Starting phenix.real_space_refine on Thu Jun 19 17:07:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6udp_20742/06_2025/6udp_20742.cif Found real_map, /net/cci-nas-00/data/ceres_data/6udp_20742/06_2025/6udp_20742.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6udp_20742/06_2025/6udp_20742.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6udp_20742/06_2025/6udp_20742.map" model { file = "/net/cci-nas-00/data/ceres_data/6udp_20742/06_2025/6udp_20742.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6udp_20742/06_2025/6udp_20742.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 22728 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "B" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "C" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "D" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "E" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "F" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "G" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "H" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "F" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "G" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 14.44, per 1000 atoms: 0.64 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: 5.65 Conformation dependent library (CDL) restraints added in 2.9 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: 3.16 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: 9.31 Time building geometry restraints manager: 6.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3816 1.31 - 1.43: 5679 1.43 - 1.56: 13337 1.56 - 1.68: 24 1.68 - 1.80: 240 Bond restraints: 23096 Sorted by residual: bond pdb=" C4 IMP C 601 " pdb=" N3 IMP C 601 " ideal model delta sigma weight residual 1.355 1.492 -0.137 2.00e-02 2.50e+03 4.72e+01 bond pdb=" C4 IMP E 601 " pdb=" N3 IMP E 601 " ideal model delta sigma weight residual 1.355 1.492 -0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" C4 IMP F 601 " pdb=" N3 IMP F 601 " ideal model delta sigma weight residual 1.355 1.492 -0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" C4 IMP D 601 " pdb=" N3 IMP D 601 " ideal model delta sigma weight residual 1.355 1.492 -0.137 2.00e-02 2.50e+03 4.68e+01 bond pdb=" C4 IMP B 601 " pdb=" N3 IMP B 601 " ideal model delta sigma weight residual 1.355 1.492 -0.137 2.00e-02 2.50e+03 4.67e+01 ... (remaining 23091 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.98: 30831 2.98 - 5.97: 320 5.97 - 8.95: 41 8.95 - 11.94: 8 11.94 - 14.92: 8 Bond angle restraints: 31208 Sorted by residual: angle pdb=" CA LEU G 235 " pdb=" CB LEU G 235 " pdb=" CG LEU G 235 " ideal model delta sigma weight residual 116.30 131.22 -14.92 3.50e+00 8.16e-02 1.82e+01 angle pdb=" CA LEU D 235 " pdb=" CB LEU D 235 " pdb=" CG LEU D 235 " ideal model delta sigma weight residual 116.30 131.18 -14.88 3.50e+00 8.16e-02 1.81e+01 angle pdb=" CA LEU C 235 " pdb=" CB LEU C 235 " pdb=" CG LEU C 235 " ideal model delta sigma weight residual 116.30 131.18 -14.88 3.50e+00 8.16e-02 1.81e+01 angle pdb=" CA LEU H 235 " pdb=" CB LEU H 235 " pdb=" CG LEU H 235 " ideal model delta sigma weight residual 116.30 131.18 -14.88 3.50e+00 8.16e-02 1.81e+01 angle pdb=" CA LEU E 235 " pdb=" CB LEU E 235 " pdb=" CG LEU E 235 " ideal model delta sigma weight residual 116.30 131.16 -14.86 3.50e+00 8.16e-02 1.80e+01 ... (remaining 31203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 13696 35.14 - 70.27: 100 70.27 - 105.41: 8 105.41 - 140.55: 0 140.55 - 175.68: 4 Dihedral angle restraints: 13808 sinusoidal: 5304 harmonic: 8504 Sorted by residual: dihedral pdb=" C5' IMP C 601 " pdb=" O5' IMP C 601 " pdb=" P IMP C 601 " pdb=" O2P IMP C 601 " ideal model delta sinusoidal sigma weight residual -168.07 7.61 -175.68 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' IMP B 601 " pdb=" O5' IMP B 601 " pdb=" P IMP B 601 " pdb=" O2P IMP B 601 " ideal model delta sinusoidal sigma weight residual -168.07 7.57 -175.64 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C5' IMP A 601 " pdb=" O5' IMP A 601 " pdb=" P IMP A 601 " pdb=" O2P IMP A 601 " ideal model delta sinusoidal sigma weight residual -168.07 7.52 -175.59 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 13805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2573 0.055 - 0.110: 850 0.110 - 0.165: 125 0.165 - 0.219: 28 0.219 - 0.274: 16 Chirality restraints: 3592 Sorted by residual: chirality pdb=" C3' IMP G 601 " pdb=" C2' IMP G 601 " pdb=" C4' IMP G 601 " pdb=" O3' IMP G 601 " both_signs ideal model delta sigma weight residual False -2.48 -2.75 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C3' IMP C 601 " pdb=" C2' IMP C 601 " pdb=" C4' IMP C 601 " pdb=" O3' IMP C 601 " both_signs ideal model delta sigma weight residual False -2.48 -2.75 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C3' IMP H 601 " pdb=" C2' IMP H 601 " pdb=" C4' IMP H 601 " pdb=" O3' IMP H 601 " both_signs ideal model delta sigma weight residual False -2.48 -2.75 0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 3589 not shown) Planarity restraints: 3976 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 233 " -0.036 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO E 234 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO E 234 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 234 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 233 " 0.036 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO A 234 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR G 233 " 0.036 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO G 234 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO G 234 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO G 234 " 0.031 5.00e-02 4.00e+02 ... (remaining 3973 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 7554 2.85 - 3.36: 20734 3.36 - 3.88: 38994 3.88 - 4.39: 45518 4.39 - 4.90: 79147 Nonbonded interactions: 191947 Sorted by model distance: nonbonded pdb=" OD1 ASN H 25 " pdb=" NZ LYS H 349 " model vdw 2.340 3.120 nonbonded pdb=" OD1 ASN C 25 " pdb=" NZ LYS C 349 " model vdw 2.340 3.120 nonbonded pdb=" OD1 ASN E 25 " pdb=" NZ LYS E 349 " model vdw 2.340 3.120 nonbonded pdb=" OD1 ASN A 25 " pdb=" NZ LYS A 349 " model vdw 2.340 3.120 nonbonded pdb=" OD1 ASN B 25 " pdb=" NZ LYS B 349 " model vdw 2.340 3.120 ... (remaining 191942 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.010 Check model and map are aligned: 0.190 Set scattering table: 0.210 Process input model: 54.780 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.137 23096 Z= 0.323 Angle : 0.868 14.920 31208 Z= 0.459 Chirality : 0.056 0.274 3592 Planarity : 0.006 0.053 3976 Dihedral : 10.711 175.684 8416 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.67 % Allowed : 5.03 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.004 0.001 HIS D 93 PHE 0.017 0.003 PHE E 401 TYR 0.020 0.003 TYR E 484 ARG 0.004 0.001 ARG B 341 Details of bonding type rmsd hydrogen bonds : bond 0.17055 ( 849) hydrogen bonds : angle 7.35189 ( 2475) covalent geometry : bond 0.00724 (23096) covalent geometry : angle 0.86751 (31208) *********************** 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 : 2.536 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: 1.2231 time to fit residues: 704.9337 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 : 2.281 ------------------------------------------------------------------------------- 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 249 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 232 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 141 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 268 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 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 = 0.3344 r_free = 0.3344 target = 0.119789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.101936 