (mm-30) REVERT: C 84 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7313 (mm) REVERT: C 254 GLU cc_start: 0.9192 (tp30) cc_final: 0.8934 (tp30) REVERT: C 269 ASP cc_start: 0.8610 (m-30) cc_final: 0.8200 (m-30) REVERT: C 399 GLU cc_start: 0.8950 (pm20) cc_final: 0.8658 (pm20) REVERT: C 410 LYS cc_start: 0.8637 (ptpp) cc_final: 0.8281 (ttmm) REVERT: C 483 MET cc_start: 0.9337 (tmm) cc_final: 0.8362 (tmm) REVERT: C 512 ARG cc_start: 0.8750 (mtp-110) cc_final: 0.8333 (ttp-110) REVERT: D 16 ASP cc_start: 0.8852 (t0) cc_final: 0.8412 (t0) REVERT: D 28 ASP cc_start: 0.8896 (m-30) cc_final: 0.8621 (m-30) REVERT: D 36 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.7335 (pp) REVERT: D 75 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7842 (mm-30) REVERT: D 269 ASP cc_start: 0.8502 (m-30) cc_final: 0.7942 (m-30) REVERT: D 399 GLU cc_start: 0.8848 (pm20) cc_final: 0.8530 (pm20) REVERT: D 410 LYS cc_start: 0.8695 (ptpp) cc_final: 0.8441 (ttmm) REVERT: D 483 MET cc_start: 0.9329 (tmm) cc_final: 0.8313 (tmm) REVERT: D 512 ARG cc_start: 0.9044 (ttp80) cc_final: 0.8520 (ttp-110) REVERT: E 28 ASP cc_start: 0.8891 (m-30) cc_final: 0.8602 (m-30) REVERT: E 78 MET cc_start: 0.8951 (tpp) cc_final: 0.8668 (tpp) REVERT: E 84 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.6207 (mm) REVERT: E 102 ASN cc_start: 0.8771 (t0) cc_final: 0.8415 (t0) REVERT: E 105 ARG cc_start: 0.8298 (ttp-110) cc_final: 0.7866 (ttp80) REVERT: E 269 ASP cc_start: 0.8463 (m-30) cc_final: 0.8083 (m-30) REVERT: E 399 GLU cc_start: 0.8908 (pm20) cc_final: 0.8608 (pm20) REVERT: E 410 LYS cc_start: 0.8584 (ptpp) cc_final: 0.8273 (ttmm) REVERT: E 512 ARG cc_start: 0.8772 (mtp-110) cc_final: 0.8307 (ttp-110) REVERT: F 15 ASP cc_start: 0.8858 (p0) cc_final: 0.8633 (p0) REVERT: F 16 ASP cc_start: 0.8694 (t0) cc_final: 0.8442 (t0) REVERT: F 36 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7300 (pp) REVERT: F 75 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7893 (mm-30) REVERT: F 84 LEU cc_start: 0.6381 (OUTLIER) cc_final: 0.5957 (mt) REVERT: F 254 GLU cc_start: 0.9080 (tp30) cc_final: 0.8560 (tp30) REVERT: F 269 ASP cc_start: 0.8472 (m-30) cc_final: 0.8001 (m-30) REVERT: F 274 ASP cc_start: 0.9252 (t0) cc_final: 0.8967 (t0) REVERT: F 300 ILE cc_start: 0.8401 (mm) cc_final: 0.8189 (mm) REVERT: F 393 THR cc_start: 0.8613 (p) cc_final: 0.8382 (p) REVERT: F 399 GLU cc_start: 0.8841 (pm20) cc_final: 0.8493 (pm20) REVERT: F 417 LEU cc_start: 0.8429 (pt) cc_final: 0.8093 (pt) REVERT: G 16 ASP cc_start: 0.8686 (t0) cc_final: 0.8211 (t0) REVERT: G 28 ASP cc_start: 0.8699 (m-30) cc_final: 0.8342 (m-30) REVERT: G 36 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7496 (pp) REVERT: G 75 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7734 (mm-30) REVERT: G 239 ASP cc_start: 0.8172 (p0) cc_final: 0.7784 (p0) REVERT: G 254 GLU cc_start: 0.8997 (tp30) cc_final: 0.8637 (tp30) REVERT: G 269 ASP cc_start: 0.8570 (m-30) cc_final: 0.8178 (m-30) REVERT: G 399 GLU cc_start: 0.8911 (pm20) cc_final: 0.8591 (pm20) REVERT: G 512 ARG cc_start: 0.8760 (mtp-110) cc_final: 0.8492 (ttp80) REVERT: H 16 ASP cc_start: 0.8864 (t0) cc_final: 0.8447 (t0) REVERT: H 28 ASP cc_start: 0.8882 (m-30) cc_final: 0.8619 (m-30) REVERT: H 36 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7265 (pp) REVERT: H 75 GLU cc_start: 0.8226 (mm-30) cc_final: 0.7809 (mm-30) REVERT: H 84 LEU cc_start: 0.6691 (OUTLIER) cc_final: 0.6301 (mt) REVERT: H 102 ASN cc_start: 0.8813 (t0) cc_final: 0.8519 (t0) REVERT: H 274 ASP cc_start: 0.9290 (t0) cc_final: 0.9024 (t0) REVERT: H 393 THR cc_start: 0.8525 (p) cc_final: 0.8229 (p) REVERT: H 399 GLU cc_start: 0.8852 (pm20) cc_final: 0.8519 (pm20) REVERT: H 512 ARG cc_start: 0.9017 (ttp80) cc_final: 0.8543 (ttp80) outliers start: 68 outliers final: 42 residues processed: 596 average