Starting phenix.real_space_refine on Thu Mar 5 13:28:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6udp_20742/03_2026/6udp_20742.cif Found real_map, /net/cci-nas-00/data/ceres_data/6udp_20742/03_2026/6udp_20742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6udp_20742/03_2026/6udp_20742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6udp_20742/03_2026/6udp_20742.map" model { file = "/net/cci-nas-00/data/ceres_data/6udp_20742/03_2026/6udp_20742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6udp_20742/03_2026/6udp_20742.cif" } resolution = 2.95 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= 0.042 sd= 3.333 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 8 5.49 5 S 144 5.16 5 C 14344 2.51 5 N 3864 2.21 5 O 4368 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22728 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "B" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "C" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "D" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "E" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "F" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "G" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "H" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 5.16, per 1000 atoms: 0.23 Number of scatterers: 22728 At special positions: 0 Unit cell: (123.149, 123.149, 119.843, 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 8 15.00 O 4368 8.00 N 3864 7.00 C 14344 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=0, symmetry=0 Time building additional restraints: 1.77 Conformation dependent library (CDL) restraints added in 1000.0 milliseconds 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5392 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 32 sheets defined 39.1% alpha, 13.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.83 Creating SS restraints... Processing helix chain 'A' and resid 1 through 6 removed outlier: 3.968A pdb=" N ILE A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.684A pdb=" N GLN A 48 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 85 removed outlier: 3.558A pdb=" N ALA A 83 " --> pdb=" O ALA A 79 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR A 85 " --> pdb=" O ALA A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 255 through 266 removed outlier: 4.020A pdb=" N ARG A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA A 266 " --> pdb=" O LEU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 removed outlier: 3.939A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 315 removed outlier: 3.525A pdb=" N ALA A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 355 removed outlier: 3.593A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.628A pdb=" N ILE A 373 " --> pdb=" O ASN A 369 " (cutoff:3.500A) 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 500 Processing helix chain 'B' and resid 2 through 6 removed outlier: 3.969A pdb=" N ILE B 6 " --> pdb=" O ALA B 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2 through 6' Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 removed outlier: 3.684A pdb=" N GLN B 48 " --> pdb=" O THR B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 85 removed outlier: 3.557A pdb=" N ALA B 83 " --> pdb=" O ALA B 79 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 85 " --> pdb=" O ALA B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 255 through 266 removed outlier: 4.020A pdb=" N ARG B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 266 " --> pdb=" O LEU B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 removed outlier: 3.939A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 315 removed outlier: 3.526A pdb=" N ALA B 310 " --> pdb=" O THR B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.593A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.628A pdb=" N ILE B 373 " --> pdb=" O ASN B 369 " (cutoff:3.500A) 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 500 Processing helix chain 'C' and resid 2 through 6 removed outlier: 3.969A pdb=" N ILE C 6 " --> pdb=" O ALA C 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2 through 6' Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.685A pdb=" N GLN C 48 " --> pdb=" O THR C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 85 removed outlier: 3.557A pdb=" N ALA C 83 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 255 through 266 removed outlier: 4.020A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA C 266 " --> pdb=" O LEU C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 removed outlier: 3.939A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 315 removed outlier: 3.526A pdb=" N ALA C 310 " --> pdb=" O THR C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 342 through 355 removed outlier: 3.592A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.628A pdb=" N ILE C 373 " --> pdb=" O ASN C 369 " (cutoff:3.500A) 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 500 Processing helix chain 'D' and resid 2 through 6 removed outlier: 3.968A pdb=" N ILE D 6 " --> pdb=" O ALA D 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2 through 6' Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 45 through 49 removed outlier: 3.684A pdb=" N GLN D 48 " --> pdb=" O THR D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 85 removed outlier: 3.557A pdb=" N ALA D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR D 85 " --> pdb=" O ALA D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 255 through 266 removed outlier: 4.019A pdb=" N ARG D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA D 266 " --> pdb=" O LEU D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 removed outlier: 3.938A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 315 removed outlier: 3.526A pdb=" N ALA D 310 " --> pdb=" O THR D 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 342 through 355 removed outlier: 3.593A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.629A pdb=" N ILE D 373 " --> pdb=" O ASN D 369 " (cutoff:3.500A) 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 500 Processing helix chain 'E' and resid 2 through 6 removed outlier: 3.968A pdb=" N ILE E 6 " --> pdb=" O ALA E 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2 through 6' Processing helix chain 'E' and resid 19 through 24 Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 45 through 49 removed outlier: 3.685A pdb=" N GLN E 48 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 85 removed outlier: 3.557A pdb=" N ALA E 83 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR E 85 " --> pdb=" O ALA E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 255 through 266 removed outlier: 4.020A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA E 266 " --> pdb=" O LEU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 removed outlier: 3.940A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 306 through 315 removed outlier: 3.525A pdb=" N ALA E 310 " --> pdb=" O THR E 306 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 355 removed outlier: 3.592A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 removed outlier: 3.628A pdb=" N ILE E 373 " --> pdb=" O ASN E 369 " (cutoff:3.500A) 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 500 Processing helix chain 'F' and resid 2 through 6 removed outlier: 3.969A pdb=" N ILE F 6 " --> pdb=" O ALA F 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 2 through 6' Processing helix chain 'F' and resid 19 through 24 Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 45 through 49 removed outlier: 3.684A pdb=" N GLN F 48 " --> pdb=" O THR F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 85 removed outlier: 3.557A pdb=" N ALA F 83 " --> pdb=" O ALA F 79 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR F 85 " --> pdb=" O ALA F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 255 through 266 removed outlier: 4.020A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA F 266 " --> pdb=" O LEU F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 removed outlier: 3.939A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 306 through 315 removed outlier: 3.525A pdb=" N ALA F 310 " --> pdb=" O THR F 306 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 342 through 355 removed outlier: 3.593A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 removed outlier: 3.628A pdb=" N ILE F 373 " --> pdb=" O ASN F 369 " (cutoff:3.500A) 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 500 Processing helix chain 'G' and resid 2 through 6 removed outlier: 3.969A pdb=" N ILE G 6 " --> pdb=" O ALA G 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 6' Processing helix chain 'G' and resid 19 through 24 Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 removed outlier: 3.684A pdb=" N GLN G 48 " --> pdb=" O THR G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 85 removed outlier: 3.557A pdb=" N ALA G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR G 85 " --> pdb=" O ALA G 81 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 255 through 266 removed