Starting phenix.real_space_refine on Thu Jun 26 06:35:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7res_24438/06_2025/7res_24438.cif Found real_map, /net/cci-nas-00/data/ceres_data/7res_24438/06_2025/7res_24438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7res_24438/06_2025/7res_24438.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7res_24438/06_2025/7res_24438.map" model { file = "/net/cci-nas-00/data/ceres_data/7res_24438/06_2025/7res_24438.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7res_24438/06_2025/7res_24438.cif" } resolution = 3.05 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= 0.000 sd= 0.256 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 72 5.49 5 S 184 5.16 5 C 18768 2.51 5 N 5152 2.21 5 O 5912 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 275 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 30088 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "B" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "C" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "D" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "E" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "F" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "G" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "H" Number of atoms: 3632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3632 Classifications: {'peptide': 482} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 463} Chain breaks: 3 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 17.47, per 1000 atoms: 0.58 Number of scatterers: 30088 At special positions: 0 Unit cell: (135.45, 136.5, 142.8, 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 184 16.00 P 72 15.00 O 5912 8.00 N 5152 7.00 C 18768 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.23 Conformation dependent library (CDL) restraints added in 3.9 seconds 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6912 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 32 sheets defined 40.1% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.02 Creating SS restraints... Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.512A pdb=" N PHE A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) 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: 3.630A pdb=" N VAL A 49 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 127 through 137 removed outlier: 3.953A pdb=" N LEU A 131 " --> pdb=" O VAL A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 224 through 230 removed outlier: 3.525A pdb=" N LYS A 229 " --> pdb=" O THR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 266 removed outlier: 3.617A pdb=" N ARG A 259 " --> pdb=" O ASP A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 Processing helix chain 'A' and resid 333 through 338 Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 369 through 379 removed outlier: 3.608A pdb=" N VAL A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 Processing helix chain 'A' and resid 452 through 472 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'B' and resid 19 through 24 removed outlier: 3.518A pdb=" N PHE B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) 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: 3.562A pdb=" N VAL B 49 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 85 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 127 through 137 removed outlier: 3.886A pdb=" N LEU B 131 " --> pdb=" O VAL B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.645A pdb=" N ARG B 259 " --> pdb=" O ASP B 255 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 Processing helix chain 'B' and resid 333 through 338 Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 356 through 358 No H-bonds generated for 'chain 'B' and resid 356 through 358' Processing helix chain 'B' and resid 369 through 379 removed outlier: 3.616A pdb=" N VAL B 373 " --> pdb=" O THR B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 421 Processing helix chain 'B' and resid 452 through 472 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 502 Processing helix chain 'C' and resid 19 through 24 removed outlier: 3.503A pdb=" N PHE C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) 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: 3.636A pdb=" N VAL C 49 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 127 through 137 removed outlier: 3.918A pdb=" N LEU C 131 " --> pdb=" O VAL C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 255 through 266 removed outlier: 3.638A pdb=" N ARG C 259 " --> pdb=" O ASP C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 Processing helix chain 'C' and resid 333 through 338 Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 356 through 358 No H-bonds generated for 'chain 'C' and resid 356 through 358' Processing helix chain 'C' and resid 369 through 379 removed outlier: 3.608A pdb=" N VAL C 373 " --> pdb=" O THR C 369 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 421 Processing helix chain 'C' and resid 452 through 472 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'D' and resid 19 through 24 removed outlier: 3.515A pdb=" N PHE D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) 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: 3.623A pdb=" N VAL D 49 " --> pdb=" O ALA D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 85 Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 127 through 137 removed outlier: 3.911A pdb=" N LEU D 131 " --> pdb=" O VAL D 127 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 255 through 266 removed outlier: 3.656A pdb=" N ARG D 259 " --> pdb=" O ASP D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 Processing helix chain 'D' and resid 333 through 338 Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 356 through 358 No H-bonds generated for 'chain 'D' and resid 356 through 358' Processing helix chain 'D' and resid 369 through 379 removed outlier: 3.610A pdb=" N VAL D 373 " --> pdb=" O THR D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 421 Processing helix chain 'D' and resid 452 through 472 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 502 Processing helix chain 'E' and resid 19 through 24 removed outlier: 3.502A pdb=" N PHE E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) 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: 3.594A pdb=" N VAL E 49 " --> pdb=" O