restraints weight = 25810.156| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.93 r_work: 0.2987 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1691 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= 0.143 Angle : 0.512 8.125 31208 Z= 0.271 Chirality : 0.042 0.156 3592 Planarity : 0.004 0.038 3976 Dihedral : 7.717 150.387 3294 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.52 % Allowed : 11.45 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.73 (0.14), residues: 2960 helix: -0.84 (0.14), residues: 1096 sheet: -1.35 (0.23), residues: 424 loop : -1.22 (0.14), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 504 PHE 0.013 0.002 PHE B 401 TYR 0.013 0.002 TYR C 353 ARG 0.003 0.001 ARG F 341 Details of bonding type rmsd hydrogen bonds : bond 0.03436 ( 849) hydrogen bonds : angle 5.00685 ( 2475) covalent geometry : bond 0.00347 (23096) covalent geometry : angle 0.51154 (31208) *********************** 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: 84 poor density : 361 time to evaluate : 2.481 Fit side-chains REVERT: A 21 GLN cc_start: 0.8817 (tm-30) cc_final: 0.8476 (tt0) REVERT: A 36 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8577 (pp) REVERT: A 50 ASP cc_start: 0.8426 (t70) cc_final: 0.8055 (t0) REVERT: A 58 LYS cc_start: 0.8899 (mttp) cc_final: 0.8541 (mtmt) REVERT: A 235 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7307 (pp) REVERT: A 474 LYS cc_start: 0.8475 (mtpt) cc_final: 0.8175 (mtpt) REVERT: A 510 GLU cc_start: 0.5754 (tp30) cc_final: 0.4290 (pt0) REVERT: B 36 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8598 (pp) REVERT: B 50 ASP cc_start: 0.8459 (t70) cc_final: 0.8093 (t0) REVERT: B 58 LYS cc_start: 0.8909 (mttp) cc_final: 0.8500 (mtmt) REVERT: B 510 GLU cc_start: 0.5752 (tp30) cc_final: 0.4501 (pt0) REVERT: C 36 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.7912 (mt) REVERT: C 58 LYS cc_start: 0.8923 (mttp) cc_final: 0.8557 (mtmt) REVERT: C 235 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7400 (pp) REVERT: C 510 GLU cc_start: 0.5762 (tp30) cc_final: 0.4380 (pt0) REVERT: D 36 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8590 (pp) REVERT: D 58 LYS cc_start: 0.8914 (mttp) cc_final: 0.8486 (mtmt) REVERT: D 91 ILE cc_start: 0.8815 (OUTLIER) cc_final: 0.8603 (mt) REVERT: D 235 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7441 (pp) REVERT: D 474 LYS cc_start: 0.8342 (mtpt) cc_final: 0.8035 (mtpt) REVERT: D 510 GLU cc_start: 0.5835 (tp30) cc_final: 0.4549 (pt0) REVERT: E 36 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.7890 (mt) REVERT: E 50 ASP cc_start: 0.8481 (t70) cc_final: 0.8093 (t0) REVERT: E 58 LYS cc_start: 0.8938 (mttp) cc_final: 0.8595 (mtmt) REVERT: E 235 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7340 (pp) REVERT: E 474 LYS cc_start: 0.8466 (mtpt) cc_final: 0.8172 (mtmt) REVERT: E 510 GLU cc_start: 0.5798 (tp30) cc_final: 0.4328 (pt0) REVERT: F 36 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8590 (pp) REVERT: F 50 ASP cc_start: 0.8510 (t70) cc_final: 0.8173 (t0) REVERT: F 58 LYS cc_start: 0.8975 (mttp) cc_final: 0.8590 (mtmt) REVERT: F 91 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8606 (mt) REVERT: F 235 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7421 (pp) REVERT: F 335 GLU cc_start: 0.6568 (mm-30) cc_final: 0.5786 (mp0) REVERT: F 474 LYS cc_start: 0.8364 (mtpt) cc_final: 0.8101 (mtpt) REVERT: F 510 GLU cc_start: 0.5614 (tp30) cc_final: 0.4304 (pt0) REVERT: G 36 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8453 (pp) REVERT: G 50 ASP cc_start: 0.8405 (t70) cc_final: 0.8031 (t0) REVERT: G 58 LYS cc_start: 0.8873 (mttp) cc_final: 0.8546 (mtmt) REVERT: G 235 LEU cc_start: 0.7946 (OUTLIER) cc_final: 0.7335 (pp) REVERT: G 474 LYS cc_start: 0.8450 (mtpt) cc_final: 0.8171 (mtpt) REVERT: G 483 MET cc_start: 0.9251 (tmm) cc_final: 0.9045 (tmm) REVERT: H 36 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8460 (pp) REVERT: H 50 ASP cc_start: 0.8500 (t70) cc_final: 0.8153 (t0) REVERT: H 58 LYS cc_start: 0.8939 (mttp) cc_final: 0.8551 (mtmt) REVERT: H 235 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7469 (pp) REVERT: H 510 GLU cc_start: 0.5726 (tp30) cc_final: 0.4459 (pt0) outliers start: 84 outliers final: 32 residues processed: 411 average time/residue: 1.1508 time to fit residues: 551.5322 Evaluate side-chains 357 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 308 time to evaluate : 2.607 ------------------------------------------------------------------------------- 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 36 LEU Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 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 107 VAL 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 36 LEU Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 153 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 130 optimal weight: 0.4980 chunk 257 optimal weight: 2.9990 chunk 177 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 169 optimal weight: 5.9990 chunk 137 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 0.0870 chunk 155 optimal weight: 0.0970 overall best weight: 0.8958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 334 GLN C 48 GLN C 303 ASN C 334 GLN ** D 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN ** D 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 48 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN H 334 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.117881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.099939 restraints weight = 25643.703| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.92 r_work: 0.2956 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2123 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= 0.145 Angle : 0.495 7.617 31208 Z= 0.258 Chirality : 0.042 0.150 3592 Planarity : 0.004 0.037 3976 Dihedral : 6.116 76.435 3294 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 4.19 % Allowed : 12.08 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.14), residues: 2960 helix: 0.01 (0.15), residues: 1104 sheet: -1.08 (0.22), residues: 424 loop : -0.93 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 504 PHE 0.010 0.001 PHE E 401 TYR 0.012 0.002 TYR B 353 ARG 0.003 0.001 ARG G 355 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 849) hydrogen bonds : angle 4.50540 ( 2475) covalent geometry : bond 0.00360 (23096) covalent geometry : angle 0.49504 (31208) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 344 time to evaluate : 2.712 Fit side-chains REVERT: A 21 GLN cc_start: 0.8835 (tm-30) cc_final: 0.8473 (tt0) REVERT: A 58 LYS cc_start: 0.8884 (mttp) cc_final: 0.8520 (mtmt) REVERT: A 235 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7250 (pp) REVERT: A 441 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7183 (mp10) REVERT: A 474 LYS cc_start: 0.8439 (mtpt) cc_final: 0.8142 (mtmt) REVERT: A 510 GLU cc_start: 0.5986 (tp30) cc_final: 0.4357 (pt0) REVERT: B 50 ASP cc_start: 0.8473 (t70) cc_final: 0.8107 (t0) REVERT: B 58 LYS cc_start: 0.8885 (mttp) cc_final: 0.8476 (mtmt) REVERT: B 510 GLU cc_start: 0.6006 (tp30) cc_final: 0.4561 (pt0) REVERT: C 58 LYS cc_start: 0.8942 (mttp) cc_final: 0.8591 (mtmt) REVERT: C 235 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7274 (pp) REVERT: C 412 ARG cc_start: 0.8682 (ptt180) cc_final: 0.8313 (ptt90) REVERT: C 510 GLU cc_start: 0.5986 (tp30) cc_final: 0.4403 (pt0) REVERT: D 21 GLN cc_start: 0.8913 (tm-30) cc_final: 0.8586 (tt0) REVERT: D 36 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8491 (pp) REVERT: D 58 LYS cc_start: 0.8923 (mttp) cc_final: 0.8510 (mtmt) REVERT: D 235 LEU cc_start: 0.7928 (OUTLIER) cc_final: 0.7385 (pp) REVERT: D 441 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.6888 (mp10) REVERT: D 510 GLU