outlier: 4.021A pdb=" N ARG G 259 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA G 266 " --> pdb=" O LEU G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 removed outlier: 3.939A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 315 removed outlier: 3.526A pdb=" N ALA G 310 " --> pdb=" O THR G 306 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'G' and resid 342 through 355 removed outlier: 3.593A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 removed outlier: 3.628A pdb=" N ILE G 373 " --> pdb=" O ASN G 369 " (cutoff:3.500A) 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 500 Processing helix chain 'H' and resid 2 through 6 removed outlier: 3.968A pdb=" N ILE H 6 " --> pdb=" O ALA H 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 2 through 6' Processing helix chain 'H' and resid 19 through 24 Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 45 through 49 removed outlier: 3.685A pdb=" N GLN H 48 " --> pdb=" O THR H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 85 removed outlier: 3.556A pdb=" N ALA H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR H 85 " --> pdb=" O ALA H 81 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 255 through 266 removed outlier: 4.020A pdb=" N ARG H 259 " --> pdb=" O ASP H 255 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA H 266 " --> pdb=" O LEU H 262 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 removed outlier: 3.939A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) Processing helix chain 'H' and resid 306 through 315 removed outlier: 3.526A pdb=" N ALA H 310 " --> pdb=" O THR H 306 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 337 Processing helix chain 'H' and resid 342 through 355 removed outlier: 3.593A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 removed outlier: 3.628A pdb=" N ILE H 373 " --> pdb=" O ASN H 369 " (cutoff:3.500A) 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 500 Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 29 Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 37 removed outlier: 8.113A pdb=" N GLY B 29 " --> pdb=" O PHE A 490 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LYS A 492 " --> pdb=" O GLY B 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.816A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLY A 89 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ALA A 249 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE A 91 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N MET A 385 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 400 through 402 Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 510 removed outlier: 4.046A pdb=" N SER A 508 " --> pdb=" O ALA B 446 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER B 444 " --> pdb=" O GLU A 510 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 35 through 37 removed outlier: 8.109A pdb=" N GLY C 29 " --> pdb=" O PHE B 490 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS B 492 " --> pdb=" O GLY C 29 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.816A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLY B 89 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ALA B 249 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE B 91 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N VAL B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N MET B 385 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 508 through 510 removed outlier: 4.050A pdb=" N SER B 508 " --> pdb=" O ALA C 446 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER C 444 " --> pdb=" O GLU B 510 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 37 removed outlier: 8.115A pdb=" N GLY D 29 " --> pdb=" O PHE C 490 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS C 492 " --> pdb=" O GLY D 29 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.816A pdb=" N ILE C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLY C 89 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ALA C 249 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE C 91 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N MET C 385 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 508 through 510 removed outlier: 4.071A pdb=" N SER C 508 " --> pdb=" O ALA D 446 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N SER D 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) 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: 3.816A pdb=" N ILE D 88 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLY D 89 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ALA D 249 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE D 91 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N MET D 385 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 28 through 29 Processing sheet with id=AB9, first strand: chain 'E' and resid 35 through 37 removed outlier: 8.114A pdb=" N GLY F 29 " --> pdb=" O PHE E 490 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LYS E 492 " --> pdb=" O GLY F 29 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC2, first strand: chain 'E' and resid 65 through 67 removed outlier: 3.817A pdb=" N ILE E 88 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE E 90 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY E 89 " --> pdb=" O GLY E 247 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ALA E 249 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE E 91 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N MET E 385 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 400 through 402 removed outlier: 3.844A pdb=" N SER E 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N SER H 508 " --> pdb=" O ALA E 446 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 508 through 510 removed outlier: 4.040A pdb=" N SER E 508 " --> pdb=" O ALA F 446 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER F 444 " --> pdb=" O GLU E 510 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 35 through 37 removed outlier: 8.108A pdb=" N GLY G 29 " --> pdb=" O PHE F 490 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LYS F 492 " --> pdb=" O GLY G 29 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC7, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.816A pdb=" N ILE F 88 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N GLY F 89 " --> pdb=" O GLY F 247 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ALA F 249 " --> pdb=" O GLY F 89 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE F 91 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N MET F 385 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 508 through 510 removed outlier: 4.047A pdb=" N SER F 508 " --> pdb=" O ALA G 446 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER G 444 " --> pdb=" O GLU F 510 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 35 through 37 removed outlier: 8.113A pdb=" N GLY H 29 " --> pdb=" O PHE G 490 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N LYS G 492 " --> pdb=" O GLY H 29 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AD2, first strand: chain 'G' and resid 65 through 67 removed outlier: 3.816A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY G 89 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ALA G 249 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE G 91 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N MET G 385 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 508 through 510 removed outlier: 4.052A pdb=" N SER G 508 " --> pdb=" O ALA H 446 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N SER H 444 " --> pdb=" O GLU G 510 " (cutoff:3.500A) 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: 3.816A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY H 89 " --> pdb=" O GLY H 247 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N ALA H 249 " --> pdb=" O GLY H 89 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE H 91 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N VAL H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N MET H 385 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) 849 hydrogen bonds defined for protein. 