time/residue: 0.1383 time to fit residues: 134.4017 Evaluate side-chains 612 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 559 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 84 LEU 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 98 GLU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 500 GLU 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 333 THR 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 333 THR 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 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 109 LYS Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 370 VAL 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 276 SER Chi-restraints excluded: chain G residue 325 MET Chi-restraints excluded: chain G residue 370 VAL 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 280 SER Chi-restraints excluded: chain H residue 325 MET Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 510 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 74 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 248 optimal weight: 3.9990 chunk 185 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 0.3980 chunk 246 optimal weight: 0.9990 chunk 217 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** ** 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 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 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 = 0.3170 r_free = 0.3170 target = 0.104130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.085993 restraints weight = 33868.126| |-----------------------------------------------------------------------------| r_work (start): 0.2887 rms_B_bonded: 3.24 r_work: 0.2732 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23384 Z= 0.139 Angle : 0.577 8.186 31640 Z= 0.289 Chirality : 0.044 0.158 3648 Planarity : 0.003 0.037 3976 Dihedral : 7.257 70.651 3320 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.61 % Allowed : 18.22 % Favored : 79.17 % 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: -0.28 (0.15), residues: 2952 helix: 1.17 (0.16), residues: 1112 sheet: -1.77 (0.22), residues: 528 loop : -0.58 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 105 TYR 0.020 0.001 TYR C 12 PHE 0.010 0.001 PHE B 401 HIS 0.004 0.001 HIS D 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (23376) covalent geometry : angle 0.57668 / 0.29 (31640) hydrogen bonds : bond 0.02427 / 1.62 ( 881) hydrogen bonds : angle 4.66621 / 3.21 ( 2547) Misc. bond : bond 0.00046 / 0.02 ( 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 630 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 568 time to evaluate : 0.827 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: 0.8688 (t0) cc_final: 0.8258 (t0) REVERT: A 36 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7490 (pp) REVERT: A 75 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7686 (mm-30) REVERT: A 102 ASN cc_start: 0.8880 (t0) cc_final: 0.8653 (t0) REVERT: A 105 ARG cc_start: 0.8190 (ttp80) cc_final: 0.7931 (ttp80) REVERT: A 269 ASP cc_start: 0.8471 (m-30) cc_final: 0.8117 (m-30) REVERT: A 399 GLU cc_start: 0.8942 (pm20) cc_final: 0.8664 (pm20) REVERT: A 410 LYS cc_start: 0.8673 (ptpp) cc_final: 0.8386 (ttmm) REVERT: A 483 MET cc_start: 0.9332 (tmm) cc_final: 0.8191 (tmm) REVERT: A 512 ARG cc_start: 0.8786 (mtp-110) cc_final: 0.8325 (ttp-110) REVERT: B 15 ASP cc_start: 0.8822 (p0) cc_final: 0.8595 (p0) REVERT: B 16 ASP cc_start: 0.8809 (t0) cc_final: 0.8515 (t0) REVERT: B 28 ASP cc_start: 0.8917 (m-30) cc_final: 0.8640 (m-30) REVERT: B 36 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7727 (pp) REVERT: B 75 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7830 (mm-30) REVERT: B 269 ASP cc_start: 0.8424 (m-30) cc_final: 0.7843 (m-30) REVERT: B 274 ASP cc_start: 0.9264 (t0) cc_final: 0.8985 (t0) REVERT: B 300 ILE cc_start: 0.8467 (mm) cc_final: 0.8240 (mm) REVERT: B 327 SER cc_start: 0.9239 (t) cc_final: 0.8888 (p) REVERT: B 385 MET cc_start: 0.8776 (ttm) cc_final: 0.8385 (ttp) REVERT: B 399 GLU cc_start: 0.8913 (pm20) cc_final: 0.8594 (pm20) REVERT: B 417 LEU cc_start: 0.8467 (pt) cc_final: 0.8143 (pt) REVERT: B 483 MET cc_start: 0.9392 (tmm) cc_final: 0.8503 (tmm) REVERT: C 16 ASP cc_start: 0.8701 (t0) cc_final: 0.8265 (t0) REVERT: C 28 ASP cc_start: 0.8958 (m-30) cc_final: 0.8683 (m-30) REVERT: C 36 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7485 (pp) REVERT: C 75 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7736 (mm-30) REVERT: C 84 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7378 (mm) REVERT: C 254 GLU cc_start: 0.9177 (tp30) cc_final: 0.8923 (tp30) REVERT: C 269 ASP cc_start: 0.8545 (m-30) cc_final: 0.8169 (m-30) REVERT: C 399 GLU cc_start: 0.8959 (pm20) cc_final: 0.8674 (pm20) REVERT: C 410 LYS cc_start: 0.8661 (ptpp) cc_final: 0.8317 (ttmm) REVERT: C 483 MET cc_start: 0.9351 (tmm) cc_final: 0.8400 (tmm) REVERT: C 512 ARG cc_start: 0.8765 (mtp-110) cc_final: 0.8368 (ttp-110) REVERT: D 16 ASP cc_start: 0.8827 (t0) cc_final: 0.8406 (t0) REVERT: D 28 ASP cc_start: 0.8926 (m-30) cc_final: 0.8644 (m-30) REVERT: D 36 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7398 (pp) REVERT: D 75 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7843 (mm-30) REVERT: D 269 ASP cc_start: 0.8456 (m-30) cc_final: 0.7842 (m-30) REVERT: D 399 GLU cc_start: 0.8893 (pm20) cc_final: 0.8588 (pm20) REVERT: D 410 LYS cc_start: 0.8697 (ptpp) cc_final: 0.8444 (ttmm) REVERT: D 483 MET cc_start: 0.9354 (tmm) cc_final: 0.8364 (tmm) REVERT: D 512 ARG cc_start: 0.9009 (ttp80) cc_final: 0.8453 (ttp-110) REVERT: E 28 ASP cc_start: 0.8941 (m-30) cc_final: 0.8658 (m-30) REVERT: E 75 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7641 (mm-30) REVERT: E 78 MET cc_start: 0.9011 (tpp) cc_final: 0.8760 (tpp) REVERT: E 84 LEU cc_start: 0.6826 (OUTLIER) cc_final: 0.6587 (mm) REVERT: E 102 ASN cc_start: 0.8792 (t0) cc_final: 0.8433 (t0) REVERT: E 105 ARG cc_start: 0.8292 (ttp-110) cc_final: 0.7857 (ttp80) REVERT: E 269 ASP cc_start: 0.8464 (m-30) cc_final: 0.8081 (m-30) REVERT: E 399 GLU cc_start: 0.8938 (pm20) cc_final: 0.8646 (pm20) REVERT: E 410 LYS cc_start: 0.8608 (ptpp) cc_final: 0.8306 (ttmm) REVERT: E 483 MET cc_start: 0.9428 (tmm) cc_final: 0.8563 (tmm) REVERT: E 487 GLU cc_start: 0.9065 (tt0) cc_final: 0.8835 (tt0) REVERT: E 512 ARG cc_start: 0.8786 (mtp-110) cc_final: 0.8309 (ttp-110) REVERT: F 15 ASP cc_start: 0.8846 (p0) cc_final: 0.8615 (p0) REVERT: F 16 ASP cc_start: 0.8693 (t0) cc_final: 0.8445 (t0) REVERT: F 36 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7556 (pp) REVERT: F 75 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7879 (mm-30) REVERT: F 84 LEU cc_start: 0.6720 (OUTLIER) cc_final: 0.6305 (mt) REVERT: F 254 GLU cc_start: 0.9073 (tp30) cc_final: 0.8845 (tp30) REVERT: F 269 ASP cc_start: 0.8469 (m-30) cc_final: 0.7997 (m-30) REVERT: F 274 ASP cc_start: 0.9260 (t0) cc_final: 0.8949 (t0) REVERT: F 300 ILE cc_start: 0.8508 (mm) cc_final: 0.8290 (mm) REVERT: F 393 THR cc_start: 0.8598 (p) cc_final: 0.8354 (p) REVERT: F 399 GLU cc_start: 0.8894 (pm20) cc_final: 0.8566 (pm20) REVERT: F 417 LEU cc_start: 0.8507 (pt) cc_final: 0.8126 (pt) REVERT: F 483 MET cc_start: 0.9389 (tmm) cc_final: 0.8467 (tmm) REVERT: G 16 ASP cc_start: 0.8733 (t0) cc_final: 0.8281 (t0) REVERT: G 28 ASP cc_start: 0.8749 (m-30) cc_final: 0.8361 (m-30) REVERT: G 36 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7432 (pp) REVERT: G 75 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7741 (mm-30) REVERT: G 239 ASP cc_start: 0.8156 (p0) cc_final: 0.7820 (p0) REVERT: G 254 GLU cc_start: 0.9005 (tp30) cc_final: 0.8619 (tp30) REVERT: G 269 ASP cc_start: 0.8566 (m-30) cc_final: 0.8178 (m-30) REVERT: G 399 GLU cc_start: 0.8920 (pm20) cc_final: 0.8615 (pm20) REVERT: G 483 MET cc_start: 0.9412 (tmm) cc_final: 0.8458 (tmm) REVERT: G 512 ARG cc_start: 0.8752 (mtp-110) cc_final: 0.8468 (ttp80) REVERT: H 16 ASP cc_start: 0.8844 (t0) cc_final: 0.8420 (t0) REVERT: H 28 ASP cc_start: 0.8904 (m-30) cc_final: 0.8650 (m-30) REVERT: H 36 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7515 (pp) REVERT: H 75 GLU cc_start: 0.8243 (mm-30) cc_final: 0.7821 (mm-30) REVERT: H 102 ASN cc_start: 0.8808 (t0) cc_final: 0.8411 (t0) REVERT: H 105 ARG cc_start: 0.8490 (ttp-110) cc_final: 0.8102 (ttp80) REVERT: H 274 ASP cc_start: 0.9272 (t0) cc_final: 0.9012 (t0) REVERT: H 393 THR cc_start: 0.8584 (p) cc_final: 0.8337 (p) REVERT: H 399 GLU cc_start: 0.8884 (pm20) cc_final: 0.8565 (pm20) REVERT: H 483 MET cc_start: 0.9460 (tmm) cc_final: 0.8519 (tmm) REVERT: H 512 ARG cc_start: 0.9016 (ttp80) cc_final: 0.8446 (ttp80) outliers start: 62 outliers final: 44 residues processed: 592 average time/residue: 0.1339 time to fit residues: 130.4741 Evaluate side-chains 601 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 547 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 84 LEU 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 98 GLU Chi-restraints excluded: chain B residue 109 LYS Chi-restraints excluded: chain B residue 333 THR Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 500 GLU 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 333 THR Chi-restraints excluded: chain C residue 361 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 333 THR 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 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 109 LYS Chi-restraints excluded: chain F residue 244 LEU Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 361 VAL 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 276 SER Chi-restraints excluded: chain G residue 325 MET Chi-restraints excluded: chain G residue 370 VAL 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 109 LYS Chi-restraints excluded: chain H residue 276 SER Chi-restraints excluded: chain H residue 280 SER Chi-restraints excluded: chain H residue 333 THR Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 510 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 191 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 251 optimal weight: 5.9990 chunk 192 optimal weight: 0.3980 chunk 125 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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 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 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 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.099697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.080750 restraints weight = 33839.475| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 3.22 r_work: 0.2664 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 23384 Z= 0.224 Angle : 0.643 9.602 31640 Z= 0.322 Chirality : 0.047 0.171 3648 Planarity : 0.003 0.036 3976 Dihedral : 7.478 69.610 3320 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.86 % Allowed : 17.85 % Favored : 79.29 % 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: 1.05 (0.16), residues: 1112 sheet: -1.36 (0.22), residues: 504 loop : -0.65 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 105 TYR 0.029 0.002 TYR C 12 PHE 0.009 0.001 PHE B 401 HIS 0.005 0.001 HIS G 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 (23376) covalent geometry : angle 0.64300 / 0.32 (31640) hydrogen bonds : bond 0.02873 / 1.92 ( 881) hydrogen bonds : angle 4.94574 / 3.40 ( 2547) Misc. bond : bond 0.00152 / 0.07 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4648.98 seconds wall clock time: 81 minutes 6.43 seconds (4866.43 seconds total)