cc_start: 0.6088 (tp30) cc_final: 0.4636 (pt0) REVERT: E 36 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8241 (pp) REVERT: E 50 ASP cc_start: 0.8441 (t70) cc_final: 0.8062 (t0) REVERT: E 58 LYS cc_start: 0.8926 (mttp) cc_final: 0.8580 (mtmt) REVERT: E 235 LEU cc_start: 0.7887 (OUTLIER) cc_final: 0.7259 (pp) REVERT: E 474 LYS cc_start: 0.8443 (mtpt) cc_final: 0.8154 (mtmt) REVERT: E 510 GLU cc_start: 0.5940 (tp30) cc_final: 0.4312 (pt0) REVERT: F 50 ASP cc_start: 0.8508 (t70) cc_final: 0.8160 (t0) REVERT: F 58 LYS cc_start: 0.8964 (mttp) cc_final: 0.8567 (mtmt) REVERT: F 235 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7293 (pp) REVERT: F 510 GLU cc_start: 0.5940 (tp30) cc_final: 0.5603 (tp30) REVERT: G 36 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8500 (pp) REVERT: G 58 LYS cc_start: 0.8900 (mttp) cc_final: 0.8562 (mtmt) REVERT: G 235 LEU cc_start: 0.7832 (OUTLIER) cc_final: 0.7248 (pp) REVERT: G 474 LYS cc_start: 0.8409 (mtpt) cc_final: 0.8137 (mtmt) REVERT: G 510 GLU cc_start: 0.5949 (tp30) cc_final: 0.5551 (tp30) REVERT: H 21 GLN cc_start: 0.8902 (tm-30) cc_final: 0.8557 (tt0) REVERT: H 36 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8401 (pp) REVERT: H 50 ASP cc_start: 0.8463 (t70) cc_final: 0.8112 (t0) REVERT: H 58 LYS cc_start: 0.8912 (mttp) cc_final: 0.8533 (mtmt) REVERT: H 235 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7410 (pp) REVERT: H 441 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7193 (mp10) REVERT: H 510 GLU cc_start: 0.5916 (tp30) cc_final: 0.4530 (pt0) outliers start: 100 outliers final: 47 residues processed: 407 average time/residue: 1.1828 time to fit residues: 560.3103 Evaluate side-chains 372 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 311 time to evaluate : 2.482 ------------------------------------------------------------------------------- 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 437 ILE Chi-restraints excluded: chain A residue 441 GLN 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 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 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 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 441 GLN Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 107 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 437 ILE Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain 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 277 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 287 optimal weight: 5.9990 chunk 171 optimal weight: 0.3980 chunk 83 optimal weight: 0.6980 chunk 247 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 172 optimal weight: 0.9980 chunk 94 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 259 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN B 48 GLN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 334 GLN ** C 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 = 0.3318 r_free = 0.3318 target = 0.118422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.100133 restraints weight = 25929.134| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.94 r_work: 0.2954 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23096 Z= 0.130 Angle : 0.482 7.279 31208 Z= 0.252 Chirality : 0.042 0.145 3592 Planarity : 0.004 0.036 3976 Dihedral : 5.818 53.426 3292 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.11 % Allowed : 12.25 % Favored : 83.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.15), residues: 2960 helix: 0.45 (0.16), residues: 1104 sheet: -0.82 (0.22), residues: 424 loop : -0.74 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 504 PHE 0.011 0.001 PHE E 401 TYR 0.010 0.001 TYR F 348 ARG 0.003 0.000 ARG B 341 Details of bonding type rmsd hydrogen bonds : bond 0.02884 ( 849) hydrogen bonds : angle 4.31882 ( 2475) covalent geometry : bond 0.00319 (23096) covalent geometry : angle 0.48195 (31208) *********************** 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 415 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 317 time to evaluate : 2.750 Fit side-chains REVERT: A 21 GLN cc_start: 0.8840 (tm-30) cc_final: 0.8518 (tt0) REVERT: A 58 LYS cc_start: 0.8864 (mttp) cc_final: 0.8514 (mtmt) REVERT: A 235 LEU cc_start: 0.7730 (OUTLIER) cc_final: 0.7163 (pp) REVERT: A 412 ARG cc_start: 0.8592 (ptt90) cc_final: 0.8346 (ptt90) REVERT: A 474 LYS cc_start: 0.8421 (mtpt) cc_final: 0.8154 (mtmt) REVERT: A 492 LYS cc_start: 0.8509 (OUTLIER) cc_final: 0.8220 (mtpp) REVERT: A 510 GLU cc_start: 0.6184 (tp30) cc_final: 0.4489 (pt0) REVERT: B 58 LYS cc_start: 0.8886 (mttp) cc_final: 0.8477 (mtmt) REVERT: B 91 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8598 (mt) REVERT: B 441 GLN cc_start: 0.8111 (OUTLIER) cc_final: 0.6827 (mp10) REVERT: B 492 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8260 (mtpp) REVERT: B 510 GLU cc_start: 0.6138 (tp30) cc_final: 0.4619 (pt0) REVERT: C 21 GLN cc_start: 0.8828 (tt0) cc_final: 0.8570 (tt0) REVERT: C 36 LEU cc_start: 0.8411 (pp) cc_final: 0.7918 (mt) REVERT: C 58 LYS cc_start: 0.8907 (mttp) cc_final: 0.8554 (mtmt) REVERT: C 235 LEU cc_start: 0.7852 (OUTLIER) cc_final: 0.7261 (pp) REVERT: C 510 GLU cc_start: 0.6125 (tp30) cc_final: 0.4486 (pt0) REVERT: D 21 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8600 (tt0) REVERT: D 36 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8580 (pp) REVERT: D 58 LYS cc_start: 0.8887 (mttp) cc_final: 0.8476 (mtmt) REVERT: D 235 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7292 (pp) REVERT: D 400 TYR cc_start: 0.8612 (m-80) cc_final: 0.8305 (m-80) REVERT: D 510 GLU cc_start: 0.6228 (tp30) cc_final: 0.4722 (pt0) REVERT: E 36 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8011 (mt) REVERT: E 58 LYS cc_start: 0.8883 (mttp) cc_final: 0.8548 (mtmt) REVERT: E 235 LEU cc_start: 0.7812 (OUTLIER) cc_final: 0.7246 (pp) REVERT: E 474 LYS cc_start: 0.8459 (mtpt) cc_final: 0.8192 (mtmt) REVERT: E 492 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8298 (mtpp) REVERT: E 510 GLU cc_start: 0.6107 (tp30) cc_final: 0.4405 (pt0) REVERT: F 16 ASP cc_start: 0.8359 (t70) cc_final: 0.8113 (t70) REVERT: F 50 ASP cc_start: 0.8526 (t70) cc_final: 0.8173 (t0) REVERT: F 58 LYS cc_start: 0.8948 (mttp) cc_final: 0.8560 (mtmt) REVERT: F 235 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7310 (pp) REVERT: F 491 GLU cc_start: 0.8957 (tp30) cc_final: 0.8716 (tt0) REVERT: F 492 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8200 (mtpp) REVERT: F 510 GLU cc_start: 0.6099 (tp30) cc_final: 0.5738 (tp30) REVERT: G 58 LYS cc_start: 0.8887 (mttp) cc_final: 0.8558 (mtmt) REVERT: G 235 LEU cc_start: 0.7747 (OUTLIER) cc_final: 0.7206 (pp) REVERT: G 410 LYS cc_start: 0.8072 (ttmm) cc_final: 0.7738 (tppp) REVERT: G 441 GLN cc_start: 0.8125 (OUTLIER) cc_final: 0.7018 (mp10) REVERT: G 492 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8190 (mtpp) REVERT: G 510 GLU cc_start: 0.6038 (tp30) cc_final: 0.5641 (tp30) REVERT: H 21 GLN cc_start: 0.8904 (tm-30) cc_final: 0.8585 (tt0) REVERT: H 36 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8387 (pp) REVERT: H 50 ASP cc_start: 0.8451 (t70) cc_final: 0.8096 (t0) REVERT: H 58 LYS cc_start: 0.8914 (mttp) cc_final: 0.8541 (mtmt) REVERT: H 235 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7383 (pp) REVERT: H 510 GLU cc_start: 0.6072 (tp30) cc_final: 0.4581 (pt0) outliers start: 98 outliers final: 47 residues processed: 381 average time/residue: 1.2417 time to fit residues: 548.0551 Evaluate side-chains 367 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 302 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 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 B residue 492 LYS 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 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 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 