2475 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: 4.18 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3816 1.31 - 1.43: 5679 1.43 - 1.56: 13337 1.56 - 1.68: 24 1.68 - 1.80: 240 Bond restraints: 23096 Sorted by residual: bond pdb=" C4 IMP C 601 " pdb=" N3 IMP C 601 " ideal model delta sigma weight residual 1.355 1.492 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C4 IMP E 601 " pdb=" N3 IMP E 601 " ideal model delta sigma weight residual 1.355 1.492 -0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" C4 IMP F 601 " pdb=" N3 IMP F 601 " ideal model delta sigma weight residual 1.355 1.492 -0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" C4 IMP D 601 " pdb=" N3 IMP D 601 " ideal model delta sigma weight residual 1.355 1.492 -0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" C4 IMP B 601 " pdb=" N3 IMP B 601 " ideal model delta sigma weight residual 1.355 1.492 -0.137 2.00e-02 2.50e+03 4.67e+01 ... (remaining 23091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 30831 2.98 - 5.97: 320 5.97 - 8.95: 41 8.95 - 11.94: 8 11.94 - 14.92: 8 Bond angle restraints: 31208 Sorted by residual: angle pdb=" CA LEU G 235 " pdb=" CB LEU G 235 " pdb=" CG LEU G 235 " ideal model delta sigma weight residual 116.30 131.22 -14.92 3.50e+00 8.16e-02 1.82e+01 angle pdb=" CA LEU D 235 " pdb=" CB LEU D 235 " pdb=" CG LEU D 235 " ideal model delta sigma weight residual 116.30 131.18 -14.88 3.50e+00 8.16e-02 1.81e+01 angle pdb=" CA LEU C 235 " pdb=" CB LEU C 235 " pdb=" CG LEU C 235 " ideal model delta sigma weight residual 116.30 131.18 -14.88 3.50e+00 8.16e-02 1.81e+01 angle pdb=" CA LEU H 235 " pdb=" CB LEU H 235 " pdb=" CG LEU H 235 " ideal model delta sigma weight residual 116.30 131.18 -14.88 3.50e+00 8.16e-02 1.81e+01 angle pdb=" CA LEU E 235 " pdb=" CB LEU E 235 " pdb=" CG LEU E 235 " ideal model delta sigma weight residual 116.30 131.16 -14.86 3.50e+00 8.16e-02 1.80e+01 ... (remaining 31203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 13696 35.14 - 70.27: 100 70.27 - 105.41: 8 105.41 - 140.55: 0 140.55 - 175.68: 4 Dihedral angle restraints: 13808 sinusoidal: 5304 harmonic: 8504 Sorted by residual: dihedral pdb=" C5' IMP C 601 " pdb=" O5' IMP C 601 " pdb=" P IMP C 601 " pdb=" O2P IMP C 601 " ideal model delta sinusoidal sigma weight residual -168.07 7.61 -175.68 1 2.00e+01 2.50e-03 4.79e+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 7.57 -175.64 1 2.00e+01 2.50e-03 4.79e+01 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 7.52 -175.59 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 13805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2573 0.055 - 0.110: 850 0.110 - 0.165: 125 0.165 - 0.219: 28 0.219 - 0.274: 16 Chirality restraints: 3592 Sorted by residual: chirality pdb=" C3' IMP G 601 " pdb=" C2' IMP G 601 " pdb=" C4' IMP G 601 " pdb=" O3' IMP G 601 " both_signs ideal model delta sigma weight residual False -2.48 -2.75 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C3' IMP C 601 " pdb=" C2' IMP C 601 " pdb=" C4' IMP C 601 " pdb=" O3' IMP C 601 " both_signs ideal model delta sigma weight residual False -2.48 -2.75 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C3' IMP H 601 " pdb=" C2' IMP H 601 " pdb=" C4' IMP H 601 " pdb=" O3' IMP H 601 " both_signs ideal model delta sigma weight residual False -2.48 -2.75 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 3589 not shown) Planarity restraints: 3976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 233 " -0.036 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO E 234 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 234 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 234 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 233 " 0.036 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO A 234 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR G 233 " 0.036 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO G 234 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO G 234 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 234 " 0.031 5.00e-02 4.00e+02 ... (remaining 3973 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 7554 2.85 - 3.36: 20734 3.36 - 3.88: 38994 3.88 - 4.39: 45518 4.39 - 4.90: 79147 Nonbonded interactions: 191947 Sorted by model distance: nonbonded pdb=" OD1 ASN H 25 " pdb=" NZ LYS H 349 " model vdw 2.340 3.120 nonbonded pdb=" OD1 ASN C 25 " pdb=" NZ LYS C 349 " model vdw 2.340 3.120 nonbonded pdb=" OD1 ASN E 25 " pdb=" NZ LYS E 349 " model vdw 2.340 3.120 nonbonded pdb=" OD1 ASN A 25 " pdb=" NZ LYS A 349 " model vdw 2.340 3.120 nonbonded pdb=" OD1 ASN B 25 " pdb=" NZ LYS B 349 " model vdw 2.340 3.120 ... (remaining 191942 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 20.230 Find NCS groups from input model: 0.310 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:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 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 : 0.007 0.137 23096 Z= 0.323 Angle : 0.868 14.920 31208 Z= 0.459 Chirality : 0.056 0.274 3592 Planarity : 0.006 0.053 3976 Dihedral : 10.711 175.684 8416 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.67 % Allowed : 5.03 % Favored : 94.30 % 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: -3.38 (0.12), residues: 2960 helix: -2.87 (0.10), residues: 1104 sheet: -1.67 (0.23), residues: 424 loop : -1.77 (0.13), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 341 TYR 0.020 0.003 TYR E 484 PHE 0.017 0.003 PHE E 401 HIS 0.004 0.001 HIS D 93 Details of bonding type rmsd covalent geometry : bond 0.00724 (23096) covalent geometry : angle 0.86751 (31208) hydrogen bonds : bond 0.17055 ( 849) hydrogen bonds : angle 7.35189 ( 2475) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 491 time to evaluate : 0.807 Fit side-chains REVERT: A 58 LYS cc_start: 0.8761 (mttp) cc_final: 0.8429 (mtmt) REVERT: A 474 LYS cc_start: 0.8480 (mtpt) cc_final: 0.8169 (mtmt) REVERT: B 58 LYS cc_start: 0.8775 (mttp) cc_final: 0.8408 (mtmt) REVERT: C 36 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8621 (pp) REVERT: C 58 LYS cc_start: 0.8729 (mttp) cc_final: 0.8424 (mtmt) REVERT: C 71 ASP cc_start: 0.8953 (p0) cc_final: 0.8745 (p0) REVERT: D 36 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8464 (pp) REVERT: D 474 LYS cc_start: 0.8326 (mtpt) cc_final: 0.8011 (mtmt) REVERT: E 36 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8623 (pp) REVERT: E 58 LYS cc_start: 0.8787 (mttp) cc_final: 0.8475 (mtmt) REVERT: E 474 LYS cc_start: 0.8485 (mtpt) cc_final: 0.8183 (mtmt) REVERT: F 50 ASP cc_start: 0.8295 (t70) cc_final: 0.8011 (t0) REVERT: F 58 LYS cc_start: 0.8829 (mttp) cc_final: 0.8477 (mtmt) REVERT: F 474 LYS cc_start: 0.8355 (mtpt) cc_final: 0.8091 (mtmt) REVERT: G 50 ASP cc_start: 0.8202 (t70) cc_final: 0.7964 (t0) REVERT: G 58 LYS cc_start: 0.8788 (mttp) cc_final: 0.8519 (mtmt) REVERT: G 483 MET cc_start: 0.9120 (tmm) cc_final: 0.8898 (tmm) REVERT: H 58 LYS cc_start: 0.8793 (mttp) cc_final: 0.8425 (mtmt) REVERT: H 483 MET cc_start: 0.9152 (tmm) cc_final: 0.8943 (tmm) outliers start: 16 outliers final: 0 residues processed: 501 average time/residue: 0.5781 time to fit residues: 332.5590 Evaluate side-chains 320 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 317 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain E residue 36 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 197 optimal weight: 0.8980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.6980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 279 ASN ** 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 334 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 368 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN C 334 GLN C 368 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 334 GLN D 368 GLN ** E 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** 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 334 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 279 ASN ** 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 334 GLN G 504 HIS ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN H 334 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.120094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.102260 restraints weight = 25985.884| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.94 r_work: 0.2992 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23096 Z= 0.141 Angle : 0.508 8.146 31208 Z= 0.269 Chirality : 0.042 0.156 3592 Planarity : 0.004 0.038 3976 Dihedral : 7.790 153.066 3294 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.52 % Allowed : 11.45 % Favored : 85.03 % 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: -1.74 (0.14), residues: 2960 helix: -0.84 (0.14), residues: 1096 sheet: -1.36 (0.23), residues: 424 loop : -1.23 (0.14), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 341 TYR 0.012 0.002 TYR C 353 PHE 0.012 0.002 PHE B 401 HIS 0.003 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00341 (23096) covalent geometry : angle 0.50802 (31208) hydrogen bonds : bond 0.03414 ( 849) hydrogen bonds : angle 5.02921 ( 2475) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 363 time to evaluate : 0.806 Fit side-chains REVERT: A 21 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8474 (tt0) REVERT: A 36 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8579 (pp) REVERT: A 50 ASP cc_start: 0.8430 (t70) cc_final: 0.8069 (t0) REVERT: A 58 LYS cc_start: 0.8898 (mttp) cc_final: 0.8541 (mtmt) REVERT: A 235 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7296 (pp) REVERT: A 474 LYS cc_start: 0.8478 (mtpt) cc_final: 0.8181 (mtpt) REVERT: A 510 GLU cc_start: 0.5778 (tp30) cc_final: 0.4285 (pt0) REVERT: B 36 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8586 (pp) REVERT: B 50 ASP cc_start: 0.8457 (t70) cc_final: 0.8098 (t0) REVERT: B 58 LYS cc_start: 0.8934 (mttp) cc_final: 0.8513 (mtmt) REVERT: B 510 GLU cc_start: 0.5745 (tp30) cc_final: 0.4504 (pt0) REVERT: C 36 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7890 (mt) REVERT: C 58 LYS cc_start: 0.8919 (mttp) cc_final: 0.8555 (mtmt) REVERT: C 235 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7383 (pp) REVERT: C 510 GLU cc_start: 0.5742 (tp30) cc_final: 0.4337 (pt0) REVERT: D 36 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8590 (pp) REVERT: D 58 LYS cc_start: 0.8909 (mttp) cc_final: 0.8482 (mtmt) REVERT: D 91 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8610 (mt) REVERT: D 235 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7429 (pp) REVERT: D 474 LYS cc_start: 0.8339 (mtpt) cc_final: 0.8031 (mtpt) REVERT: D 510 GLU cc_start: 0.5736 (tp30) cc_final: 0.4474 (pt0) REVERT: E 36 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.7875 (mt) REVERT: E 50 ASP cc_start: 0.8445 (t70) cc_final: 0.8079 (t0) REVERT: E 58 LYS cc_start: 0.8914 (mttp) cc_final: 0.8568 (mtmt) REVERT: E 235 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7335 (pp) REVERT: E 474 LYS cc_start: 0.8463 (mtpt) cc_final: 0.8167 (mtmt) REVERT: E 510 GLU cc_start: 0.5736 (tp30) cc_final: 0.4278 (pt0) REVERT: F 50 ASP cc_start: 0.8512 (t70) cc_final: 0.8169 (t0) REVERT: F 58 LYS cc_start: 0.8983 (mttp) cc_final: 0.8598 (mtmt) REVERT: F 235 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7443 (pp) REVERT: F 335 GLU cc_start: 0.6566 (mm-30) cc_final: 0.5801 (mp0) REVERT: F 474 LYS cc_start: 0.8366 (mtpt) cc_final: 0.8098 (mtpt) REVERT: F 510 GLU cc_start: 0.5673 (tp30) cc_final: 0.4357 (pt0) REVERT: G 36 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8449 (pp) REVERT: G 50 ASP cc_start: 0.8411 (t70) cc_final: 0.8036 (t0) REVERT: G 58 LYS cc_start: 0.8876 (mttp) cc_final: 0.8543 (mtmt) REVERT: G 235 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7276 (pp) REVERT: G 474 LYS cc_start: 0.8447 (mtpt) cc_final: 0.8171 (mtpt) REVERT: H 36 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8428 (pp) REVERT: H 50 ASP cc_start: 0.8500 (t70) cc_final: 0.8159 (t0) REVERT: H 58 LYS cc_start: 0.8938 (mttp) cc_final: 0.8551 (mtmt) REVERT: H 235 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7446 (pp) REVERT: H 394 THR cc_start: 0.8833 (m) cc_final: 0.8621 (m) REVERT: H 510 GLU cc_start: 0.5696 (tp30) cc_final: 0.4396 (pt0) outliers start: 84 outliers final: 31 residues processed: 414 average time/residue: 0.5412 time to fit residues: 260.6018 Evaluate side-chains 353 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 307 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 140 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 189 optimal weight: 0.7980 chunk 173 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 40 optimal weight: 0.0980 chunk 204 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 233 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 334 GLN C 303 ASN C 334 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN H 334 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.114324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.096295 restraints weight = 26189.264| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.91 r_work: 0.2933 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23096 Z= 0.179 Angle : 0.526 7.762 31208 Z= 0.274 Chirality : 0.044 0.150 3592 Planarity : 0.004 0.038 3976 Dihedral : 6.313 81.096 3294 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 4.70 % Allowed : 11.54 % Favored : 83.77 % 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: -1.04 (0.14), residues: 2960 helix: -0.06 (0.15), residues: 1096 sheet: -1.07 (0.22), residues: 424 loop : -0.97 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 341 TYR 0.013 0.002 TYR B 353 PHE 0.009 0.002 PHE E 401 HIS 0.004 0.001 HIS G 504 Details of bonding type rmsd covalent geometry : bond 0.00447 (23096) covalent geometry : angle 0.52568 (31208) hydrogen bonds : bond 0.03577 ( 849) hydrogen bonds : angle 4.61811 ( 2475) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 332 time to evaluate : 0.751 Fit side-chains REVERT: A 21 GLN cc_start: 0.8729 (tm-30) cc_final: 0.8430 (tt0) REVERT: A 58 LYS cc_start: 0.8721 (mttp) cc_final: 0.8313 (mtmt) REVERT: A 235 LEU cc_start: 0.7574 (OUTLIER) cc_final: 0.6972 (pp) REVERT: A 474 LYS cc_start: 0.8170 (mtpt) cc_final: 0.7891 (mtmt) REVERT: A 492 LYS cc_start: 0.8389 (OUTLIER) cc_final: 0.8128 (mtpp) REVERT: A 510 GLU cc_start: 0.5843 (tp30) cc_final: 0.4138 (pt0) REVERT: B 58 LYS cc_start: 0.8742 (mttp) cc_final: 0.8291 (mtmt) REVERT: B 510 GLU cc_start: 0.5804 (tp30) cc_final: 0.4286 (pt0) REVERT: C 36 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8466 (pp) REVERT: C 58 LYS cc_start: 0.8744 (mttp) cc_final: 0.8330 (mtmt) REVERT: C 235 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7070 (pp) REVERT: C 277 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.6459 (tm-30) REVERT: C 510 GLU cc_start: 0.5793 (tp30) cc_final: 0.4118 (pt0) REVERT: D 21 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8466 (tt0) REVERT: D 36 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8305 (pp) REVERT: D 58 LYS cc_start: 0.8728 (mttp) cc_final: 0.8266 (mtmt) REVERT: D 235 LEU cc_start: 0.7677 (OUTLIER) cc_final: 0.7092 (pp) REVERT: D 441 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.6850 (mp10) REVERT: D 510 GLU cc_start: 0.5958 (tp30) cc_final: 0.4374 (pt0) REVERT: E 36 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8108 (pp) REVERT: E 50 ASP cc_start: 0.8335 (t70) cc_final: 0.7915 (t0) REVERT: E 58 LYS cc_start: 0.8785 (mttp) cc_final: 0.8403 (mtmt) REVERT: E 235 LEU cc_start: 0.7660 (OUTLIER) cc_final: 0.7048 (pp) REVERT: E 474 LYS cc_start: 0.8205 (mtpt) cc_final: 0.7915 (mtmt) REVERT: E 510 GLU cc_start: 0.5688 (tp30) cc_final: 0.3980 (pt0) REVERT: F 50 ASP cc_start: 0.8408 (t70) cc_final: 0.8024 (t0) REVERT: F 58 LYS cc_start: 0.8810 (mttp) cc_final: 0.8363 (mtmt) REVERT: F 235 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7075 (pp) REVERT: F 492 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.7989 (mtpp) REVERT: F 510 GLU cc_start: 0.5737 (tp30) cc_final: 0.5420 (tp30) REVERT: G 36 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8339 (pp) REVERT: G 58 LYS cc_start: 0.8734 (mttp) cc_final: 0.8365 (mtmt) REVERT: G 235 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.6991 (pp) REVERT: G 492 LYS cc_start: 0.8302 (OUTLIER) cc_final: 0.8087 (mtpp) REVERT: G 510 GLU cc_start: 0.5697 (tp30) cc_final: 0.5333 (tp30) REVERT: H 21 GLN cc_start: 0.8786 (tm-30) cc_final: 0.8446 (tt0) REVERT: H 36 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8262 (pp) REVERT: H 50 ASP cc_start: 0.8320 (t70) cc_final: 0.7918 (t0) REVERT: H 58 LYS cc_start: 0.8751 (mttp) cc_final: 0.8324 (mtmt) REVERT: H 235 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7153 (pp) REVERT: H 441 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7090 (mp10) REVERT: H 510 GLU cc_start: 0.5736 (tp30) cc_final: 0.4257 (pt0) outliers start: 112 outliers final: 53 residues processed: 403 average time/residue: 0.5518 time to fit residues: 257.2952 Evaluate side-chains 369 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 298 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 262 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain F residue 492 LYS Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain G residue 492 LYS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 177 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 295 optimal weight: 0.0470 chunk 241 optimal weight: 2.9990 chunk 216 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 195 optimal weight: 0.9990 chunk 219 optimal weight: 0.9990 chunk 271 optimal weight: 2.9990 overall best weight: 0.7682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN B 48 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 334 GLN C 48 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN C 334 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN E 48 GLN E 334 GLN F 48 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN G 48 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN H 334 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.117745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.099484 restraints weight = 25860.671| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.94 r_work: 0.2919 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23096 Z= 0.131 Angle : 0.484 7.429 31208 Z= 0.253 Chirality : 0.042 0.144 3592 Planarity : 0.004 0.036 3976 Dihedral : 5.912 54.979 3294 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.19 % Allowed : 11.95 % Favored : 83.85 % 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: -0.59 (0.15), residues: 2960 helix: 0.36 (0.16), residues: 1104 sheet: -0.87 (0.22), residues: 424 loop : -0.74 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 341 TYR 0.010 0.001 TYR B 353 PHE 0.011 0.001 PHE B 401 HIS 0.003 0.001 HIS H 504 Details of bonding type rmsd covalent geometry : bond 0.00323 (23096) covalent geometry : angle 0.48362 (31208) hydrogen bonds : bond 0.02940 ( 849) hydrogen bonds : angle 4.37181 ( 2475) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 319 time to evaluate : 0.867 Fit side-chains REVERT: A 21 GLN cc_start: 