Starting phenix.real_space_refine on Sun Sep 13 10:27:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6udp_20742/09_2026/6udp_20742.cif Found real_map, /net/cci-nas-00/data/ceres_data/6udp_20742/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6udp_20742/09_2026/6udp_20742.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6udp_20742/09_2026/6udp_20742.cif" model { file = "/net/cci-nas-00/data/ceres_data/6udp_20742/09_2026/6udp_20742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6udp_20742/09_2026/6udp_20742.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6udp_20742/09_2026/6udp_20742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6udp_20742/09_2026/6udp_20742.map" } 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): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNAv2': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 5.24, 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: 1.98 Conformation dependent library (CDL) restraints added in 1.2 seconds 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5392 Finding SS restraints... Secondary structure from input PDB file: 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: 0.71 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: 4.39 Time building geometry restraints manager: 2.58 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: 30810 2.98 - 5.97: 325 5.97 - 8.95: 57 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 - 0.056: 2607 0.056 - 0.112: 835 0.112 - 0.168: 119 0.168 - 0.224: 23 0.224 - 0.280: 8 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 -2.47 -2.75 0.28 2.00e-01 2.50e+01 1.96e+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 -2.47 -2.75 0.28 2.00e-01 2.50e+01 1.96e+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 -2.47 -2.75 0.28 2.00e-01 2.50e+01 1.95e+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: 0.09 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: 6.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 22.090 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 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= 0.325 Angle : 0.893 14.920 31208 Z= 0.457 Chirality : 0.055 0.280 3592 Planarity : 0.006 0.053 3976 Dihedral : 10.712 175.684 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/Z covalent geometry : bond 0.00729 / 0.33 (23096) covalent geometry : angle 0.89302 / 0.46 (31208) hydrogen bonds : bond 0.17055 / 11.35 ( 849) hydrogen bonds : angle 7.35189 / 5.19 ( 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 : 0.870 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: 0.6046 time to fit residues: 350.1029 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 : 0.881 ------------------------------------------------------------------------------- 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... ** 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 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 = 0.3349 r_free = 0.3349 target = 0.120146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.102367 restraints weight = 25966.011| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.94 r_work: 0.2968 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23096 Z= 0.139 Angle : 0.529 8.052 31208 Z= 0.273 Chirality : 0.043 0.157 3592 Planarity : 0.004 0.038 3976 Dihedral : 7.623 138.610 3294 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.44 % Allowed : 11.54 % 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: -1.75 (0.14), residues: 2960 helix: -0.86 (0.14), residues: 1096 sheet: -1.35 (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 A 412 TYR 0.012 0.001 TYR C 353 PHE 0.011 0.001 PHE B 401 HIS 0.003 0.001 HIS A 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 (23096) covalent geometry : angle 0.52873 / 0.27 (31208) hydrogen bonds : bond 0.03461 / 2.32 ( 849) hydrogen bonds : angle 5.05250 / 3.57 ( 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 445 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 363 time to evaluate : 0.931 Fit side-chains REVERT: A 21 GLN cc_start: 0.8791 (tm-30) cc_final: 0.8456 (tt0) REVERT: A 36 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8576 (pp) REVERT: A 50 ASP cc_start: 0.8429 (t70) cc_final: 0.8092 (t0) REVERT: A 58 LYS cc_start: 0.8887 (mttp) cc_final: 0.8530 (mtmt) REVERT: A 235 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7247 (pp) REVERT: A 474 LYS cc_start: 0.8458 (mtpt) cc_final: 0.8163 (mtpt) REVERT: A 510 GLU cc_start: 0.5757 (tp30) cc_final: 0.4259 (pt0) REVERT: B 50 ASP cc_start: 0.8453 (t70) cc_final: 0.8091 (t0) REVERT: B 58 LYS cc_start: 0.8924 (mttp) cc_final: 0.8498 (mtmt) REVERT: B 510 GLU cc_start: 0.5721 (tp30) cc_final: 0.4462 (pt0) REVERT: C 36 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.7879 (mt) REVERT: C 58 LYS cc_start: 0.8908 (mttp) cc_final: 0.8540 (mtmt) REVERT: C 235 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7321 (pp) REVERT: C 510 GLU cc_start: 0.5725 (tp30) cc_final: 0.4298 (pt0) REVERT: D 36 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8573 (pp) REVERT: D 58 LYS cc_start: 0.8897 (mttp) cc_final: 0.8467 (mtmt) REVERT: D 91 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8601 (mt) REVERT: D 235 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7421 (pp) REVERT: D 474 LYS cc_start: 0.8318 (mtpt) cc_final: 0.8013 (mtpt) REVERT: D 510 GLU cc_start: 0.5707 (tp30) cc_final: 0.4444 (pt0) REVERT: E 36 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.7856 (mt) REVERT: E 50 ASP cc_start: 0.8440 (t70) cc_final: 0.8071 (t0) REVERT: E 58 LYS cc_start: 0.8905 (mttp) cc_final: 0.8555 (mtmt) REVERT: E 235 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7317 (pp) REVERT: E 474 LYS cc_start: 0.8452 (mtpt) cc_final: 0.8157 (mtmt) REVERT: E 510 GLU cc_start: 0.5710 (tp30) cc_final: 0.4248 (pt0) REVERT: F 50 ASP cc_start: 0.8508 (t70) cc_final: 0.8163 (t0) REVERT: F 58 LYS cc_start: 0.8976 (mttp) cc_final: 0.8590 (mtmt) REVERT: F 235 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7425 (pp) REVERT: F 335 GLU cc_start: 0.6550 (mm-30) cc_final: 0.5794 (mp0) REVERT: F 474 LYS cc_start: 0.8345 (mtpt) cc_final: 0.8079 (mtpt) REVERT: F 510 GLU cc_start: 0.5642 (tp30) cc_final: 0.4329 (pt0) REVERT: G 50 ASP cc_start: 0.8406 (t70) cc_final: 0.8029 (t0) REVERT: G 58 LYS cc_start: 0.8868 (mttp) cc_final: 0.8533 (mtmt) REVERT: G 235 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7279 (pp) REVERT: G 474 LYS cc_start: 0.8420 (mtpt) cc_final: 0.8142 (mtpt) REVERT: G 483 MET cc_start: 0.9245 (tmm) cc_final: 0.9037 (tmm) REVERT: H 36 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8418 (pp) REVERT: H 50 ASP cc_start: 0.8497 (t70) cc_final: 0.8152 (t0) REVERT: H 58 LYS cc_start: 0.8927 (mttp) cc_final: 0.8536 (mtmt) REVERT: H 235 LEU cc_start: 0.8045 (OUTLIER) cc_final: 0.7426 (pp) REVERT: H 394 THR cc_start: 0.8824 (m) cc_final: 0.8613 (m) REVERT: H 510 GLU cc_start: 