437 ILE Chi-restraints excluded: chain E residue 492 LYS 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 492 LYS Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain G residue 492 LYS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 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 96 optimal weight: 0.5980 chunk 209 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 106 optimal weight: 2.9990 chunk 217 optimal weight: 0.6980 chunk 227 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 220 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN B 303 ASN B 334 GLN 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 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN H 334 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.115302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.097236 restraints weight = 26004.162| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.90 r_work: 0.2942 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 23096 Z= 0.149 Angle : 0.489 5.532 31208 Z= 0.255 Chirality : 0.043 0.144 3592 Planarity : 0.004 0.036 3976 Dihedral : 5.884 58.677 3292 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 4.57 % Allowed : 12.04 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 2960 helix: 0.67 (0.16), residues: 1104 sheet: -0.73 (0.22), residues: 424 loop : -0.63 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 504 PHE 0.010 0.001 PHE F 401 TYR 0.011 0.001 TYR C 348 ARG 0.002 0.000 ARG B 341 Details of bonding type rmsd hydrogen bonds : bond 0.03026 ( 849) hydrogen bonds : angle 4.30096 ( 2475) covalent geometry : bond 0.00370 (23096) covalent geometry : angle 0.48902 (31208) *********************** 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 414 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 305 time to evaluate : 2.502 Fit side-chains REVERT: A 21 GLN cc_start: 0.8654 (tt0) cc_final: 0.8345 (tt0) REVERT: A 58 LYS cc_start: 0.8700 (mttp) cc_final: 0.8284 (mtmt) REVERT: A 235 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6882 (pp) REVERT: A 441 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.6622 (mp10) REVERT: A 474 LYS cc_start: 0.8144 (mtpt) cc_final: 0.7881 (mtmt) REVERT: A 492 LYS cc_start: 0.8305 (OUTLIER) cc_final: 0.7923 (mtpp) REVERT: A 510 GLU cc_start: 0.6006 (tp30) cc_final: 0.4238 (pt0) REVERT: B 50 ASP cc_start: 0.8328 (t70) cc_final: 0.7965 (t0) REVERT: B 58 LYS cc_start: 0.8691 (mttp) cc_final: 0.8238 (mtmt) REVERT: B 91 ILE cc_start: 0.8615 (OUTLIER) cc_final: 0.8403 (mt) REVERT: B 235 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.6997 (pp) REVERT: B 412 ARG cc_start: 0.8517 (ptt90) cc_final: 0.8297 (ptt90) REVERT: B 441 GLN cc_start: 0.7853 (OUTLIER) cc_final: 0.6600 (mp10) REVERT: B 492 LYS cc_start: 0.8258 (OUTLIER) cc_final: 0.8009 (mtpp) REVERT: B 510 GLU cc_start: 0.5984 (tp30) cc_final: 0.4437 (pt0) REVERT: C 36 LEU cc_start: 0.8276 (OUTLIER) cc_final: 0.8037 (pp) REVERT: C 58 LYS cc_start: 0.8788 (mttp) cc_final: 0.8385 (mtmt) REVERT: C 235 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.6916 (pp) REVERT: C 325 MET cc_start: 0.9255 (ttt) cc_final: 0.9016 (ttt) REVERT: C 510 GLU cc_start: 0.5966 (tp30) cc_final: 0.4247 (pt0) REVERT: D 21 GLN cc_start: 0.8739 (tt0) cc_final: 0.8442 (tt0) REVERT: D 36 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8327 (pp) REVERT: D 58 LYS cc_start: 0.8693 (mttp) cc_final: 0.8232 (mtmt) REVERT: D 235 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.6975 (pp) REVERT: D 441 GLN cc_start: 0.7884 (OUTLIER) cc_final: 0.6416 (mp10) REVERT: D 510 GLU cc_start: 0.6012 (tp30) cc_final: 0.4434 (pt0) REVERT: E 58 LYS cc_start: 0.8770 (mttp) cc_final: 0.8392 (mtmt) REVERT: E 235 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.6962 (pp) REVERT: E 492 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.7948 (mtpp) REVERT: E 510 GLU cc_start: 0.5869 (tp30) cc_final: 0.4137 (pt0) REVERT: F 58 LYS cc_start: 0.8825 (mttp) cc_final: 0.8383 (mtmt) REVERT: F 235 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6990 (pp) REVERT: F 491 GLU cc_start: 0.8870 (tp30) cc_final: 0.8622 (tt0) REVERT: F 492 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7972 (mtpp) REVERT: G 58 LYS cc_start: 0.8768 (mttp) cc_final: 0.8398 (mtmt) REVERT: G 235 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.6874 (pp) REVERT: G 410 LYS cc_start: 0.7913 (ttmm) cc_final: 0.7579 (tppp) REVERT: G 412 ARG cc_start: 0.8496 (ptt90) cc_final: 0.8296 (ptt90) REVERT: G 441 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.6709 (mp10) REVERT: G 492 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7833 (mtpp) REVERT: G 510 GLU cc_start: 0.5855 (tp30) cc_final: 0.5563 (tp30) REVERT: H 21 GLN cc_start: 0.8728 (tt0) cc_final: 0.8382 (tt0) REVERT: H 36 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8195 (pp) REVERT: H 58 LYS cc_start: 0.8752 (mttp) cc_final: 0.8335 (mtmt) REVERT: H 235 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7064 (pp) REVERT: H 412 ARG cc_start: 0.8573 (ptt90) cc_final: 0.8348 (ptt90) REVERT: H 441 GLN cc_start: 0.7965 (OUTLIER) cc_final: 0.6630 (mp10) REVERT: H 510 GLU cc_start: 0.5892 (tp30) cc_final: 0.4309 (pt0) outliers start: 109 outliers final: 65 residues processed: 375 average time/residue: 1.2097 time to fit residues: 524.9225 Evaluate side-chains 381 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 294 time to evaluate : 2.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain A residue 492 LYS Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 91 ILE 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 B residue 492 LYS Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 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 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 66 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain G residue 492 LYS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 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 178 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 232 optimal weight: 0.7980 chunk 269 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 132 optimal weight: 7.9990 chunk 87 optimal weight: 3.9990 chunk 216 optimal weight: 0.0030 chunk 294 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN B 303 ASN B 334 GLN C 303 ASN C 334 GLN D 303 ASN D 334 GLN E 309 GLN E 334 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.115890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.097389 restraints weight = 25886.179| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.98 r_work: 0.2955 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23096 Z= 0.138 Angle : 0.482 5.549 31208 Z= 0.251 Chirality : 0.042 0.142 3592 Planarity : 0.004 0.035 3976 Dihedral : 5.816 59.797 3290 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 4.66 % Allowed : 12.12 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.15), residues: 2960 helix: 0.83 (0.16), residues: 1104 sheet: -0.61 (0.23), residues: 424 loop : -0.56 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 504 PHE 0.009 0.001 PHE E 401 TYR 0.010 0.001 TYR F 348 ARG 0.002 0.000 ARG B 341 Details of bonding type rmsd hydrogen bonds : bond 0.02901 ( 849) hydrogen bonds : angle 4.22340 ( 2475) covalent geometry : bond 0.00342 (23096) covalent geometry : angle 0.48158 (31208) *********************** 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 423 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 312 time to evaluate : 2.498 Fit side-chains REVERT: A 21 GLN cc_start: 0.8874 (tt0) cc_final: 0.8583 (tt0) REVERT: A 36 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8190 (pp) REVERT: A 58 LYS cc_start: 0.8969 (mttp) cc_final: 0.8636 (mtmt) REVERT: A 235 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7307 (pp) REVERT: A 441 