0.8632 (tt0) cc_final: 0.8320 (tt0) REVERT: A 58 LYS cc_start: 0.8636 (mttp) cc_final: 0.8242 (mtmt) REVERT: A 235 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.6812 (pp) REVERT: A 412 ARG cc_start: 0.8462 (ptt90) cc_final: 0.8183 (ptt90) REVERT: A 474 LYS cc_start: 0.8094 (mtpt) cc_final: 0.7827 (mtmt) REVERT: A 510 GLU cc_start: 0.5876 (tp30) cc_final: 0.4126 (pt0) REVERT: B 58 LYS cc_start: 0.8645 (mttp) cc_final: 0.8187 (mtmt) REVERT: B 412 ARG cc_start: 0.8470 (ptt90) cc_final: 0.8185 (ptt90) REVERT: B 441 GLN cc_start: 0.7771 (OUTLIER) cc_final: 0.6546 (mp10) REVERT: B 510 GLU cc_start: 0.5828 (tp30) cc_final: 0.4272 (pt0) REVERT: C 21 GLN cc_start: 0.8649 (tt0) cc_final: 0.8333 (tt0) REVERT: C 36 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8086 (pp) REVERT: C 58 LYS cc_start: 0.8694 (mttp) cc_final: 0.8303 (mtmt) REVERT: C 235 LEU cc_start: 0.7451 (OUTLIER) cc_final: 0.6884 (pp) REVERT: C 510 GLU cc_start: 0.5812 (tp30) cc_final: 0.4109 (pt0) REVERT: D 21 GLN cc_start: 0.8722 (tt0) cc_final: 0.8424 (tt0) REVERT: D 36 LEU cc_start: 0.8574 (OUTLIER) cc_final: 0.8303 (pp) REVERT: D 58 LYS cc_start: 0.8641 (mttp) cc_final: 0.8174 (mtmt) REVERT: D 235 LEU cc_start: 0.7484 (OUTLIER) cc_final: 0.6959 (pp) REVERT: D 412 ARG cc_start: 0.8493 (ptt90) cc_final: 0.8280 (ptt90) REVERT: D 510 GLU cc_start: 0.5984 (tp30) cc_final: 0.4403 (pt0) REVERT: E 36 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7793 (mt) REVERT: E 58 LYS cc_start: 0.8672 (mttp) cc_final: 0.8295 (mtmt) REVERT: E 235 LEU cc_start: 0.7422 (OUTLIER) cc_final: 0.6873 (pp) REVERT: E 412 ARG cc_start: 0.8364 (ptt90) cc_final: 0.8128 (ptt90) REVERT: E 510 GLU cc_start: 0.5764 (tp30) cc_final: 0.4026 (pt0) REVERT: F 36 LEU cc_start: 0.8226 (OUTLIER) cc_final: 0.7989 (pp) REVERT: F 58 LYS cc_start: 0.8722 (mttp) cc_final: 0.8278 (mtmt) REVERT: F 235 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.6929 (pp) REVERT: F 412 ARG cc_start: 0.8398 (ptt90) cc_final: 0.8164 (ptt90) REVERT: G 58 LYS cc_start: 0.8660 (mttp) cc_final: 0.8269 (mtmt) REVERT: G 235 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.6850 (pp) REVERT: G 410 LYS cc_start: 0.7859 (ttmm) cc_final: 0.7492 (tppp) REVERT: G 412 ARG cc_start: 0.8390 (ptt90) cc_final: 0.8048 (ptt90) REVERT: G 510 GLU cc_start: 0.5750 (tp30) cc_final: 0.5362 (tp30) REVERT: H 21 GLN cc_start: 0.8730 (tt0) cc_final: 0.8402 (tt0) REVERT: H 36 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8160 (pp) REVERT: H 58 LYS cc_start: 0.8659 (mttp) cc_final: 0.8252 (mtmt) REVERT: H 235 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7030 (pp) REVERT: H 412 ARG cc_start: 0.8531 (ptt90) cc_final: 0.8281 (ptt90) REVERT: H 414 MET cc_start: 0.8427 (mmm) cc_final: 0.8167 (mmm) REVERT: H 510 GLU cc_start: 0.5768 (tp30) cc_final: 0.4220 (pt0) outliers start: 100 outliers final: 51 residues processed: 382 average time/residue: 0.5392 time to fit residues: 239.1918 Evaluate side-chains 354 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 290 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 477 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 184 optimal weight: 4.9990 chunk 270 optimal weight: 4.9990 chunk 243 optimal weight: 1.9990 chunk 242 optimal weight: 0.0570 chunk 74 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 282 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 218 optimal weight: 0.9980 chunk 280 optimal weight: 2.9990 overall best weight: 1.3502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN B 48 GLN B 303 ASN B 334 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN C 334 GLN D 303 ASN D 334 GLN E 334 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN H 283 GLN H 303 ASN H 334 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.103115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.084544 restraints weight = 26944.886| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.04 r_work: 0.2906 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2764 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23096 Z= 0.196 Angle : 0.531 5.601 31208 Z= 0.276 Chirality : 0.044 0.146 3592 Planarity : 0.004 0.035 3976 Dihedral : 6.138 59.293 3294 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.82 % Allowed : 12.08 % Favored : 83.10 % 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: -0.44 (0.15), residues: 2960 helix: 0.48 (0.16), residues: 1104 sheet: -0.71 (0.22), residues: 424 loop : -0.69 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 341 TYR 0.013 0.002 TYR H 348 PHE 0.009 0.002 PHE C 401 HIS 0.004 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00493 (23096) covalent geometry : angle 0.53105 (31208) hydrogen bonds : bond 0.03473 ( 849) hydrogen bonds : angle 4.46592 ( 2475) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 402 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 287 time to evaluate : 0.784 Fit side-chains REVERT: A 21 GLN cc_start: 0.8843 (tt0) cc_final: 0.8548 (tt0) REVERT: A 58 LYS cc_start: 0.8916 (mttp) cc_final: 0.8532 (mtmt) REVERT: A 235 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7227 (pp) REVERT: A 492 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8157 (mtpp) REVERT: A 510 GLU cc_start: 0.6243 (tp30) cc_final: 0.4429 (pt0) REVERT: B 50 ASP cc_start: 0.8511 (t70) cc_final: 0.8178 (t0) REVERT: B 58 LYS cc_start: 0.8905 (mttp) cc_final: 0.8485 (mtmt) REVERT: B 235 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7307 (pp) REVERT: B 510 GLU cc_start: 0.6230 (tp30) cc_final: 0.4631 (pt0) REVERT: C 36 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8228 (pp) REVERT: C 58 LYS cc_start: 0.8943 (mttp) cc_final: 0.8570 (mtmt) REVERT: C 235 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7220 (pp) REVERT: C 510 GLU cc_start: 0.6280 (tp30) cc_final: 0.4474 (pt0) REVERT: D 21 GLN cc_start: 0.8916 (tt0) cc_final: 0.8618 (tt0) REVERT: D 36 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8449 (pp) REVERT: D 58 LYS cc_start: 0.8899 (mttp) cc_final: 0.8481 (mtmt) REVERT: D 235 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7276 (pp) REVERT: D 441 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.6775 (mp10) REVERT: D 510 GLU cc_start: 0.6305 (tp30) cc_final: 0.4713 (pt0) REVERT: D 512 ARG cc_start: 0.5390 (mmt180) cc_final: 0.5103 (mmt90) REVERT: E 36 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8578 (pp) REVERT: E 58 LYS cc_start: 0.8940 (mttp) cc_final: 0.8586 (mtmt) REVERT: E 235 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7273 (pp) REVERT: E 412 ARG cc_start: 0.8619 (ptt90) cc_final: 0.8402 (ptt90) REVERT: E 510 GLU cc_start: 0.6192 (tp30) cc_final: 0.4412 (pt0) REVERT: F 36 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8170 (pp) REVERT: F 58 LYS cc_start: 0.8988 (mttp) cc_final: 0.8574 (mtmt) REVERT: F 235 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7207 (pp) REVERT: F 491 GLU cc_start: 0.8987 (tp30) cc_final: 0.8751 (tt0) REVERT: G 58 LYS cc_start: 0.8928 (mttp) cc_final: 0.8588 (mtmt) REVERT: G 235 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7214 (pp) REVERT: G 412 ARG cc_start: 0.8656 (ptt90) cc_final: 0.8378 (ptt90) REVERT: G 492 LYS cc_start: 0.8425 (OUTLIER) cc_final: 0.8100 (mtpp) REVERT: H 36 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8402 (pp) REVERT: H 58 LYS cc_start: 0.8955 (mttp) cc_final: 0.8559 (mtmt) REVERT: H 235 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7357 (pp) REVERT: H 441 GLN cc_start: 0.8173 (OUTLIER) cc_final: 0.7056 (mp10) REVERT: H 510 GLU cc_start: 0.6149 (tp30) cc_final: 0.4527 (pt0) outliers start: 115 outliers final: 72 residues processed: 364 average time/residue: 0.5846 time to fit residues: 245.0363 Evaluate side-chains 362 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 273 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain G residue 492 LYS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 27 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 129 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 216 optimal weight: 0.1980 chunk 231 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 269 optimal weight: 0.6980 chunk 104 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN B 48 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 334 GLN ** C 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN C 309 GLN C 334 GLN D 48 GLN D 303 ASN D 334 GLN E 334 GLN F 303 ASN F 334 GLN G 334 GLN H 48 GLN H 303 ASN H 334 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.114513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.096000 restraints weight = 26148.482| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.98 r_work: 0.2917 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23096 Z= 0.150 Angle : 0.495 5.603 31208 Z= 0.258 Chirality : 0.043 0.143 3592 Planarity : 0.004 0.035 3976 Dihedral : 6.019 59.623 3294 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 4.24 % Allowed : 12.96 % Favored : 82.80 % 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: -0.25 (0.15), residues: 2960 helix: 0.69 (0.16), residues: 1104 sheet: -0.62 (0.22), residues: 424 loop : -0.62 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 341 TYR 0.010 0.001 TYR F 348 PHE 0.010 0.001 PHE E 401 HIS 0.003 0.001 HIS H 504 Details of bonding type rmsd covalent geometry : bond 0.00371 (23096) covalent geometry : angle 0.49476 (31208) hydrogen bonds : bond 0.03037 ( 849) hydrogen bonds : angle 4.32779 ( 2475) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 295 time to evaluate : 0.866 Fit side-chains REVERT: A 21 GLN cc_start: 0.8872 (tt0) cc_final: 0.8584 (tt0) REVERT: A 36 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8187 (pp) REVERT: A 58 LYS cc_start: 0.8954 (mttp) cc_final: 0.8614 (mtmt) REVERT: A 235 LEU cc_start: 0.7809 (OUTLIER) cc_final: 0.7279 (pp) REVERT: A 277 GLN cc_start: 0.9011 (OUTLIER) cc_final: 0.6760 (tm-30) REVERT: A 441 GLN cc_start: 0.8236 (OUTLIER) cc_final: 0.7114 (mp10) REVERT: A 492 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8274 (mtpp) REVERT: A 510 GLU cc_start: 0.6343 (tp30) cc_final: 0.4641 (pt0) REVERT: B 36 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8273 (pp) REVERT: B 58 LYS cc_start: 0.8987 (mttp) cc_final: 0.8577 (mtmt) REVERT: B 235 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7439 (pp) REVERT: B 441 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7085 (mp10) REVERT: B 510 GLU cc_start: 0.6395 (tp30) cc_final: 0.4835 (pt0) REVERT: C 36 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8238 (pp) REVERT: C 58 LYS cc_start: 0.9001 (mttp) cc_final: 0.8660 (mtmt) REVERT: C 235 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7324 (pp) REVERT: C 510 GLU cc_start: 0.6352 (tp30) cc_final: 0.4593 (pt0) REVERT: D 36 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8484 (pp) REVERT: D 58 LYS cc_start: 0.8967 (mttp) cc_final: 0.8576 (mtmt) REVERT: D 235 LEU cc_start: 0.7846 (OUTLIER) cc_final: 0.7367 (pp) REVERT: D 441 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.6743 (mp10) REVERT: D 510 GLU cc_start: 0.6380 (tp30) cc_final: 0.4830 (pt0) REVERT: E 36 LEU cc_start: 0.8553 (OUTLIER) cc_final: 0.8239 (pp) REVERT: E 58 LYS cc_start: 0.9001 (mttp) cc_final: 0.8679 (mtmt) REVERT: E 235 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7347 (pp) REVERT: E 510 GLU cc_start: 0.6283 (tp30) cc_final: 0.4540 (pt0) REVERT: F 36 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8196 (pp) REVERT: F 58 LYS cc_start: 0.9047 (mttp) cc_final: 0.8670 (mtmt) REVERT: F 235 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7378 (pp) REVERT: F 491 GLU cc_start: 0.8981 (tp30) cc_final: 0.8698 (tp30) REVERT: F 510 GLU cc_start: 0.6183 (tp30) cc_final: 0.4520 (pt0) REVERT: G 58 LYS cc_start: 0.8999 (mttp) cc_final: 0.8669 (mtmt) REVERT: G 235 LEU cc_start: 0.7818 (OUTLIER) cc_final: 0.7346 (pp) REVERT: G 277 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.6749 (tm-30) REVERT: G 410 LYS cc_start: 0.8188 (ttmm) cc_final: 0.7824 (tppp) REVERT: G 412 ARG cc_start: 0.8682 (ptt90) cc_final: 0.8452 (ptt90) REVERT: G 492 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8232 (mtpp) REVERT: H 36 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8462 (pp) REVERT: H 58 LYS cc_start: 0.9020 (mttp) cc_final: 0.8656 (mtmt) REVERT: H 235 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7490 (pp) REVERT: H 441 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.6966 (mp10) REVERT: H 510 GLU cc_start: 0.6306 (tp30) cc_final: 0.4742 (pt0) outliers start: 101 outliers final: 66 residues processed: 355 average time/residue: 0.5645 time to fit residues: 231.0795 Evaluate side-chains 372 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 283 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain G residue 492 LYS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 477 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 204 optimal weight: 0.4980 chunk 217 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 112 optimal weight: 4.9990 chunk 125 optimal weight: 0.5980 chunk 123 optimal weight: 1.9990 chunk 188 optimal weight: 0.5980 chunk 83 optimal weight: 0.9990 chunk 178 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN B 303 ASN B 334 GLN C 303 ASN C 334 GLN D 303 ASN D 334 GLN E 309 GLN E 334 GLN F 303 ASN F 334 GLN G 334 GLN H 303 ASN H 334 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.109304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.090761 restraints weight = 26525.243| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.97 r_work: 0.2960 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23096 Z= 0.124 Angle : 0.475 5.607 31208 Z= 0.247 Chirality : 0.042 0.140 3592 Planarity : 0.004 0.035 3976 Dihedral : 5.798 58.405 3294 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 4.53 % Allowed : 13.09 % Favored : 82.38 % 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: -0.09 (0.15), residues: 2960 helix: 0.89 (0.16), residues: 1104 sheet: -0.56 (0.23), residues: 424 loop : -0.57 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 341 TYR 0.009 0.001 TYR F 348 PHE 0.010 0.001 PHE E 401 HIS 0.003 0.001 HIS H 504 Details of bonding type rmsd covalent geometry : bond 0.00305 (23096) covalent geometry : angle 0.47457 (31208) hydrogen bonds : bond 0.02768 ( 849) hydrogen bonds : angle 4.19863 ( 2475) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 305 time to evaluate : 0.736 Fit side-chains REVERT: A 1 MET cc_start: 0.5572 (mtm) cc_final: 0.5337 (mtt) REVERT: A 21 GLN cc_start: 0.8912 (tt0) cc_final: 0.8629 (tt0) REVERT: A 36 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8187 (pp) REVERT: A 58 LYS cc_start: 0.8978 (mttp) cc_final: 0.8651 (mtmt) REVERT: A 235 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7290 (pp) REVERT: A 277 GLN cc_start: 0.8976 (OUTLIER) cc_final: 0.6763 (tm-30) REVERT: A 441 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.6957 (mp10) REVERT: A 492 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8254 (mtpp) REVERT: A 510 GLU cc_start: 0.6421 (tp30) cc_final: 0.4762 (pt0) REVERT: B 36 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8240 (pp) REVERT: B 58 LYS cc_start: 0.8950 (mttp) cc_final: 0.8555 (mtmt) REVERT: B 235 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7421 (pp) REVERT: B 412 ARG cc_start: 0.8660 (ptt90) cc_final: 0.8442 (ptt90) REVERT: B 510 GLU cc_start: 0.6393 (tp30) cc_final: 0.4860 (pt0) REVERT: C 21 GLN cc_start: 0.8912 (tt0) cc_final: 0.8654 (tt0) REVERT: C 36 LEU cc_start: 0.8551 (OUTLIER) cc_final: 0.8256 (pp) REVERT: C 58 LYS cc_start: 0.9032 (mttp) cc_final: 0.8715 (mtmt) REVERT: C 235 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7293 (pp) REVERT: D 36 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8614 (pp) REVERT: D 50 ASP cc_start: 0.8522 (t70) cc_final: 0.8199 (t0) REVERT: D 58 LYS cc_start: 0.8976 (mttp) cc_final: 0.8589 (mtmt) REVERT: D 235 LEU cc_start: 0.7807 (OUTLIER) cc_final: 0.7344 (pp) REVERT: D 441 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.6612 (mp10) REVERT: D 510 GLU cc_start: 0.6407 (tp30) cc_final: 0.4871 (pt0) REVERT: E 21 GLN cc_start: 0.8930 (tt0) cc_final: 0.8631 (tt0) REVERT: E 36 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8250 (pp) REVERT: E 58 LYS cc_start: 0.9024 (mttp) cc_final: 0.8712 (mtmt) REVERT: E 235 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7328 (pp) REVERT: E 453 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.7988 (tt) REVERT: E 510 GLU cc_start: 0.6305 (tp30) cc_final: 0.4608 (pt0) REVERT: F 36 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8228 (pp) REVERT: F 58 LYS cc_start: 0.9047 (mttp) cc_final: 0.8676 (mtmt) REVERT: F 235 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7317 (pp) REVERT: F 510 GLU cc_start: 0.6248 (tp30) cc_final: 0.4625 (pt0) REVERT: G 58 LYS cc_start: 0.9000 (mttp) cc_final: 0.8686 (mtmt) REVERT: G 235 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7300 (pp) REVERT: G 410 LYS cc_start: 0.8195 (ttmm) cc_final: 0.7839 (tppp) REVERT: G 412 ARG cc_start: 0.8642 (ptt90) cc_final: 0.8373 (ptt90) REVERT: G 441 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7245 (mp10) REVERT: G 491 GLU cc_start: 0.9110 (tp30) cc_final: 0.8718 (tt0) REVERT: G 492 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8300 (mtpp) REVERT: H 36 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8463 (pp) REVERT: H 58 LYS cc_start: 0.8999 (mttp) cc_final: 0.8644 (mtmt) REVERT: H 235 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7455 (pp) REVERT: H 412 ARG cc_start: 0.8745 (ptt90) cc_final: 0.8490 (ptt90) REVERT: H 441 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.6761 (mp10) REVERT: H 510 GLU cc_start: 0.6360 (tp30) cc_final: 0.4825 (pt0) outliers start: 108 outliers final: 56 residues processed: 375 average time/residue: 0.5538 time to fit residues: 240.4252 Evaluate side-chains 379 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 300 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 438 LYS Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain G residue 492 LYS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 477 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 