ALA E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 85 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 127 through 137 removed outlier: 3.901A pdb=" N LEU E 131 " --> pdb=" O VAL E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 163 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 224 through 228 Processing helix chain 'E' and resid 255 through 266 removed outlier: 3.661A pdb=" N ARG E 259 " --> pdb=" O ASP E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 Processing helix chain 'E' and resid 333 through 338 Processing helix chain 'E' and resid 342 through 355 Processing helix chain 'E' and resid 356 through 358 No H-bonds generated for 'chain 'E' and resid 356 through 358' Processing helix chain 'E' and resid 369 through 379 removed outlier: 3.612A pdb=" N VAL E 373 " --> pdb=" O THR E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 421 Processing helix chain 'E' and resid 452 through 472 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 502 Processing helix chain 'F' and resid 19 through 24 removed outlier: 3.507A pdb=" N PHE F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) 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: 3.620A pdb=" N VAL F 49 " --> pdb=" O ALA F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 85 Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 127 through 137 removed outlier: 3.797A pdb=" N LEU F 131 " --> pdb=" O VAL F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 255 through 266 removed outlier: 3.661A pdb=" N ARG F 259 " --> pdb=" O ASP F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 Processing helix chain 'F' and resid 333 through 338 Processing helix chain 'F' and resid 342 through 355 Processing helix chain 'F' and resid 356 through 358 No H-bonds generated for 'chain 'F' and resid 356 through 358' Processing helix chain 'F' and resid 369 through 379 removed outlier: 3.607A pdb=" N VAL F 373 " --> pdb=" O THR F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 421 Processing helix chain 'F' and resid 452 through 472 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 502 Processing helix chain 'G' and resid 19 through 24 removed outlier: 3.511A pdb=" N PHE G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) 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: 3.703A pdb=" N VAL G 49 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 85 Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 127 through 137 removed outlier: 3.816A pdb=" N LEU G 131 " --> pdb=" O VAL G 127 " (cutoff:3.500A) Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 193 through 205 Processing helix chain 'G' and resid 224 through 228 Processing helix chain 'G' and resid 255 through 266 removed outlier: 3.647A pdb=" N ARG G 259 " --> pdb=" O ASP G 255 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 Processing helix chain 'G' and resid 333 through 338 Processing helix chain 'G' and resid 342 through 355 Processing helix chain 'G' and resid 356 through 358 No H-bonds generated for 'chain 'G' and resid 356 through 358' Processing helix chain 'G' and resid 369 through 379 removed outlier: 3.614A pdb=" N VAL G 373 " --> pdb=" O THR G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 421 Processing helix chain 'G' and resid 452 through 472 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 475 through 485 Processing helix chain 'G' and resid 494 through 502 Processing helix chain 'H' and resid 19 through 24 removed outlier: 3.511A pdb=" N PHE H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) 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: 3.657A pdb=" N VAL H 49 " --> pdb=" O ALA H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 85 Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 127 through 137 removed outlier: 3.939A pdb=" N LEU H 131 " --> pdb=" O VAL H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 163 Processing helix chain 'H' and resid 193 through 205 Processing helix chain 'H' and resid 224 through 228 Processing helix chain 'H' and resid 255 through 266 removed outlier: 3.606A pdb=" N ARG H 259 " --> pdb=" O ASP H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 Processing helix chain 'H' and resid 333 through 338 Processing helix chain 'H' and resid 342 through 355 Processing helix chain 'H' and resid 356 through 358 No H-bonds generated for 'chain 'H' and resid 356 through 358' Processing helix chain 'H' and resid 369 through 379 removed outlier: 3.616A pdb=" N VAL H 373 " --> pdb=" O THR H 369 " (cutoff:3.500A) Processing helix chain 'H' and resid 416 through 421 Processing helix chain 'H' and resid 452 through 472 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 475 through 485 Processing helix chain 'H' and resid 494 through 502 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.526A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N ILE A 271 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLY A 302 " --> pdb=" O ILE A 271 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU A 273 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL A 304 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ILE A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 211 removed outlier: 3.733A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 401 through 403 removed outlier: 3.661A pdb=" N SER A 403 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER A 444 " --> pdb=" O GLU D 510 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER D 508 " --> pdb=" O SER A 446 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.827A pdb=" N SER A 508 " --> pdb=" O SER B 446 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N SER B 444 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER B 403 " --> pdb=" O VAL B 406 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA7, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.525A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE B 271 " --> pdb=" O ILE B 300 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N GLY B 302 " --> pdb=" O ILE B 271 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LEU B 273 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N VAL B 304 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.287A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.794A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.813A