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.6986 (mp10) REVERT: A 492 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8295 (mtpp) REVERT: A 510 GLU cc_start: 0.6441 (tp30) cc_final: 0.4752 (pt0) REVERT: B 36 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8280 (pp) REVERT: B 50 ASP cc_start: 0.8524 (t70) cc_final: 0.8220 (t0) REVERT: B 58 LYS cc_start: 0.8959 (mttp) cc_final: 0.8573 (mtmt) REVERT: B 91 ILE cc_start: 0.8935 (OUTLIER) cc_final: 0.8700 (mt) REVERT: B 235 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7505 (pp) REVERT: B 412 ARG cc_start: 0.8717 (ptt90) cc_final: 0.8499 (ptt90) REVERT: B 441 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.6860 (mp10) REVERT: B 492 LYS cc_start: 0.8553 (OUTLIER) cc_final: 0.8176 (mtpt) REVERT: B 510 GLU cc_start: 0.6354 (tp30) cc_final: 0.4866 (pt0) REVERT: C 36 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8306 (pp) REVERT: C 58 LYS cc_start: 0.9015 (mttp) cc_final: 0.8695 (mtmt) REVERT: C 235 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7337 (pp) REVERT: D 21 GLN cc_start: 0.8940 (tt0) cc_final: 0.8626 (tt0) REVERT: D 36 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8608 (pp) REVERT: D 58 LYS cc_start: 0.8968 (mttp) cc_final: 0.8576 (mtmt) REVERT: D 235 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7409 (pp) REVERT: D 441 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.6700 (mp10) REVERT: D 510 GLU cc_start: 0.6438 (tp30) cc_final: 0.4944 (pt0) REVERT: E 21 GLN cc_start: 0.8908 (tt0) cc_final: 0.8599 (tt0) REVERT: E 36 LEU cc_start: 0.8396 (pp) cc_final: 0.8018 (mt) REVERT: E 58 LYS cc_start: 0.9013 (mttp) cc_final: 0.8717 (mtmt) REVERT: E 235 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7333 (pp) REVERT: E 492 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8272 (mtpp) REVERT: E 510 GLU cc_start: 0.6248 (tp30) cc_final: 0.4567 (pt0) REVERT: F 36 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8200 (pp) REVERT: F 58 LYS cc_start: 0.9066 (mttp) cc_final: 0.8705 (mtmt) REVERT: F 235 LEU cc_start: 0.7811 (OUTLIER) cc_final: 0.7385 (pp) REVERT: F 491 GLU cc_start: 0.8977 (tp30) cc_final: 0.8690 (tp30) REVERT: F 492 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8289 (mtpp) REVERT: G 58 LYS cc_start: 0.9034 (mttp) cc_final: 0.8719 (mtmt) REVERT: G 235 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7357 (pp) REVERT: G 410 LYS cc_start: 0.8203 (ttmm) cc_final: 0.7865 (tppp) REVERT: G 414 MET cc_start: 0.8508 (mmm) cc_final: 0.8003 (mmm) REVERT: G 441 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7022 (mp10) REVERT: G 492 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8235 (mtpp) REVERT: H 21 GLN cc_start: 0.8927 (tt0) cc_final: 0.8608 (tt0) REVERT: H 36 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8449 (pp) REVERT: H 50 ASP cc_start: 0.8506 (t70) cc_final: 0.8175 (t0) REVERT: H 58 LYS cc_start: 0.9014 (mttp) cc_final: 0.8657 (mtmt) REVERT: H 235 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7451 (pp) REVERT: H 441 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.6942 (mp10) REVERT: H 510 GLU cc_start: 0.6354 (tp30) cc_final: 0.4866 (pt0) outliers start: 111 outliers final: 64 residues processed: 384 average time/residue: 1.1879 time to fit residues: 529.4357 Evaluate side-chains 387 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 298 time to evaluate : 2.533 ------------------------------------------------------------------------------- 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 91 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain E residue 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 441 GLN Chi-restraints excluded: chain F residue 492 LYS 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 318 VAL Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain G residue 492 LYS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 477 THR Chi-restraints excluded: chain H residue 485 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 189 optimal weight: 0.2980 chunk 102 optimal weight: 5.9990 chunk 262 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 178 optimal weight: 7.9990 chunk 208 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 276 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 chunk 164 optimal weight: 2.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN B 303 ASN B 334 GLN C 303 ASN C 334 GLN D 303 ASN D 334 GLN E 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: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.116163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.097726 restraints weight = 26007.227| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.95 r_work: 0.2971 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23096 Z= 0.126 Angle : 0.479 5.559 31208 Z= 0.249 Chirality : 0.042 0.144 3592 Planarity : 0.004 0.036 3976 Dihedral : 5.705 59.179 3290 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 4.53 % Allowed : 13.21 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 2960 helix: 0.96 (0.16), residues: 1104 sheet: -0.59 (0.23), residues: 424 loop : -0.52 (0.16), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 92 PHE 0.010 0.001 PHE E 401 TYR 0.010 0.001 TYR F 348 ARG 0.004 0.000 ARG H 412 Details of bonding type rmsd hydrogen bonds : bond 0.02759 ( 849) hydrogen bonds : angle 4.15652 ( 2475) covalent geometry : bond 0.00310 (23096) covalent geometry : angle 0.47943 (31208) *********************** 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 423 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 315 time to evaluate : 2.443 Fit side-chains REVERT: A 21 GLN cc_start: 0.8911 (tt0) cc_final: 0.8617 (tt0) REVERT: A 36 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8190 (pp) REVERT: A 58 LYS cc_start: 0.9001 (mttp) cc_final: 0.8675 (mtmt) REVERT: A 235 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7311 (pp) REVERT: A 441 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.6922 (mp10) REVERT: A 492 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8315 (mtpp) REVERT: A 510 GLU cc_start: 0.6435 (tp30) cc_final: 0.4795 (pt0) REVERT: B 36 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8177 (pp) REVERT: B 50 ASP cc_start: 0.8528 (t70) cc_final: 0.8224 (t0) REVERT: B 58 LYS cc_start: 0.8984 (mttp) cc_final: 0.8595 (mtmt) REVERT: B 91 ILE cc_start: 0.8967 (OUTLIER) cc_final: 0.8746 (mt) REVERT: B 235 LEU cc_start: 0.7968 (OUTLIER) cc_final: 0.7474 (pp) REVERT: B 441 GLN cc_start: 0.8097 (OUTLIER) cc_final: 0.6842 (mp10) REVERT: B 492 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8369 (mtpp) REVERT: B 510 GLU cc_start: 0.6395 (tp30) cc_final: 0.4901 (pt0) REVERT: C 21 GLN cc_start: 0.8921 (tt0) cc_final: 0.8708 (tt0) REVERT: C 36 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8122 (mt) REVERT: C 58 LYS cc_start: 0.9038 (mttp) cc_final: 0.8731 (mtmt) REVERT: C 235 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7325 (pp) REVERT: D 36 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8648 (pp) REVERT: D 58 LYS cc_start: 0.8961 (mttp) cc_final: 0.8571 (mtmt) REVERT: D 235 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7420 (pp) REVERT: D 441 GLN cc_start: 0.8118 (OUTLIER) cc_final: 0.6639 (mp10) REVERT: D 510 GLU cc_start: 0.6515 (tp30) cc_final: 0.4994 (pt0) REVERT: E 21 GLN cc_start: 0.8920 (tt0) cc_final: 0.8624 (tt0) REVERT: E 58 LYS cc_start: 0.9035 (mttp) cc_final: 0.8728 (mtmt) REVERT: E 235 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7319 (pp) REVERT: E 491 GLU cc_start: 0.9064 (tp30) cc_final: 0.8789 (tt0) REVERT: E 492 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8388 (mtpp) REVERT: E 510 GLU cc_start: 0.6343 (tp30) cc_final: 0.4724 (pt0) REVERT: F 36 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8190 (pp) REVERT: F 58 LYS cc_start: 