161 optimal weight: 0.0870 chunk 0 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 276 optimal weight: 0.0470 chunk 93 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 295 optimal weight: 7.9990 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 303 ASN B 334 GLN C 303 ASN C 334 GLN D 303 ASN D 334 GLN E 334 GLN F 303 ASN F 334 GLN G 334 GLN H 303 ASN H 334 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.114265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.095647 restraints weight = 25867.378| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.99 r_work: 0.2930 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23096 Z= 0.155 Angle : 0.505 5.825 31208 Z= 0.262 Chirality : 0.043 0.146 3592 Planarity : 0.004 0.034 3976 Dihedral : 5.873 56.951 3294 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.32 % Allowed : 13.34 % Favored : 82.34 % 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: -0.07 (0.15), residues: 2960 helix: 0.90 (0.16), residues: 1104 sheet: -0.57 (0.22), residues: 424 loop : -0.56 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 412 TYR 0.011 0.001 TYR F 348 PHE 0.010 0.001 PHE F 401 HIS 0.003 0.001 HIS H 504 Details of bonding type rmsd covalent geometry : bond 0.00385 (23096) covalent geometry : angle 0.50461 (31208) hydrogen bonds : bond 0.03026 ( 849) hydrogen bonds : angle 4.24679 ( 2475) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 300 time to evaluate : 0.825 Fit side-chains REVERT: A 21 GLN cc_start: 0.8926 (tt0) cc_final: 0.8638 (tt0) REVERT: A 36 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8190 (pp) REVERT: A 58 LYS cc_start: 0.9017 (mttp) cc_final: 0.8683 (mtmt) REVERT: A 235 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7310 (pp) REVERT: A 277 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.6742 (tm-30) REVERT: A 441 GLN cc_start: 0.8253 (OUTLIER) cc_final: 0.7086 (mp10) REVERT: A 492 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8275 (mtpp) REVERT: A 510 GLU cc_start: 0.6442 (tp30) cc_final: 0.4742 (pt0) REVERT: B 36 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8287 (pp) REVERT: B 50 ASP cc_start: 0.8532 (t70) cc_final: 0.8216 (t0) REVERT: B 58 LYS cc_start: 0.8977 (mttp) cc_final: 0.8580 (mtmt) REVERT: B 235 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7429 (pp) REVERT: B 412 ARG cc_start: 0.8728 (ptt90) cc_final: 0.8500 (ptt90) REVERT: B 441 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.6886 (mp10) REVERT: B 510 GLU cc_start: 0.6443 (tp30) cc_final: 0.4847 (pt0) REVERT: C 21 GLN cc_start: 0.8899 (tt0) cc_final: 0.8642 (tt0) REVERT: C 36 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8242 (pp) REVERT: C 58 LYS cc_start: 0.9045 (mttp) cc_final: 0.8718 (mtmt) REVERT: C 235 LEU cc_start: 0.7841 (OUTLIER) cc_final: 0.7337 (pp) REVERT: C 510 GLU cc_start: 0.6477 (tp30) cc_final: 0.4714 (pt0) REVERT: D 36 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8524 (pp) REVERT: D 50 ASP cc_start: 0.8556 (t70) cc_final: 0.8227 (t0) REVERT: D 58 LYS cc_start: 0.8986 (mttp) cc_final: 0.8605 (mtmt) REVERT: D 235 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7385 (pp) REVERT: D 441 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.6653 (mp10) REVERT: D 453 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8155 (tt) REVERT: E 21 GLN cc_start: 0.8940 (tt0) cc_final: 0.8634 (tt0) REVERT: E 36 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8207 (pp) REVERT: E 58 LYS cc_start: 0.9023 (mttp) cc_final: 0.8713 (mtmt) REVERT: E 235 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7374 (pp) REVERT: E 453 ILE cc_start: 0.8393 (OUTLIER) cc_final: 0.8016 (tt) REVERT: E 510 GLU cc_start: 0.6390 (tp30) cc_final: 0.4699 (pt0) REVERT: F 36 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8240 (pp) REVERT: F 58 LYS cc_start: 0.9061 (mttp) cc_final: 0.8696 (mtmt) REVERT: F 235 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7347 (pp) REVERT: F 510 GLU cc_start: 0.6200 (tp30) cc_final: 0.4573 (pt0) REVERT: G 36 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8146 (pp) REVERT: G 58 LYS cc_start: 0.9004 (mttp) cc_final: 0.8696 (mtmt) REVERT: G 235 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7364 (pp) REVERT: G 410 LYS cc_start: 0.8193 (ttmm) cc_final: 0.7847 (tppp) REVERT: G 412 ARG cc_start: 0.8666 (ptt90) cc_final: 0.8457 (ptt90) REVERT: G 441 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7244 (mp10) REVERT: G 491 GLU cc_start: 0.9124 (tp30) cc_final: 0.8743 (tt0) REVERT: G 492 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8307 (mtpp) REVERT: H 36 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8475 (pp) REVERT: H 50 ASP cc_start: 0.8514 (t70) cc_final: 0.8192 (t0) REVERT: H 58 LYS cc_start: 0.9016 (mttp) cc_final: 0.8650 (mtmt) REVERT: H 235 LEU cc_start: 0.7960 (OUTLIER) cc_final: 0.7499 (pp) REVERT: H 412 ARG cc_start: 0.8787 (ptt90) cc_final: 0.8572 (ptt90) REVERT: H 441 GLN cc_start: 0.8160 (OUTLIER) cc_final: 0.6792 (mp10) REVERT: H 510 GLU cc_start: 0.6400 (tp30) cc_final: 0.4819 (pt0) outliers start: 103 outliers final: 63 residues processed: 362 average time/residue: 0.5702 time to fit residues: 238.1040 Evaluate side-chains 379 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 290 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 441 GLN 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 107 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain G residue 492 LYS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 477 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 72 optimal weight: 0.0570 chunk 260 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 121 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 246 optimal weight: 0.8980 overall best weight: 0.9902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 303 ASN B 334 GLN C 303 ASN C 334 GLN D 303 ASN D 334 GLN E 334 GLN F 303 ASN F 334 GLN G 334 GLN H 303 ASN H 334 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.116119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.097647 restraints weight = 25937.434| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.94 r_work: 0.2939 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 23096 Z= 0.153 Angle : 0.510 8.020 31208 Z= 0.264 Chirality : 0.043 0.145 3592 Planarity : 0.004 0.034 3976 Dihedral : 5.843 57.544 3294 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.45 % Allowed : 13.55 % Favored : 82.01 % 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: 0.00 (0.15), residues: 2960 helix: 0.94 (0.16), residues: 1104 sheet: -0.44 (0.23), residues: 408 loop : -0.53 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 412 TYR 0.011 0.001 TYR C 348 PHE 0.010 0.001 PHE D 401 HIS 0.003 0.001 HIS H 504 Details of bonding type rmsd covalent geometry : bond 0.00381 (23096) covalent geometry : angle 0.50995 (31208) hydrogen bonds : bond 0.02993 ( 849) hydrogen bonds : angle 4.23643 ( 2475) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 283 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 36 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8170 (pp) REVERT: A 58 LYS cc_start: 0.9003 (mttp) cc_final: 0.8671 (mtmt) REVERT: A 235 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7316 (pp) REVERT: A 277 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.6710 (tm-30) REVERT: A 441 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.6950 (mp10) REVERT: A 492 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8214 (mtpp) REVERT: B 36 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8255 (pp) REVERT: B 50 ASP cc_start: 0.8530 (t70) cc_final: 0.8193 (t0) REVERT: B 58 LYS cc_start: 0.8974 (mttp) cc_final: 0.8567 (mtmt) REVERT: B 235 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7422 (pp) REVERT: B 412 ARG cc_start: 0.8696 (ptt90) cc_final: 0.8467 (ptt90) REVERT: B 441 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.6831 (mp10) REVERT: B 510 GLU cc_start: 0.6410 (tp30) cc_final: 0.4826 (pt0) REVERT: C 21 GLN cc_start: 0.8903 (tt0) cc_final: 0.8652 (tt0) REVERT: C 36 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8239 (pp) REVERT: C 58 LYS cc_start: 0.9036 (mttp) cc_final: 0.8705 (mtmt) REVERT: C 235 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7305 (pp) REVERT: D 36 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8511 (pp) REVERT: D 50 ASP cc_start: 0.8531 (t70) cc_final: 0.8199 (t0) REVERT: D 58 LYS cc_start: 0.8981 (mttp) cc_final: 0.8598 (mtmt) REVERT: D 235 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7342 (pp) REVERT: D 441 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.6566 (mp10) REVERT: D 453 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8135 (tt) REVERT: D 510 GLU cc_start: 0.6452 (tp30) cc_final: 0.4875 (pt0) REVERT: D 512 ARG cc_start: 0.5465 (mmt180) cc_final: 0.5215 (mmt90) REVERT: E 21 GLN cc_start: 0.8945 (tt0) cc_final: 0.8641 (tt0) REVERT: E 36 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8201 (pp) REVERT: E 58 LYS cc_start: 0.9028 (mttp) cc_final: 0.8718 (mtmt) REVERT: E 235 