0.5673 (tp30) cc_final: 0.4369 (pt0) outliers start: 82 outliers final: 30 residues processed: 414 average time/residue: 0.5564 time to fit residues: 268.8925 Evaluate side-chains 351 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 308 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 485 SER Chi-restraints excluded: chain B residue 11 SER 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 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: 5.9990 chunk 241 optimal weight: 3.9990 chunk 189 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 204 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 233 optimal weight: 0.0980 chunk 106 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 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 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 303 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 334 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.117852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.099867 restraints weight = 25974.867| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.94 r_work: 0.2953 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 23096 Z= 0.149 Angle : 0.517 7.705 31208 Z= 0.263 Chirality : 0.043 0.150 3592 Planarity : 0.004 0.037 3976 Dihedral : 6.316 73.642 3294 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.28 % Allowed : 11.83 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.00 (0.14), residues: 2960 helix: -0.01 (0.15), residues: 1096 sheet: -1.07 (0.23), residues: 424 loop : -0.96 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 341 TYR 0.012 0.002 TYR B 353 PHE 0.010 0.001 PHE E 401 HIS 0.003 0.001 HIS G 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 (23096) covalent geometry : angle 0.51706 / 0.26 (31208) hydrogen bonds : bond 0.03258 / 2.18 ( 849) hydrogen bonds : angle 4.54396 / 3.21 ( 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 440 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 338 time to evaluate : 0.902 Fit side-chains REVERT: A 21 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8463 (tt0) REVERT: A 58 LYS cc_start: 0.8901 (mttp) cc_final: 0.8545 (mtmt) REVERT: A 235 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7234 (pp) REVERT: A 474 LYS cc_start: 0.8454 (mtpt) cc_final: 0.8155 (mtmt) REVERT: A 510 GLU cc_start: 0.5955 (tp30) cc_final: 0.4328 (pt0) REVERT: B 50 ASP cc_start: 0.8464 (t70) cc_final: 0.8095 (t0) REVERT: B 58 LYS cc_start: 0.8884 (mttp) cc_final: 0.8476 (mtmt) REVERT: B 510 GLU cc_start: 0.5881 (tp30) cc_final: 0.4477 (pt0) REVERT: C 58 LYS cc_start: 0.8943 (mttp) cc_final: 0.8584 (mtmt) REVERT: C 235 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7286 (pp) REVERT: C 412 ARG cc_start: 0.8686 (ptt180) cc_final: 0.8320 (ptt90) REVERT: C 510 GLU cc_start: 0.5926 (tp30) cc_final: 0.4355 (pt0) REVERT: D 21 GLN cc_start: 0.8909 (tm-30) cc_final: 0.8579 (tt0) REVERT: D 36 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8485 (pp) REVERT: D 58 LYS cc_start: 0.8912 (mttp) cc_final: 0.8484 (mtmt) REVERT: D 235 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7352 (pp) REVERT: D 441 GLN cc_start: 0.8254 (OUTLIER) cc_final: 0.6973 (mp10) REVERT: D 510 GLU cc_start: 0.6122 (tp30) cc_final: 0.4669 (pt0) REVERT: E 16 ASP cc_start: 0.8452 (t70) cc_final: 0.8074 (t70) REVERT: E 36 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8246 (pp) REVERT: E 50 ASP cc_start: 0.8447 (t70) cc_final: 0.8059 (t0) REVERT: E 58 LYS cc_start: 0.8918 (mttp) cc_final: 0.8580 (mtmt) REVERT: E 235 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7284 (pp) REVERT: E 474 LYS cc_start: 0.8448 (mtpt) cc_final: 0.8165 (mtmt) REVERT: E 510 GLU cc_start: 0.5909 (tp30) cc_final: 0.4291 (pt0) REVERT: F 50 ASP cc_start: 0.8517 (t70) cc_final: 0.8162 (t0) REVERT: F 58 LYS cc_start: 0.8968 (mttp) cc_final: 0.8573 (mtmt) REVERT: F 235 LEU cc_start: 0.7886 (OUTLIER) cc_final: 0.7309 (pp) REVERT: F 510 GLU cc_start: 0.5934 (tp30) cc_final: 0.5608 (tp30) REVERT: G 58 LYS cc_start: 0.8890 (mttp) cc_final: 0.8554 (mtmt) REVERT: G 235 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7273 (pp) REVERT: G 474 LYS cc_start: 0.8427 (mtpt) cc_final: 0.8151 (mtmt) REVERT: G 510 GLU cc_start: 0.5851 (tp30) cc_final: 0.5491 (tp30) REVERT: H 21 GLN cc_start: 0.8899 (tm-30) cc_final: 0.8560 (tt0) REVERT: H 36 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8406 (pp) REVERT: H 50 ASP cc_start: 0.8476 (t70) cc_final: 0.8104 (t0) REVERT: H 58 LYS cc_start: 0.8918 (mttp) cc_final: 0.8538 (mtmt) REVERT: H 235 LEU cc_start: 0.7975 (OUTLIER) cc_final: 0.7383 (pp) REVERT: H 441 GLN cc_start: 0.8363 (OUTLIER) cc_final: 0.7182 (mp10) REVERT: H 510 GLU cc_start: 0.5873 (tp30) cc_final: 0.4473 (pt0) outliers start: 102 outliers final: 51 residues processed: 402 average time/residue: 0.5641 time to fit residues: 264.8832 Evaluate side-chains 369 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 306 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 437 ILE Chi-restraints excluded: chain A residue 485 SER 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 441 GLN Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 11 SER 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 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 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 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 235 LEU Chi-restraints excluded: chain F residue 245 LEU 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 235 LEU Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 441 GLN 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 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: 5.9990 chunk 0 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 295 optimal weight: 0.5980 chunk 241 optimal weight: 0.8980 chunk 216 optimal weight: 0.0370 chunk 145 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 195 optimal weight: 0.8980 chunk 219 optimal weight: 0.9990 chunk 271 optimal weight: 1.