0.9065 (mttp) cc_final: 0.8713 (mtmt) REVERT: F 235 LEU cc_start: 0.7820 (OUTLIER) cc_final: 0.7371 (pp) REVERT: F 492 LYS cc_start: 0.8584 (OUTLIER) cc_final: 0.8298 (mtpp) REVERT: G 58 LYS cc_start: 0.9019 (mttp) cc_final: 0.8708 (mtmt) REVERT: G 235 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7365 (pp) REVERT: G 410 LYS cc_start: 0.8173 (ttmm) cc_final: 0.7832 (tppp) REVERT: G 441 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.6857 (mp10) REVERT: G 491 GLU cc_start: 0.9154 (tp30) cc_final: 0.8780 (tt0) REVERT: G 492 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8341 (mtpp) REVERT: H 36 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8472 (pp) REVERT: H 50 ASP cc_start: 0.8505 (t70) cc_final: 0.8193 (t0) REVERT: H 58 LYS cc_start: 0.9003 (mttp) cc_final: 0.8649 (mtmt) REVERT: H 235 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7537 (pp) REVERT: H 412 ARG cc_start: 0.8729 (ptt90) cc_final: 0.8505 (ptt90) REVERT: H 441 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.6844 (mp10) REVERT: H 510 GLU cc_start: 0.6347 (tp30) cc_final: 0.4891 (pt0) outliers start: 108 outliers final: 60 residues processed: 386 average time/residue: 1.2292 time to fit residues: 551.3113 Evaluate side-chains 390 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 305 time to evaluate : 2.723 ------------------------------------------------------------------------------- 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 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 91 ILE Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 437 ILE Chi-restraints excluded: chain B residue 441 GLN Chi-restraints excluded: chain B residue 492 LYS Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 438 LYS Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 107 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 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 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 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 441 GLN Chi-restraints excluded: chain F residue 492 LYS Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 361 VAL Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain G residue 492 LYS Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 477 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 30 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 193 optimal weight: 0.9990 chunk 196 optimal weight: 0.0770 chunk 148 optimal weight: 0.0770 chunk 199 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 260 optimal weight: 1.9990 chunk 217 optimal weight: 0.7980 chunk 153 optimal weight: 0.0370 chunk 17 optimal weight: 0.5980 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 303 ASN B 334 GLN C 303 ASN C 334 GLN D 303 ASN 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.121760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.103411 restraints weight = 25594.583| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.90 r_work: 0.3029 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2895 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 23096 Z= 0.094 Angle : 0.464 7.708 31208 Z= 0.240 Chirality : 0.041 0.141 3592 Planarity : 0.003 0.036 3976 Dihedral : 5.357 53.261 3290 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.61 % Allowed : 14.22 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.15), residues: 2960 helix: 1.18 (0.16), residues: 1104 sheet: -0.46 (0.24), residues: 392 loop : -0.43 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 92 PHE 0.010 0.001 PHE C 401 TYR 0.009 0.001 TYR F 289 ARG 0.003 0.000 ARG H 412 Details of bonding type rmsd hydrogen bonds : bond 0.02299 ( 849) hydrogen bonds : angle 3.98085 ( 2475) covalent geometry : bond 0.00215 (23096) covalent geometry : angle 0.46409 (31208) *********************** 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 441 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 355 time to evaluate : 2.798 Fit side-chains REVERT: A 1 MET cc_start: 0.5582 (mtm) cc_final: 0.5365 (mtt) REVERT: A 21 GLN cc_start: 0.8892 (tt0) cc_final: 0.8607 (tt0) REVERT: A 36 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8141 (mt) REVERT: A 58 LYS cc_start: 0.8982 (mttp) cc_final: 0.8616 (mtmt) REVERT: A 235 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7330 (pp) REVERT: A 277 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: A 400 TYR cc_start: 0.8480 (m-80) cc_final: 0.8230 (m-80) REVERT: A 441 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.6963 (mp10) REVERT: A 474 LYS cc_start: 0.8585 (mtpt) cc_final: 0.8352 (mtmt) REVERT: A 491 GLU cc_start: 0.8995 (tp30) cc_final: 0.8546 (tp30) REVERT: B 50 ASP cc_start: 0.8516 (t70) cc_final: 0.8213 (t0) REVERT: B 58 LYS cc_start: 0.8975 (mttp) cc_final: 0.8571 (mtmt) REVERT: B 235 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7472 (pp) REVERT: B 412 ARG cc_start: 0.8556 (ptt90) cc_final: 0.8353 (ptt90) REVERT: B 441 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.6605 (mp10) REVERT: B 491 GLU cc_start: 0.8968 (tp30) cc_final: 0.8587 (tp30) REVERT: C 21 GLN cc_start: 0.8880 (tt0) cc_final: 0.8672 (tt0) REVERT: C 36 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8166 (mt) REVERT: C 58 LYS cc_start: 0.9025 (mttp) cc_final: 0.8683 (mtmt) REVERT: C 235 LEU cc_start: 0.7765 (OUTLIER) cc_final: 0.7314 (pp) REVERT: C 277 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.6741 (tm-30) REVERT: C 400 TYR cc_start: 0.8535 (m-80) cc_final: 0.8224 (m-80) REVERT: C 410 LYS cc_start: 0.8151 (ttmm) cc_final: 0.7677 (tppp) REVERT: C 441 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7260 (mp10) REVERT: D 21 GLN cc_start: 0.8884 (tt0) cc_final: 0.8562 (tt0) REVERT: D 36 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8642 (pp) REVERT: D 50 ASP cc_start: 0.8540 (t70) cc_final: 0.8252 (t0) REVERT: D 58 LYS cc_start: 0.8960 (mttp) cc_final: 0.8562 (mtmt) REVERT: D 235 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7386 (pp) REVERT: D 400 TYR cc_start: 0.8615 (m-80) cc_final: 0.8401 (m-80) REVERT: D 441 GLN cc_start: 0.8143 (OUTLIER) cc_final: 0.6585 (mp10) REVERT: D 491 GLU cc_start: 0.9180 (tp30) cc_final: 0.8850 (tp30) REVERT: E 21 GLN cc_start: 0.8871 (tt0) cc_final: 0.8608 (tt0) REVERT: E 58 LYS cc_start: 0.9003 (mttp) cc_final: 0.8705 (mtmt) REVERT: E 235 LEU cc_start: 0.7759 (OUTLIER) cc_final: 0.7305 (pp) REVERT: E 492 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8358 (mtpp) REVERT: E 510 GLU cc_start: 0.6303 (tp30) cc_final: 0.4894 (pt0) REVERT: F 36 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8166 (mt) REVERT: F 58 LYS cc_start: 0.9054 (mttp) cc_final: 0.8694 (mtmt) REVERT: F 235 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7548 (pp) REVERT: F 400 TYR cc_start: 0.8583 (m-80) cc_final: 0.8375 (m-80) REVERT: F 441 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.7122 (mp10) REVERT: F 492 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8304 (mtpt) REVERT: G 58 LYS cc_start: 0.9012 (mttp) cc_final: 0.8678 (mtmt) REVERT: G 235 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7384 (pp) REVERT: G 410 LYS cc_start: 0.8175 (ttmm) cc_final: 0.7720 (tppp) REVERT: G 441 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.6629 (mp10) REVERT: G 491 GLU cc_start: 0.9126 (tp30) cc_final: 0.8707 (tt0) REVERT: G 492 LYS cc_start: 0.8569 (OUTLIER) cc_final: 0.8329 (mtpp) REVERT: H 21 GLN cc_start: 0.8897 (tt0) cc_final: 0.8595 (tt0) REVERT: H 50 ASP cc_start: 0.8500 (t70) cc_final: 0.8196 (t0) REVERT: H 58 LYS cc_start: 0.9008 (mttp) cc_final: 0.8613 (mtmt) REVERT: H 235 LEU cc_start: 0.7953 (OUTLIER) cc_final: 0.7551 (pp) REVERT: H 441 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.6645 (mp10) REVERT: H 510 GLU cc_start: 0.6252 (tp30) cc_final: 0.5019 (pt0) outliers start: 86 outliers final: 