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7334 (pp) REVERT: E 453 ILE cc_start: 0.8384 (OUTLIER) cc_final: 0.8010 (tt) REVERT: E 510 GLU cc_start: 0.6355 (tp30) cc_final: 0.4671 (pt0) REVERT: F 36 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8210 (pp) REVERT: F 58 LYS cc_start: 0.9057 (mttp) cc_final: 0.8691 (mtmt) REVERT: F 235 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7283 (pp) REVERT: F 510 GLU cc_start: 0.6204 (tp30) cc_final: 0.4603 (pt0) REVERT: G 36 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8126 (pp) REVERT: G 58 LYS cc_start: 0.8999 (mttp) cc_final: 0.8688 (mtmt) REVERT: G 235 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7323 (pp) REVERT: G 410 LYS cc_start: 0.8177 (ttmm) cc_final: 0.7821 (tppp) REVERT: G 412 ARG cc_start: 0.8647 (ptt90) cc_final: 0.8423 (ptt90) REVERT: G 441 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7097 (mp10) REVERT: G 491 GLU cc_start: 0.9114 (tp30) cc_final: 0.8738 (tt0) REVERT: G 492 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8294 (mtpp) REVERT: G 510 GLU cc_start: 0.6281 (tp30) cc_final: 0.4618 (pt0) REVERT: H 36 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8437 (pp) REVERT: H 58 LYS cc_start: 0.9017 (mttp) cc_final: 0.8650 (mtmt) REVERT: H 235 LEU cc_start: 0.7898 (OUTLIER) cc_final: 0.7439 (pp) REVERT: H 412 ARG cc_start: 0.8798 (ptt90) cc_final: 0.8530 (ptt90) REVERT: H 441 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.6718 (mp10) REVERT: H 510 GLU cc_start: 0.6362 (tp30) cc_final: 0.4800 (pt0) outliers start: 106 outliers final: 66 residues processed: 348 average time/residue: 0.5716 time to fit residues: 229.2467 Evaluate side-chains 371 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 279 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 107 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain G residue 492 LYS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 477 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 54 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 239 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 108 optimal weight: 0.8980 chunk 182 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 303 ASN B 334 GLN C 303 ASN C 334 GLN D 303 ASN D 334 GLN F 303 ASN F 334 GLN G 334 GLN H 303 ASN H 334 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.116248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.097481 restraints weight = 25862.708| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.99 r_work: 0.2950 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 23096 Z= 0.121 Angle : 0.495 7.759 31208 Z= 0.254 Chirality : 0.042 0.143 3592 Planarity : 0.004 0.035 3976 Dihedral : 5.653 56.405 3294 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.86 % Allowed : 14.39 % Favored : 81.75 % 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: 0.14 (0.15), residues: 2960 helix: 1.08 (0.16), residues: 1104 sheet: -0.39 (0.24), residues: 392 loop : -0.46 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 412 TYR 0.010 0.001 TYR H 459 PHE 0.011 0.001 PHE C 401 HIS 0.003 0.001 HIS H 504 Details of bonding type rmsd covalent geometry : bond 0.00295 (23096) covalent geometry : angle 0.49545 (31208) hydrogen bonds : bond 0.02687 ( 849) hydrogen bonds : angle 4.13243 ( 2475) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 305 time to evaluate : 0.837 Fit side-chains REVERT: A 21 GLN cc_start: 0.8884 (tt0) cc_final: 0.8600 (tt0) REVERT: A 36 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8087 (mt) REVERT: A 58 LYS cc_start: 0.8999 (mttp) cc_final: 0.8656 (mtmt) REVERT: A 235 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7257 (pp) REVERT: A 441 GLN cc_start: 0.8138 (OUTLIER) cc_final: 0.6887 (mp10) REVERT: A 453 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8088 (tt) REVERT: A 492 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.8207 (mtpp) REVERT: A 510 GLU cc_start: 0.6355 (tp30) cc_final: 0.4604 (pt0) REVERT: B 36 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8206 (pp) REVERT: B 58 LYS cc_start: 0.8956 (mttp) cc_final: 0.8536 (mtmt) REVERT: B 235 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7394 (pp) REVERT: B 412 ARG cc_start: 0.8645 (ptt90) cc_final: 0.8419 (ptt90) REVERT: B 441 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.6633 (mp10) REVERT: B 510 GLU cc_start: 0.6349 (tp30) cc_final: 0.4838 (pt0) REVERT: C 36 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8146 (mt) REVERT: C 58 LYS cc_start: 0.9039 (mttp) cc_final: 0.8713 (mtmt) REVERT: C 235 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7263 (pp) REVERT: C 510 GLU cc_start: 0.6434 (tp30) cc_final: 0.4807 (pt0) REVERT: D 36 LEU cc_start: 0.8841 (OUTLIER) cc_final: 0.8600 (pp) REVERT: D 50 ASP cc_start: 0.8546 (t70) cc_final: 0.8229 (t0) REVERT: D 58 LYS cc_start: 0.8985 (mttp) cc_final: 0.8596 (mtmt) REVERT: D 235 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7309 (pp) REVERT: D 441 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.6497 (mp10) REVERT: D 453 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8022 (tt) REVERT: E 21 GLN cc_start: 0.8911 (tt0) cc_final: 0.8615 (tt0) REVERT: E 36 LEU cc_start: 0.8501 (OUTLIER) cc_final: 0.8179 (pp) REVERT: E 58 LYS cc_start: 0.9022 (mttp) cc_final: 0.8708 (mtmt) REVERT: E 235 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7304 (pp) REVERT: E 453 ILE cc_start: 0.8357 (OUTLIER) cc_final: 0.7987 (tt) REVERT: E 510 GLU cc_start: 0.6286 (tp30) cc_final: 0.4573 (pt0) REVERT: F 36 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8160 (mt) REVERT: F 58 LYS cc_start: 0.9048 (mttp) cc_final: 0.8678 (mtmt) REVERT: F 235 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.7310 (pp) REVERT: F 453 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7943 (tt) REVERT: F 510 GLU cc_start: 0.6235 (tp30) cc_final: 0.4624 (pt0) REVERT: G 36 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8093 (pp) REVERT: G 58 LYS cc_start: 0.8996 (mttp) cc_final: 0.8684 (mtmt) REVERT: G 235 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7269 (pp) REVERT: G 410 LYS cc_start: 0.8148 (ttmm) cc_final: 0.7789 (tppp) REVERT: G 412 ARG cc_start: 0.8571 (ptt90) cc_final: 0.8363 (ptt90) REVERT: G 441 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.6686 (mp10) REVERT: G 492 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8272 (mtpp) REVERT: G 510 GLU cc_start: 0.6268 (tp30) cc_final: 0.4638 (pt0) REVERT: H 36 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8440 (pp) REVERT: H 58 LYS cc_start: 0.9013 (mttp) cc_final: 0.8645 (mtmt) REVERT: H 235 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7394 (pp) REVERT: H 412 ARG cc_start: 0.8723 (ptt90) cc_final: 0.8460 (ptt90) REVERT: H 441 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.6498 (mp10) REVERT: H 510 GLU cc_start: 0.6288 (tp30) cc_final: 0.4724 (pt0) outliers start: 92 outliers final: 53 residues processed: 359 average time/residue: 0.5611 time to fit residues: 233.2107 Evaluate side-chains 381 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 301 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 441 GLN 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 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 453 ILE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain F residue 453 ILE Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain G residue 492 LYS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 477 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 100 optimal weight: 3.9990 chunk 67 optimal weight: 0.0670 chunk 5 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 269 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 211 optimal weight: 0.8980 chunk 31 optimal weight: 0.0570 chunk 203 optimal weight: 2.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 303 ASN C 303 ASN C 334 GLN D 303 ASN F 303 ASN F 334 GLN H 303 ASN H 334 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.115618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.096830 restraints weight = 25862.386| |-----------------------------------------------------------------------------| r_work (start): 0.2859 rms_B_bonded: 1.99 r_work: 0.2750 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23096 Z= 0.135 Angle : 0.512 7.755 31208 Z= 0.263 Chirality : 0.043 0.149 3592 Planarity : 0.004 0.035 3976 Dihedral : 5.666 56.685 3294 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.94 % Allowed : 14.56 % Favored : 81.50 % 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: 0.16 (0.15), residues: 2960 helix: 1.07 (0.16), residues: 1112 sheet: -0.39 (0.24), residues: 392 loop : -0.43 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 412 TYR 0.011 0.001 TYR H 459 PHE 0.009 0.001 PHE C 401 HIS 0.003 0.001 HIS H 504 Details of bonding type rmsd covalent geometry : bond 0.00333 (23096) covalent geometry : angle 0.51219 (31208) hydrogen bonds : bond 0.02807 ( 849) hydrogen bonds : angle 4.13875 ( 2475) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6846.49 seconds wall clock time: 117 minutes 30.44 seconds (7050.44 seconds total)