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN C 334 GLN D 48 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 334 GLN E 48 GLN E 334 GLN F 48 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN H 48 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN H 334 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.119144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.100846 restraints weight = 25783.542| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.94 r_work: 0.2968 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23096 Z= 0.121 Angle : 0.496 7.301 31208 Z= 0.252 Chirality : 0.042 0.145 3592 Planarity : 0.004 0.036 3976 Dihedral : 6.066 59.771 3292 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 4.03 % Allowed : 12.37 % Favored : 83.60 % 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: -0.52 (0.15), residues: 2960 helix: 0.45 (0.16), residues: 1104 sheet: -0.82 (0.23), 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 F 348 PHE 0.011 0.001 PHE E 401 HIS 0.003 0.001 HIS H 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (23096) covalent geometry : angle 0.49567 / 0.25 (31208) hydrogen bonds : bond 0.02797 / 1.86 ( 849) hydrogen bonds : angle 4.29636 / 3.03 ( 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 422 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 326 time to evaluate : 1.039 Fit side-chains REVERT: A 21 GLN cc_start: 0.8819 (tm-30) cc_final: 0.8490 (tt0) REVERT: A 36 LEU cc_start: 0.8282 (pp) cc_final: 0.7905 (mt) REVERT: A 58 LYS cc_start: 0.8860 (mttp) cc_final: 0.8489 (mtmt) REVERT: A 235 LEU cc_start: 0.7679 (OUTLIER) cc_final: 0.7127 (pp) REVERT: A 412 ARG cc_start: 0.8558 (ptt90) cc_final: 0.8315 (ptt90) REVERT: A 441 GLN cc_start: 0.8228 (OUTLIER) cc_final: 0.6764 (mp10) REVERT: A 474 LYS cc_start: 0.8379 (mtpt) cc_final: 0.8103 (mtmt) REVERT: A 492 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8296 (mtpp) REVERT: A 510 GLU cc_start: 0.6107 (tp30) cc_final: 0.4422 (pt0) REVERT: B 36 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8144 (pp) REVERT: B 58 LYS cc_start: 0.8863 (mttp) cc_final: 0.8413 (mtmt) REVERT: B 91 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8567 (mt) REVERT: B 412 ARG cc_start: 0.8624 (ptt90) cc_final: 0.8392 (ptt90) REVERT: B 441 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.6747 (mp10) REVERT: B 510 GLU cc_start: 0.6061 (tp30) cc_final: 0.4551 (pt0) REVERT: C 21 GLN cc_start: 0.8771 (tt0) cc_final: 0.8446 (tt0) REVERT: C 36 LEU cc_start: 0.8339 (pp) cc_final: 0.7945 (mt) REVERT: C 58 LYS cc_start: 0.8882 (mttp) cc_final: 0.8527 (mtmt) REVERT: C 235 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7234 (pp) REVERT: C 412 ARG cc_start: 0.8645 (ptt180) cc_final: 0.8266 (ptt90) REVERT: C 492 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8274 (mtpp) REVERT: C 510 GLU cc_start: 0.6099 (tp30) cc_final: 0.4436 (pt0) REVERT: D 21 GLN cc_start: 0.8883 (tm-30) cc_final: 0.8532 (tt0) REVERT: D 36 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8557 (pp) REVERT: D 58 LYS cc_start: 0.8860 (mttp) cc_final: 0.8440 (mtmt) REVERT: D 235 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7241 (pp) REVERT: D 400 TYR cc_start: 0.8618 (m-80) cc_final: 0.8297 (m-80) REVERT: D 510 GLU cc_start: 0.6222 (tp30) cc_final: 0.4695 (pt0) REVERT: E 36 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7997 (mt) REVERT: E 58 LYS cc_start: 0.8878 (mttp) cc_final: 0.8534 (mtmt) REVERT: E 78 MET cc_start: 0.8709 (tpt) cc_final: 0.8498 (tpp) REVERT: E 235 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7169 (pp) REVERT: E 474 LYS cc_start: 0.8405 (mtpt) cc_final: 0.8113 (mtmt) REVERT: E 492 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8290 (mtpp) REVERT: E 510 GLU cc_start: 0.5978 (tp30) cc_final: 0.4320 (pt0) REVERT: F 36 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8141 (pp) REVERT: F 58 LYS cc_start: 0.8919 (mttp) cc_final: 0.8517 (mtmt) REVERT: F 235 LEU cc_start: 0.7766 (OUTLIER) cc_final: 0.7280 (pp) REVERT: F 492 LYS cc_start: 0.8460 (OUTLIER) cc_final: 0.8211 (mtpp) REVERT: G 36 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8088 (pp) REVERT: G 58 LYS cc_start: 0.8867 (mttp) cc_final: 0.8518 (mtmt) REVERT: G 235 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7118 (pp) REVERT: G 410 LYS cc_start: 0.8036 (ttmm) cc_final: 0.7702 (tppp) REVERT: G 412 ARG cc_start: 0.8532 (ptt90) cc_final: 0.8257 (ptt90) REVERT: G 492 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8189 (mtpp) REVERT: G 510 GLU cc_start: 0.5975 (tp30) cc_final: 0.5610 (tp30) REVERT: H 36 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8348 (pp) REVERT: H 58 LYS cc_start: 0.8884 (mttp) cc_final: 0.8504 (mtmt) REVERT: H 91 ILE cc_start: 0.8805 (OUTLIER) cc_final: 0.8580 (mt) REVERT: H 235 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7327 (pp) REVERT: H 510 GLU cc_start: 0.5983 (tp30) cc_final: 0.4475 (pt0) outliers start: 96 outliers final: 43 residues processed: 389 average time/residue: 0.5846 time to fit residues: 264.5327 Evaluate side-chains 372 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 307 time to evaluate : 0.897 ------------------------------------------------------------------------------- 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 318 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 91 ILE 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 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 437 ILE Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain C residue 492 LYS 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 437 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 269 ASP Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 437 ILE Chi-restraints excluded: chain E residue 492 LYS Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 66 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 437 ILE 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 235 LEU Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 437 ILE 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 91 ILE 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 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: 5.9990 chunk 270 optimal weight: 4.9990 chunk 243 optimal weight: 0.9990 chunk 242 optimal weight: 4.9990 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: 0.4980 chunk 280 optimal weight: 0.4980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 C 303 ASN C 334 GLN D 303 ASN 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 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 = 0.3255 r_free = 0.3255 target = 0.113887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.095570 restraints weight = 26057.222| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.95 r_work: 0.2931 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23096 Z= 0.172 Angle : 0.534 7.002 31208 Z= 0.270 Chirality : 0.044 0.145 3592 Planarity : 0.004 0.036 3976 Dihedral : 6.145 61.133 3292 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.61 % Allowed : 12.12 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.15), residues: 2960 helix: 0.60 (0.16), residues: 1104 sheet: -0.70 (0.22), residues: 424 loop : -0.65 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 355 TYR 0.011 0.002 TYR H 348 PHE 0.010 0.001 PHE F 401 HIS 0.003 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.17 (23096) covalent geometry : angle 0.53378 / 0.27 (31208) hydrogen bonds : bond 0.03244 / 2.17 ( 849) hydrogen bonds : angle 4.36814 / 3.09 ( 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 409 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 299 time to evaluate : 0.877 Fit side-chains REVERT: A 21 GLN cc_start: 0.8914 (tt0) cc_final: 0.8600 (tt0) REVERT: A 58 LYS cc_start: 0.8973 (mttp) cc_final: 0.8634 (mtmt) REVERT: A 235 