37 residues processed: 409 average time/residue: 1.2470 time to fit residues: 590.9613 Evaluate side-chains 385 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 324 time to evaluate : 2.328 ------------------------------------------------------------------------------- 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 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 277 GLN 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 B residue 11 SER 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 441 GLN Chi-restraints excluded: chain C residue 1 MET 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 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 438 LYS Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 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 D residue 441 GLN 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 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 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 441 GLN Chi-restraints excluded: chain F residue 492 LYS Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 361 VAL 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 66 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 235 LEU 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 151 optimal weight: 0.8980 chunk 284 optimal weight: 1.9990 chunk 269 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 123 optimal weight: 0.7980 chunk 233 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 285 optimal weight: 2.9990 chunk 264 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN D 303 ASN 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.103519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.084696 restraints weight = 27031.680| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.06 r_work: 0.2907 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 23096 Z= 0.192 Angle : 0.538 7.718 31208 Z= 0.278 Chirality : 0.045 0.161 3592 Planarity : 0.004 0.034 3976 Dihedral : 5.795 56.839 3290 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.94 % Allowed : 15.02 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.15), residues: 2960 helix: 0.93 (0.16), residues: 1104 sheet: -0.65 (0.22), residues: 448 loop : -0.46 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 93 PHE 0.009 0.002 PHE E 401 TYR 0.012 0.002 TYR B 348 ARG 0.005 0.001 ARG F 412 Details of bonding type rmsd hydrogen bonds : bond 0.03310 ( 849) hydrogen bonds : angle 4.30239 ( 2475) covalent geometry : bond 0.00481 (23096) covalent geometry : angle 0.53820 (31208) *********************** 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 394 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 300 time to evaluate : 2.615 Fit side-chains REVERT: A 21 GLN cc_start: 0.8897 (tt0) cc_final: 0.8604 (tt0) REVERT: A 36 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8147 (pp) REVERT: A 58 LYS cc_start: 0.8890 (mttp) cc_final: 0.8518 (mtmt) REVERT: A 235 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7163 (pp) REVERT: A 441 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7017 (mp10) REVERT: B 50 ASP cc_start: 0.8498 (t70) cc_final: 0.8146 (t0) REVERT: B 58 LYS cc_start: 0.8885 (mttp) cc_final: 0.8453 (mtmt) REVERT: B 91 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8613 (mp) REVERT: B 235 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7324 (pp) REVERT: B 412 ARG cc_start: 0.8705 (ptt90) cc_final: 0.8451 (ptt90) REVERT: B 441 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.6949 (mp10) REVERT: B 510 GLU cc_start: 0.6326 (tp30) cc_final: 0.4678 (pt0) REVERT: C 21 GLN cc_start: 0.8840 (tt0) cc_final: 0.8639 (tt0) REVERT: C 36 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8172 (pp) REVERT: C 58 LYS cc_start: 0.8925 (mttp) cc_final: 0.8559 (mtmt) REVERT: C 235 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7220 (pp) REVERT: C 277 GLN cc_start: 0.9002 (OUTLIER) cc_final: 0.6517 (tm-30) REVERT: C 455 LYS cc_start: 0.8546 (mtpt) cc_final: 0.8285 (mtmt) REVERT: C 510 GLU cc_start: 0.6375 (tp30) cc_final: 0.4601 (pt0) REVERT: D 36 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8440 (pp) REVERT: D 50 ASP cc_start: 0.8486 (t70) cc_final: 0.8145 (t0) REVERT: D 58 LYS cc_start: 0.8889 (mttp) cc_final: 0.8469 (mtmt) REVERT: D 235 LEU cc_start: 0.7621 (OUTLIER) cc_final: 0.7162 (pp) REVERT: D 441 GLN cc_start: 0.8064 (OUTLIER) cc_final: 0.6530 (mp10) REVERT: D 510 GLU cc_start: 0.6333 (tp30) cc_final: 0.4737 (pt0) REVERT: D 512 ARG cc_start: 0.5257 (mmt180) cc_final: 0.4984 (mmt90) REVERT: E 21 GLN cc_start: 0.8881 (tt0) cc_final: 0.8570 (tt0) REVERT: E 58 LYS cc_start: 0.8952 (mttp) cc_final: 0.8611 (mtmt) REVERT: E 235 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7195 (pp) REVERT: E 491 GLU cc_start: 0.9024 (tp30) cc_final: 0.8728 (tt0) REVERT: E 492 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8229 (mtpp) REVERT: E 510 GLU cc_start: 0.6252 (tp30) cc_final: 0.4524 (pt0) REVERT: F 36 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8179 (pp) REVERT: F 50 ASP cc_start: 0.8536 (t70) cc_final: 0.8191 (t0) REVERT: F 58 LYS cc_start: 0.8980 (mttp) cc_final: 0.8576 (mtmt) REVERT: F 235 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7224 (pp) REVERT: F 325 MET cc_start: 0.9230 (ttt) cc_final: 0.9024 (ttt) REVERT: F 412 ARG cc_start: 0.8615 (ptt-90) cc_final: 0.8213 (ptt90) REVERT: F 491 GLU cc_start: 0.9059 (tp30) cc_final: 0.8751 (tt0) REVERT: F 492 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8130 (mtpt) REVERT: G 36 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8088 (pp) REVERT: G 58 LYS cc_start: 0.8909 (mttp) cc_final: 0.8572 (mtmt) REVERT: G 235 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7183 (pp) REVERT: G 441 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.6993 (mp10) REVERT: G 491 GLU cc_start: 0.9119 (tp30) cc_final: 0.8754 (tt0) REVERT: H 21 GLN cc_start: 0.8877 (tt0) cc_final: 0.8563 (tt0) REVERT: H 36 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8266 (pp) REVERT: H 50 ASP cc_start: 0.8457 (t70) cc_final: 0.8109 (t0) REVERT: H 58 LYS cc_start: 0.8874 (mttp) cc_final: 0.8482 (mtmt) REVERT: H 235 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7319 (pp) REVERT: H 441 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.6727 (mp10) REVERT: H 453 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7876 (tt) REVERT: H 510 GLU cc_start: 0.6259 (tp30) cc_final: 0.4683 (pt0) outliers start: 94 outliers final: 51 residues processed: 363 average time/residue: 1.2541 time to fit residues: 524.7455 Evaluate side-chains 367 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 292 time to evaluate : 2.368 ------------------------------------------------------------------------------- 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 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain B residue 11 SER Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 91 ILE 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 441 GLN Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 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 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 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 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 441 GLN Chi-restraints excluded: chain F residue 492 LYS 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 361 VAL Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 477 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 48 optimal weight: 0.0980 chunk 179 optimal weight: 0.8980 chunk 46 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 129 optimal weight: 0.9990 chunk 152 optimal weight: 0.9990 chunk 253 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 194 optimal weight: 0.6980 chunk 122 optimal weight: 0.4980 chunk 244 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN C 303 ASN ** C 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 334 GLN E 334 GLN F 303 ASN F 334 GLN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN ** H 309 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 = 0.3288 r_free = 0.3288 target = 0.117009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.098150 restraints weight = 25848.160| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.01 r_work: 0.2962 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23096 Z= 0.116 Angle : 0.499 7.540 31208 Z= 0.256 Chirality : 0.042 0.160 3592 Planarity : 0.004 0.034 3976 Dihedral : 5.501 56.488 3290 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 3.15 % Allowed : 16.15 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.15), residues: 2960 helix: 1.11 (0.16), residues: 1104 sheet: -0.57 (0.23), residues: 432 loop : -0.38 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 504 PHE 0.012 0.001 PHE F 401 TYR 0.009 0.001 TYR F 348 ARG 0.005 0.000 ARG F 412 Details of bonding type rmsd hydrogen bonds : bond 0.02621 ( 849) hydrogen bonds : angle 4.11168 ( 2475) covalent geometry : bond 0.00280 (23096) covalent geometry : angle 0.49944 (31208) ********************** 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 376 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 301 time to evaluate : 2.659 Fit side-chains REVERT: A 1 MET cc_start: 0.5577 (mtm) cc_final: 0.5339 (mtt) REVERT: A 21 GLN cc_start: 0.8891 (tt0) cc_final: 0.8603 (tt0) REVERT: A 36 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8188 (pp) REVERT: A 58 LYS cc_start: 0.8933 (mttp) cc_final: 0.8598 (mtmt) REVERT: A 235 LEU cc_start: 0.7706 (OUTLIER) cc_final: 0.7245 (pp) REVERT: A 441 GLN cc_start: 0.8202 (OUTLIER) cc_final: 0.6976 (mp10) REVERT: A 510 GLU cc_start: 0.6386 (tp30) cc_final: 0.4811 (pt0) REVERT: B 50 ASP cc_start: 0.8508 (t70) cc_final: 0.8188 (t0) REVERT: B 58 LYS cc_start: 0.8944 (mttp) cc_final: 0.8565 (mtmt) REVERT: B 235 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7364 (pp) REVERT: B 441 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.6643 (mp10) REVERT: B 491 GLU cc_start: 0.9073 (tp30) cc_final: 0.8858 (tt0) REVERT: C 21 GLN cc_start: 0.8891 (tt0) cc_final: 0.8680 (tt0) REVERT: C 36 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8180 (pp) REVERT: C 58 LYS cc_start: 0.9002 (mttp) cc_final: 0.8679 (mtmt) REVERT: C 235 LEU cc_start: 0.7745 (OUTLIER) cc_final: 0.7291 (pp) REVERT: D 21 GLN cc_start: 0.8903 (tt0) cc_final: 0.8608 (tt0) REVERT: D 36 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8653 (pp) REVERT: D 50 ASP cc_start: 0.8550 (t70) cc_final: 0.8239 (t0) REVERT: D 58 LYS cc_start: 0.8932 (mttp) cc_final: 0.8552 (mtmt) REVERT: D 235 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7304 (pp) REVERT: D 410 LYS cc_start: 0.8119 (ttmm) cc_final: 0.7665 (tppp) REVERT: D 441 GLN cc_start: 0.8077 (OUTLIER) cc_final: 0.6486 (mp10) REVERT: E 21 GLN cc_start: 0.8916 (tt0) cc_final: 0.8626 (tt0) REVERT: E 36 LEU cc_start: 0.8451 (pp) cc_final: 0.8033 (mt) REVERT: E 58 LYS cc_start: 0.9003 (mttp) cc_final: 0.8698 (mtmt) REVERT: E 235 LEU cc_start: 0.7760 (OUTLIER) cc_final: 0.7298 (pp) REVERT: E 492 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8297 (mtpp) REVERT: E 510 GLU cc_start: 0.6280 (tp30) cc_final: 0.4639 (pt0) REVERT: F 36 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8144 (pp) REVERT: F 50 ASP cc_start: 0.8573 (t70) cc_final: 0.8265 (t0) REVERT: F 58 LYS cc_start: 0.9047 (mttp) cc_final: 0.8681 (mtmt) REVERT: F 235 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7356 (pp) REVERT: F 491 GLU cc_start: 0.9061 (tp30) cc_final: 0.8763 (tt0) REVERT: F 492 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8245 (mtpp) REVERT: F 510 GLU cc_start: 0.6298 (tp30) cc_final: 0.4717 (pt0) REVERT: G 36 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8092 (pp) REVERT: G 50 ASP cc_start: 0.8516 (t70) cc_final: 0.8166 (t0) REVERT: G 58 LYS cc_start: 0.8972 (mttp) cc_final: 0.8672 (mtmt) REVERT: G 235 LEU cc_start: 0.7726 (OUTLIER) cc_final: 0.7274 (pp) REVERT: G 399 GLU cc_start: 0.8461 (mm-30) cc_final: 0.8122 (mm-30) REVERT: G 441 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.6722 (mp10) REVERT: G 510 GLU cc_start: 0.6223 (tp30) cc_final: 0.4637 (pt0) REVERT: H 21 GLN cc_start: 0.8901 (tt0) cc_final: 0.8591 (tt0) REVERT: H 36 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8495 (pp) REVERT: H 50 ASP cc_start: 0.8518 (t70) cc_final: 0.8210 (t0) REVERT: H 58 LYS cc_start: 0.8951 (mttp) cc_final: 0.8589 (mtmt) REVERT: H 235 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7475 (pp) REVERT: H 412 ARG cc_start: 0.8727 (ptt90) cc_final: 0.8519 (ptt90) REVERT: H 441 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.6561 (mp10) REVERT: H 510 GLU cc_start: 0.6228 (tp30) cc_final: 0.4857 (pt0) outliers start: 75 outliers final: 47 residues processed: 348 average time/residue: 1.3011 time to fit residues: 522.8436 Evaluate side-chains 365 residues out of total 2384 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 297 time to evaluate : 2.359 ------------------------------------------------------------------------------- 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 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 437 ILE Chi-restraints excluded: chain A residue 438 LYS Chi-restraints excluded: chain A residue 441 GLN Chi-restraints excluded: chain B residue 11 SER 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 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 269 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 441 GLN Chi-restraints excluded: chain C residue 477 THR Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 441 GLN Chi-restraints excluded: chain 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 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 441 GLN Chi-restraints excluded: chain F residue 492 LYS 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 441 GLN Chi-restraints excluded: chain H residue 11 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 361 VAL Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 441 GLN Chi-restraints excluded: chain H residue 477 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 134 optimal weight: 0.3980 chunk 217 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 chunk 130 optimal weight: 0.8980 chunk 102 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 122 optimal weight: 0.0060 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN C 303 ASN D 303 ASN D 334 GLN F 303 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.117659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.098731 restraints weight = 25715.639| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 2.01 r_work: 0.2875 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2738 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2773 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= 0.113 Angle : 0.497 7.313 31208 Z= 0.254 Chirality : 0.042 0.158 3592 Planarity : 0.003 0.034 3976 Dihedral : 5.385 55.714 3290 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.06 % Allowed : 16.36 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 2960 helix: 1.19 (0.16), residues: 1104 sheet: -0.29 (0.24), residues: 392 loop : -0.32 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 92 PHE 0.010 0.001 PHE B 401 TYR 0.010 0.001 TYR E 459 ARG 0.005 0.000 ARG E 412 Details of bonding type rmsd hydrogen bonds : bond 0.02582 ( 849) hydrogen bonds : angle 4.06448 ( 2475) covalent geometry : bond 0.00273 (23096) covalent geometry : angle 0.49663 (31208) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14461.15 seconds wall clock time: 249 minutes 11.23 seconds (14951.23 seconds total)