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7350 (pp) REVERT: A 492 LYS cc_start: 0.8651 (OUTLIER) cc_final: 0.8317 (mtpp) REVERT: A 510 GLU cc_start: 0.6331 (tp30) cc_final: 0.4601 (pt0) REVERT: B 36 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8262 (pp) REVERT: B 50 ASP cc_start: 0.8537 (t70) cc_final: 0.8227 (t0) REVERT: B 58 LYS cc_start: 0.8924 (mttp) cc_final: 0.8536 (mtmt) REVERT: B 235 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7485 (pp) REVERT: B 510 GLU cc_start: 0.6449 (tp30) cc_final: 0.4910 (pt0) REVERT: C 36 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8326 (pp) REVERT: C 58 LYS cc_start: 0.9000 (mttp) cc_final: 0.8652 (mtmt) REVERT: C 235 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7385 (pp) REVERT: C 492 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8363 (mtpp) REVERT: C 510 GLU cc_start: 0.6376 (tp30) cc_final: 0.4652 (pt0) REVERT: D 21 GLN cc_start: 0.8950 (tt0) cc_final: 0.8649 (tt0) REVERT: D 36 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8511 (pp) REVERT: D 58 LYS cc_start: 0.8952 (mttp) cc_final: 0.8558 (mtmt) REVERT: D 235 LEU cc_start: 0.7963 (OUTLIER) cc_final: 0.7473 (pp) REVERT: D 441 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.6885 (mp10) REVERT: D 510 GLU cc_start: 0.6504 (tp30) cc_final: 0.4958 (pt0) REVERT: E 36 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8611 (pp) REVERT: E 58 LYS cc_start: 0.9013 (mttp) cc_final: 0.8707 (mtmt) REVERT: E 235 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7397 (pp) REVERT: E 492 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8420 (mtpp) REVERT: E 510 GLU cc_start: 0.6351 (tp30) cc_final: 0.4655 (pt0) REVERT: F 36 LEU cc_start: 0.8540 (OUTLIER) cc_final: 0.8227 (pp) REVERT: F 58 LYS cc_start: 0.9048 (mttp) cc_final: 0.8679 (mtmt) REVERT: F 235 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7409 (pp) REVERT: F 492 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8301 (mtpp) REVERT: G 36 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8166 (pp) REVERT: G 58 LYS cc_start: 0.8987 (mttp) cc_final: 0.8673 (mtmt) REVERT: G 235 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7384 (pp) REVERT: G 410 LYS cc_start: 0.8207 (ttmm) cc_final: 0.7860 (tppp) REVERT: G 412 ARG cc_start: 0.8699 (ptt90) cc_final: 0.8444 (ptt90) REVERT: G 492 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8331 (mtpp) REVERT: H 21 GLN cc_start: 0.8919 (tt0) cc_final: 0.8594 (tt0) REVERT: H 36 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8458 (pp) REVERT: H 50 ASP cc_start: 0.8504 (t70) cc_final: 0.8170 (t0) REVERT: H 58 LYS cc_start: 0.8964 (mttp) cc_final: 0.8606 (mtmt) REVERT: H 91 ILE cc_start: 0.8968 (OUTLIER) cc_final: 0.8745 (mp) REVERT: H 235 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7560 (pp) REVERT: H 441 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7045 (mp10) REVERT: H 510 GLU cc_start: 0.6358 (tp30) cc_final: 0.4813 (pt0) outliers start: 110 outliers final: 64 residues processed: 368 average time/residue: 0.6073 time to fit residues: 258.4625 Evaluate side-chains 371 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 284 time to evaluate : 0.826 ------------------------------------------------------------------------------- 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 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 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 492 LYS 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 E residue 492 LYS 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 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 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 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 91 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 27 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 chunk 129 optimal weight: 0.9980 chunk 191 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 216 optimal weight: 4.9990 chunk 231 optimal weight: 0.3980 chunk 79 optimal weight: 1.9990 chunk 269 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 GLN B 48 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN 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 = 0.3315 r_free = 0.3315 target = 0.117931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.099781 restraints weight = 25942.565| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.90 r_work: 0.2972 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8902 moved from start: 0.2520 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= 0.127 Angle : 0.498 6.852 31208 Z= 0.252 Chirality : 0.043 0.142 3592 Planarity : 0.004 0.036 3976 Dihedral : 5.963 60.708 3292 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 4.57 % Allowed : 12.42 % Favored : 83.01 % 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: -0.09 (0.15), residues: 2960 helix: 0.87 (0.16), residues: 1104 sheet: -0.59 (0.23), residues: 424 loop : -0.55 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 341 TYR 0.010 0.001 TYR G 348 PHE 0.010 0.001 PHE E 401 HIS 0.003 0.001 HIS B 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (23096) covalent geometry : angle 0.49846 / 0.25 (31208) hydrogen bonds : bond 0.02795 / 1.86 ( 849) hydrogen bonds : angle 4.20533 / 2.97 ( 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 422 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 313 time to evaluate : 0.660 Fit side-chains REVERT: A 21 GLN cc_start: 0.8896 (tt0) cc_final: 0.8607 (tt0) REVERT: A 36 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8207 (pp) REVERT: A 58 LYS cc_start: 0.8967 (mttp) cc_final: 0.8639 (mtmt) REVERT: A 235 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7342 (pp) REVERT: A 277 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.6873 (tm-30) REVERT: A 441 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.6981 (mp10) REVERT: A 492 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8368 (mtpp) REVERT: A 510 GLU cc_start: 0.6437 (tp30) cc_final: 0.4808 (pt0) REVERT: B 36 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8250 (pp) REVERT: B 50 ASP cc_start: 0.8508 (t70) cc_final: 0.8191 (t0) REVERT: B 58 LYS cc_start: 0.8906 (mttp) cc_final: 0.8530 (mtmt) REVERT: B 235 LEU cc_start: 0.8010 (OUTLIER) cc_final: 0.7497 (pp) REVERT: B 441 GLN cc_start: 0.8140 (OUTLIER) cc_final: 0.6875 (mp10) REVERT: B 510 GLU cc_start: 0.6401 (tp30) cc_final: 0.4935 (pt0) REVERT: C 21 GLN cc_start: 0.8917 (tt0) cc_final: 0.8651 (tt0) REVERT: C 36 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8081 (mt) REVERT: C 58 LYS cc_start: 0.9006 (mttp) cc_final: 0.8700 (mtmt) REVERT: C 235 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7370 (pp) REVERT: C 277 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.6722 (tm-30) REVERT: C 492 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8329 (mtpp) REVERT: D 36 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8675 (pp) REVERT: D 58 LYS cc_start: 0.8964 (mttp) cc_final: 0.8583 (mtmt) REVERT: D 235 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7443 (pp) REVERT: D 441 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.6698 (mp10) REVERT: D 510 GLU cc_start: 0.6531 (tp30) cc_final: 0.5064 (pt0) REVERT: E 21 GLN cc_start: 0.8907 (tt0) cc_final: 0.8601 (tt0) REVERT: E 36 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8278 (pp) REVERT: E 58 LYS cc_start: 0.9009 (mttp) cc_final: 0.8728 (mtmt) REVERT: E 235 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7410 (pp) REVERT: E 492 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8363 (mtpp) REVERT: E 510 GLU cc_start: 0.6330 (tp30) cc_final: 0.4706 (pt0) REVERT: F 36 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8149 (mt) REVERT: F 58 LYS cc_start: 0.9064 (mttp) cc_final: 0.8706 (mtmt) REVERT: F 235 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7415 (pp) REVERT: F 492 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8311 (mtpp) REVERT: G 36 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8165 (pp) REVERT: G 58 LYS cc_start: 0.9015 (mttp) cc_final: 0.8705 (mtmt) REVERT: G 91 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8626 (mp) REVERT: G 235 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7391 (pp) REVERT: G 410 LYS cc_start: 0.8236 (ttmm) cc_final: 0.7900 (tppp) REVERT: G 412 ARG cc_start: 0.8657 (ptt90) cc_final: 0.8450 (ptt90) REVERT: G 441 GLN cc_start: 0.8113 (OUTLIER) cc_final: 0.7218 (mp10) REVERT: G 492 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8253 (mtpp) REVERT: H 36 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8455 (pp) REVERT: H 50 ASP cc_start: 0.8531 (t70) cc_final: 0.8219 (t0) REVERT: H 58 LYS cc_start: 0.8974 (mttp) cc_final: 0.8622 (mtmt) REVERT: H 91 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8762 (mt) REVERT: H 235 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7544 (pp) REVERT: H 441 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.6910 (mp10) REVERT: H 510 GLU cc_start: 0.6400 (tp30) cc_final: 0.4939 (pt0) outliers start: 109 outliers final: 54 residues processed: 383 average time/residue: 0.5526 time to fit residues: 246.8793 Evaluate side-chains 381 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 297 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 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 235 LEU 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 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 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 C residue 492 LYS 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 269 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 437 ILE 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 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 492 LYS 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 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 91 ILE 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 91 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 204 optimal weight: 2.9990 chunk 217 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 125 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 178 optimal weight: 0.0870 chunk 9 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 GLN B 303 ASN B 334 GLN C 303 ASN C 334 GLN D 303 ASN E 334 GLN F 303 ASN F 334 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 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 = 0.3249 r_free = 0.3249 target = 0.113448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.095157 restraints weight = 26298.908| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.94 r_work: 0.2926 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8918 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23096 Z= 0.174 Angle : 0.539 6.983 31208 Z= 0.272 Chirality : 0.044 0.145 3592 Planarity : 0.004 0.035 3976 Dihedral : 6.097 61.222 3292 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.57 % Allowed : 13.21 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.15), residues: 2960 helix: 0.82 (0.16), residues: 1104 sheet: -0.55 (0.22), residues: 424 loop : -0.59 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 412 TYR 0.011 0.001 TYR H 348 PHE 0.009 0.001 PHE E 401 HIS 0.003 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.17 (23096) covalent geometry : angle 0.53887 / 0.27 (31208) hydrogen bonds : bond 0.03197 / 2.13 ( 849) hydrogen bonds : angle 4.31296 / 3.05 ( 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 401 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 292 time to evaluate : 0.906 Fit side-chains revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8923 (tt0) cc_final: 0.8627 (tt0) REVERT: A 36 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8188 (pp) REVERT: A 58 LYS cc_start: 0.9002 (mttp) cc_final: 0.8661 (mtmt) REVERT: A 235 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7285 (pp) REVERT: A 277 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.6693 (tm-30) REVERT: A 441 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.7200 (mp10) REVERT: A 492 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8335 (mtpp) REVERT: A 510 GLU cc_start: 0.6429 (tp30) cc_final: 0.4713 (pt0) REVERT: B 36 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8269 (pp) REVERT: B 50 ASP cc_start: 0.8540 (t70) cc_final: 0.8232 (t0) REVERT: B 58 LYS cc_start: 0.8960 (mttp) cc_final: 0.8554 (mtmt) REVERT: B 235 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7499 (pp) REVERT: B 441 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7214 (mp10) REVERT: B 510 GLU cc_start: 0.6448 (tp30) cc_final: 0.4883 (pt0) REVERT: C 21 GLN cc_start: 0.8926 (tt0) cc_final: 0.8709 (tt0) REVERT: C 36 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8264 (pp) REVERT: C 58 LYS cc_start: 0.9023 (mttp) cc_final: 0.8689 (mtmt) REVERT: C 235 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7349 (pp) REVERT: C 245 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8064 (mp) REVERT: C 510 GLU cc_start: 0.6381 (tp30) cc_final: 0.4680 (pt0) REVERT: D 36 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8516 (pp) REVERT: D 50 ASP cc_start: 0.8531 (t70) cc_final: 0.8203 (t0) REVERT: D 58 LYS cc_start: 0.8963 (mttp) cc_final: 0.8565 (mtmt) REVERT: D 235 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7405 (pp) REVERT: D 441 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.6784 (mp10) REVERT: D 510 GLU cc_start: 0.6491 (tp30) cc_final: 0.4947 (pt0) REVERT: E 21 GLN cc_start: 0.8916 (tt0) cc_final: 0.8612 (tt0) REVERT: E 36 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8270 (pp) REVERT: E 58 LYS cc_start: 0.9042 (mttp) cc_final: 0.8731 (mtmt) REVERT: E 235 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7385 (pp) REVERT: E 453 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7965 (tt) REVERT: E 492 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8405 (mtpp) REVERT: E 510 GLU cc_start: 0.6388 (tp30) cc_final: 0.4700 (pt0) REVERT: F 36 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8256 (pp) REVERT: F 58 LYS cc_start: 0.9069 (mttp) cc_final: 0.8701 (mtmt) REVERT: F 235 LEU cc_start: 0.7835 (OUTLIER) cc_final: 0.7385 (pp) REVERT: F 491 GLU cc_start: 0.9134 (tp30) cc_final: 0.8790 (tt0) REVERT: F 492 LYS cc_start: 0.8617 (OUTLIER) cc_final: 0.8325 (mtpt) REVERT: G 36 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8163 (pp) REVERT: G 58 LYS cc_start: 0.9005 (mttp) cc_final: 0.8691 (mtmt) REVERT: G 235 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7393 (pp) REVERT: G 410 LYS cc_start: 0.8196 (ttmm) cc_final: 0.7849 (tppp) REVERT: G 412 ARG cc_start: 0.8692 (ptt90) cc_final: 0.8470 (ptt90) REVERT: G 492 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8282 (mtpp) REVERT: H 36 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8440 (pp) REVERT: H 50 ASP cc_start: 0.8526 (t70) cc_final: 0.8202 (t0) REVERT: H 58 LYS cc_start: 0.9025 (mttp) cc_final: 0.8657 (mtmt) REVERT: H 91 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8746 (mp) REVERT: H 235 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7498 (pp) REVERT: H 441 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7007 (mp10) REVERT: H 510 GLU cc_start: 0.6422 (tp30) cc_final: 0.4866 (pt0) outliers start: 109 outliers final: 66 residues processed: 360 average time/residue: 0.6030 time to fit residues: 251.1235 Evaluate side-chains 379 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 285 time to evaluate : 0.854 ------------------------------------------------------------------------------- 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 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 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 E residue 492 LYS 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 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 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 91 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 0.6980 chunk 106 optimal weight: 0.7980 chunk 161 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 160 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 276 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 158 optimal weight: 0.7980 chunk 295 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 334 GLN 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN H 303 ASN H 334 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.116244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.097923 restraints weight = 25833.819| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.94 r_work: 0.2971 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8899 moved from start: 0.2646 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 : 0.504 7.602 31208 Z= 0.254 Chirality : 0.042 0.141 3592 Planarity : 0.003 0.035 3976 Dihedral : 5.878 59.638 3292 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.40 % Allowed : 13.26 % 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: 0.05 (0.15), residues: 2960 helix: 1.00 (0.16), residues: 1104 sheet: -0.51 (0.23), residues: 408 loop : -0.48 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 412 TYR 0.009 0.001 TYR G 348 PHE 0.010 0.001 PHE C 401 HIS 0.003 0.001 HIS G 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (23096) covalent geometry : angle 0.50437 / 0.25 (31208) hydrogen bonds : bond 0.02668 / 1.77 ( 849) hydrogen bonds : angle 4.14913 / 2.94 ( 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 416 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 311 time to evaluate : 0.862 Fit side-chains REVERT: A 21 GLN cc_start: 0.8924 (tt0) cc_final: 0.8631 (tt0) REVERT: A 36 LEU cc_start: 0.8496 (OUTLIER) cc_final: 0.8204 (pp) REVERT: A 58 LYS cc_start: 0.9015 (mttp) cc_final: 0.8696 (mtmt) REVERT: A 235 LEU cc_start: 0.7752 (OUTLIER) cc_final: 0.7265 (pp) REVERT: A 277 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.6680 (tm-30) REVERT: A 441 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.6898 (mp10) REVERT: A 492 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8306 (mtpp) REVERT: B 36 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8255 (pp) REVERT: B 58 LYS cc_start: 0.8950 (mttp) cc_final: 0.8569 (mtmt) REVERT: B 235 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7439 (pp) REVERT: B 441 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.6835 (mp10) REVERT: B 510 GLU cc_start: 0.6389 (tp30) cc_final: 0.4918 (pt0) REVERT: C 21 GLN cc_start: 0.8914 (tt0) cc_final: 0.8656 (tt0) REVERT: C 36 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8077 (mt) REVERT: C 58 LYS cc_start: 0.9051 (mttp) cc_final: 0.8728 (mtmt) REVERT: C 235 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7310 (pp) REVERT: D 36 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8648 (pp) REVERT: D 50 ASP cc_start: 0.8530 (t70) cc_final: 0.8213 (t0) REVERT: D 58 LYS cc_start: 0.8965 (mttp) cc_final: 0.8590 (mtmt) REVERT: D 235 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7379 (pp) REVERT: D 441 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.6621 (mp10) REVERT: D 510 GLU cc_start: 0.6521 (tp30) cc_final: 0.5099 (pt0) REVERT: E 21 GLN cc_start: 0.8907 (tt0) cc_final: 0.8610 (tt0) REVERT: E 36 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8145 (mt) REVERT: E 58 LYS cc_start: 0.9041 (mttp) cc_final: 0.8740 (mtmt) REVERT: E 235 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7376 (pp) REVERT: E 453 ILE cc_start: 0.8351 (OUTLIER) cc_final: 0.7997 (tt) REVERT: E 492 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8326 (mtpp) REVERT: E 510 GLU cc_start: 0.6357 (tp30) cc_final: 0.4733 (pt0) REVERT: F 36 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8154 (mt) REVERT: F 58 LYS cc_start: 0.9069 (mttp) cc_final: 0.8711 (mtmt) REVERT: F 235 LEU cc_start: 0.7749 (OUTLIER) cc_final: 0.7319 (pp) REVERT: F 492 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8332 (mtpp) REVERT: G 36 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8150 (pp) REVERT: G 58 LYS cc_start: 0.9007 (mttp) cc_final: 0.8701 (mtmt) REVERT: G 235 LEU cc_start: 0.7795 (OUTLIER) cc_final: 0.7314 (pp) REVERT: G 410 LYS cc_start: 0.8197 (ttmm) cc_final: 0.7861 (tppp) REVERT: G 441 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7163 (mp10) REVERT: G 492 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8218 (mtpp) REVERT: G 510 GLU cc_start: 0.6310 (tp30) cc_final: 0.4697 (pt0) REVERT: H 36 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8481 (pp) REVERT: H 50 ASP cc_start: 0.8514 (t70) cc_final: 0.8201 (t0) REVERT: H 58 LYS cc_start: 0.9012 (mttp) cc_final: 0.8670 (mtmt) REVERT: H 235 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7497 (pp) REVERT: H 441 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.6740 (mp10) REVERT: H 510 GLU cc_start: 0.6349 (tp30) cc_final: 0.4877 (pt0) outliers start: 105 outliers final: 51 residues processed: 378 average time/residue: 0.5823 time to fit residues: 256.3113 Evaluate side-chains 380 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 302 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 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 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 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 E residue 492 LYS 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 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 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 437 ILE Chi-restraints excluded: chain H residue 441 GLN 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: 2.9990 chunk 9 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 72 optimal weight: 0.5980 chunk 260 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 246 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 303 ASN B 334 GLN C 303 ASN C 334 GLN D 303 ASN F 303 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3305 r_free = 0.3305 target = 0.117248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.099046 restraints weight = 25999.631| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.90 r_work: 0.2965 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8919 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 23096 Z= 0.142 Angle : 0.525 7.403 31208 Z= 0.264 Chirality : 0.043 0.147 3592 Planarity : 0.004 0.034 3976 Dihedral : 5.903 59.250 3292 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.19 % Allowed : 14.35 % Favored : 81.46 % 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: 1.03 (0.16), residues: 1104 sheet: -0.49 (0.23), residues: 408 loop : -0.46 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 412 TYR 0.010 0.001 TYR C 348 PHE 0.010 0.001 PHE E 401 HIS 0.003 0.001 HIS H 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.14 (23096) covalent geometry : angle 0.52497 / 0.26 (31208) hydrogen bonds : bond 0.02876 / 1.92 ( 849) hydrogen bonds : angle 4.17059 / 2.95 ( 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 393 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 293 time to evaluate : 0.917 Fit side-chains REVERT: A 1 MET cc_start: 0.5632 (mtm) cc_final: 0.5388 (mtt) REVERT: A 21 GLN cc_start: 0.8917 (tt0) cc_final: 0.8634 (tt0) REVERT: A 36 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8205 (pp) REVERT: A 50 ASP cc_start: 0.8475 (t70) cc_final: 0.8152 (t0) REVERT: A 58 LYS cc_start: 0.9012 (mttp) cc_final: 0.8705 (mtmt) REVERT: A 235 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7341 (pp) REVERT: A 441 GLN cc_start: 0.8203 (OUTLIER) cc_final: 0.6930 (mp10) REVERT: A 492 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8327 (mtpp) REVERT: B 36 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8251 (pp) REVERT: B 58 LYS cc_start: 0.8979 (mttp) cc_final: 0.8610 (mtmt) REVERT: B 235 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7505 (pp) REVERT: B 441 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.6955 (mp10) REVERT: B 510 GLU cc_start: 0.6448 (tp30) cc_final: 0.4985 (pt0) REVERT: C 21 GLN cc_start: 0.8924 (tt0) cc_final: 0.8700 (tt0) REVERT: C 36 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8227 (pp) REVERT: C 58 LYS cc_start: 0.9054 (mttp) cc_final: 0.8743 (mtmt) REVERT: C 235 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7363 (pp) REVERT: C 510 GLU cc_start: 0.6504 (tp30) cc_final: 0.4854 (pt0) REVERT: D 36 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8628 (pp) REVERT: D 50 ASP cc_start: 0.8523 (t70) cc_final: 0.8215 (t0) REVERT: D 58 LYS cc_start: 0.8994 (mttp) cc_final: 0.8632 (mtmt) REVERT: D 235 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7447 (pp) REVERT: D 441 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.6601 (mp10) REVERT: D 510 GLU cc_start: 0.6507 (tp30) cc_final: 0.5060 (pt0) REVERT: E 21 GLN cc_start: 0.8930 (tt0) cc_final: 0.8630 (tt0) REVERT: E 36 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8281 (pp) REVERT: E 58 LYS cc_start: 0.9043 (mttp) cc_final: 0.8751 (mtmt) REVERT: E 235 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7435 (pp) REVERT: E 277 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.6669 (tm-30) REVERT: E 453 ILE cc_start: 0.8419 (OUTLIER) cc_final: 0.8054 (tt) REVERT: E 492 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8285 (mtpt) REVERT: E 510 GLU cc_start: 0.6413 (tp30) cc_final: 0.4822 (pt0) REVERT: F 36 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8244 (pp) REVERT: F 58 LYS cc_start: 0.9082 (mttp) cc_final: 0.8735 (mtmt) REVERT: F 235 LEU cc_start: 0.7778 (OUTLIER) cc_final: 0.7355 (pp) REVERT: F 492 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8324 (mtpp) REVERT: F 510 GLU cc_start: 0.6243 (tp30) cc_final: 0.4668 (pt0) REVERT: G 36 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8162 (pp) REVERT: G 58 LYS cc_start: 0.9003 (mttp) cc_final: 0.8709 (mtmt) REVERT: G 235 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7386 (pp) REVERT: G 410 LYS cc_start: 0.8222 (ttmm) cc_final: 0.7873 (tppp) REVERT: G 441 GLN cc_start: 0.8136 (OUTLIER) cc_final: 0.7351 (mp10) REVERT: G 492 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8238 (mtpp) REVERT: G 510 GLU cc_start: 0.6371 (tp30) cc_final: 0.4779 (pt0) REVERT: H 36 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8385 (pp) REVERT: H 50 ASP cc_start: 0.8502 (t70) cc_final: 0.8194 (t0) REVERT: H 58 LYS cc_start: 0.9033 (mttp) cc_final: 0.8694 (mtmt) REVERT: H 91 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8742 (mp) REVERT: H 235 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7532 (pp) REVERT: H 441 GLN cc_start: 0.8192 (OUTLIER) cc_final: 0.6810 (mp10) REVERT: H 510 GLU cc_start: 0.6424 (tp30) cc_final: 0.4966 (pt0) outliers start: 100 outliers final: 57 residues processed: 358 average time/residue: 0.5971 time to fit residues: 248.0976 Evaluate side-chains 379 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 294 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 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 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 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 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 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 269 ASP Chi-restraints excluded: chain E residue 277 GLN 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 E residue 492 LYS 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 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 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 91 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 54 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 239 optimal weight: 1.9990 chunk 1 optimal weight: 0.0770 chunk 108 optimal weight: 0.8980 chunk 182 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 80 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 overall best weight: 0.9540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3291 r_free = 0.3291 target = 0.116765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.098318 restraints weight = 25864.975| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 1.95 r_work: 0.2934 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.2702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23096 Z= 0.151 Angle : 0.542 7.590 31208 Z= 0.272 Chirality : 0.044 0.143 3592 Planarity : 0.004 0.034 3976 Dihedral : 5.949 59.068 3292 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.78 % Allowed : 14.97 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.10 (0.15), residues: 2960 helix: 1.02 (0.16), residues: 1104 sheet: -0.46 (0.23), residues: 408 loop : -0.45 (0.16), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 412 TYR 0.011 0.001 TYR C 348 PHE 0.009 0.001 PHE D 401 HIS 0.003 0.001 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.15 (23096) covalent geometry : angle 0.54206 / 0.27 (31208) hydrogen bonds : bond 0.02936 / 1.96 ( 849) hydrogen bonds : angle 4.19847 / 2.97 ( 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 378 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 288 time to evaluate : 0.900 Fit side-chains REVERT: A 1 MET cc_start: 0.5318 (mtm) cc_final: 0.5089 (mtt) REVERT: A 21 GLN cc_start: 0.8854 (tt0) cc_final: 0.8561 (tt0) REVERT: A 36 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8101 (pp) REVERT: A 50 ASP cc_start: 0.8439 (t70) cc_final: 0.8082 (t0) REVERT: A 58 LYS cc_start: 0.8940 (mttp) cc_final: 0.8574 (mtmt) REVERT: A 235 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7100 (pp) REVERT: A 441 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.6808 (mp10) REVERT: A 492 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8102 (mtpp) REVERT: B 36 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8163 (pp) REVERT: B 58 LYS cc_start: 0.8883 (mttp) cc_final: 0.8463 (mtmt) REVERT: B 235 LEU cc_start: 0.7753 (OUTLIER) cc_final: 0.7286 (pp) REVERT: B 441 GLN cc_start: 0.7946 (OUTLIER) cc_final: 0.6639 (mp10) REVERT: C 21 GLN cc_start: 0.8842 (tt0) cc_final: 0.8591 (tt0) REVERT: C 36 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8108 (pp) REVERT: C 58 LYS cc_start: 0.8981 (mttp) cc_final: 0.8624 (mtmt) REVERT: C 235 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7183 (pp) REVERT: D 36 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8435 (pp) REVERT: D 50 ASP cc_start: 0.8478 (t70) cc_final: 0.8138 (t0) REVERT: D 58 LYS cc_start: 0.8904 (mttp) cc_final: 0.8493 (mtmt) REVERT: D 235 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7143 (pp) REVERT: D 441 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.6441 (mp10) REVERT: E 36 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8018 (mt) REVERT: E 58 LYS cc_start: 0.8962 (mttp) cc_final: 0.8624 (mtmt) REVERT: E 235 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7224 (pp) REVERT: E 453 ILE cc_start: 0.8273 (OUTLIER) cc_final: 0.7904 (tt) REVERT: E 492 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8153 (mtpp) REVERT: E 510 GLU cc_start: 0.6223 (tp30) cc_final: 0.4482 (pt0) REVERT: F 36 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8126 (pp) REVERT: F 58 LYS cc_start: 0.8996 (mttp) cc_final: 0.8605 (mtmt) REVERT: F 235 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7160 (pp) REVERT: F 491 GLU cc_start: 0.9036 (tp30) cc_final: 0.8704 (tt0) REVERT: F 492 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8179 (mtpp) REVERT: G 36 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8065 (pp) REVERT: G 58 LYS cc_start: 0.8940 (mttp) cc_final: 0.8606 (mtmt) REVERT: G 235 LEU cc_start: 0.7615 (OUTLIER) cc_final: 0.7143 (pp) REVERT: G 441 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7016 (mp10) REVERT: G 492 LYS cc_start: 0.8381 (OUTLIER) cc_final: 0.8085 (mtpp) REVERT: G 510 GLU cc_start: 0.6166 (tp30) cc_final: 0.4484 (pt0) REVERT: H 36 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8381 (pp) REVERT: H 50 ASP cc_start: 0.8449 (t70) cc_final: 0.8103 (t0) REVERT: H 58 LYS cc_start: 0.8958 (mttp) cc_final: 0.8561 (mtmt) REVERT: H 91 ILE cc_start: 0.8870 (OUTLIER) cc_final: 0.8631 (mp) REVERT: H 235 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7304 (pp) REVERT: H 441 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.6544 (mp10) REVERT: H 510 GLU cc_start: 0.6237 (tp30) cc_final: 0.4678 (pt0) outliers start: 90 outliers final: 57 residues processed: 343 average time/residue: 0.6147 time to fit residues: 243.3402 Evaluate side-chains 368 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 284 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 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 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 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 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 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 E residue 492 LYS 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 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 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 91 ILE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 100 optimal weight: 0.1980 chunk 67 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 219 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 269 optimal weight: 1.9990 chunk 195 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 211 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 303 ASN B 334 GLN C 303 ASN C 334 GLN D 303 ASN D 334 GLN F 303 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN H 303 ASN H 334 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.116225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.097492 restraints weight = 25832.147| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.00 r_work: 0.2861 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.2724 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= 0.128 Angle : 0.525 7.371 31208 Z= 0.262 Chirality : 0.043 0.143 3592 Planarity : 0.004 0.035 3976 Dihedral : 5.851 58.162 3292 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 3.57 % Allowed : 15.44 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.15), residues: 2960 helix: 1.11 (0.16), residues: 1104 sheet: -0.33 (0.24), residues: 392 loop : -0.41 (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 E 459 PHE 0.009 0.001 PHE E 401 HIS 0.003 0.001 HIS H 504 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (23096) covalent geometry : angle 0.52494 / 0.26 (31208) hydrogen bonds : bond 0.02722 / 1.81 ( 849) hydrogen bonds : angle 4.12109 / 2.92 ( 2475) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6809.87 seconds wall clock time: 117 minutes 45.30 seconds (7065.30 seconds total)