pdb=" N SER B 508 " --> pdb=" O SER C 446 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N SER C 444 " --> pdb=" O GLU B 510 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N SER C 403 " --> pdb=" O VAL C 406 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB2, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.525A pdb=" N ILE C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE C 271 " --> pdb=" O ILE C 300 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLY C 302 " --> pdb=" O ILE C 271 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N LEU C 273 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL C 304 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N ILE C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 208 through 211 removed outlier: 3.816A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 508 through 510 removed outlier: 3.829A pdb=" N SER C 508 " --> pdb=" O SER D 446 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER D 444 " --> pdb=" O GLU C 510 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER D 403 " --> pdb=" O VAL D 406 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.524A pdb=" N ILE D 88 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE D 271 " --> pdb=" O ILE D 300 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N GLY D 302 " --> pdb=" O ILE D 271 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N LEU D 273 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 8.265A pdb=" N VAL D 304 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 208 through 211 removed outlier: 3.818A pdb=" N ALA D 220 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AB9, first strand: chain 'E' and resid 65 through 67 removed outlier: 3.528A pdb=" N ILE E 88 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE E 90 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE E 271 " --> pdb=" O ILE E 300 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY E 302 " --> pdb=" O ILE E 271 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU E 273 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N VAL E 304 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 208 through 211 removed outlier: 3.699A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 401 through 403 removed outlier: 3.628A pdb=" N SER E 403 " --> pdb=" O VAL E 406 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER E 444 " --> pdb=" O GLU H 510 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER H 508 " --> pdb=" O SER E 446 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 508 through 510 removed outlier: 3.801A pdb=" N SER E 508 " --> pdb=" O SER F 446 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER F 444 " --> pdb=" O GLU E 510 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER F 403 " --> pdb=" O VAL F 406 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AC5, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.526A pdb=" N ILE F 88 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE F 271 " --> pdb=" O ILE F 300 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N GLY F 302 " --> pdb=" O ILE F 271 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N LEU F 273 " --> pdb=" O GLY F 302 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N VAL F 304 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N ILE F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 208 through 211 removed outlier: 3.829A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 508 through 510 removed outlier: 3.812A pdb=" N SER F 508 " --> pdb=" O SER G 446 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER G 444 " --> pdb=" O GLU F 510 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER G 403 " --> pdb=" O VAL G 406 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AC9, first strand: chain 'G' and resid 65 through 67 removed outlier: 3.525A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ILE G 271 " --> pdb=" O ILE G 300 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY G 302 " --> pdb=" O ILE G 271 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N LEU G 273 " --> pdb=" O GLY G 302 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N VAL G 304 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ILE G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 208 through 211 removed outlier: 3.813A pdb=" N ALA G 220 " --> pdb=" O ILE G 211 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 508 through 510 removed outlier: 3.827A pdb=" N SER G 508 " --> pdb=" O SER H 446 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N SER H 444 " --> pdb=" O GLU G 510 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER H 403 " --> pdb=" O VAL H 406 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AD4, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.530A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N ILE H 271 " --> pdb=" O ILE H 300 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N GLY H 302 " --> pdb=" O ILE H 271 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LEU H 273 " --> pdb=" O GLY H 302 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N VAL H 304 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 208 through 211 removed outlier: 3.698A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) 1090 hydrogen bonds defined for protein. 3078 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: 11.69 Time building geometry restraints manager: 9.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 4987 1.26 - 1.40: 6918 1.40 - 1.53: 17690 1.53 - 1.67: 669 1.67 - 1.81: 328 Bond restraints: 30592 Sorted by residual: bond pdb=" C2' ATP B 601 " pdb=" C3' ATP B 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.84e+02 bond pdb=" C2' ATP E 601 " pdb=" C3' ATP E 601 " ideal model delta sigma weight residual 1.531 1.241 0.290 1.20e-02 6.94e+03 5.83e+02 bond pdb=" C2' ATP G 601 " pdb=" C3' ATP G 601 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.81e+02 bond pdb=" C2' ATP H 601 " pdb=" C3' ATP H 601 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.79e+02 bond pdb=" C2' ATP F 601 " pdb=" C3' ATP F 601 " ideal model delta sigma weight residual 1.531 1.242 0.289 1.20e-02 6.94e+03 5.79e+02 ... (remaining 30587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.53: 40968 4.53 - 9.05: 367 9.05 - 13.58: 57 13.58 - 18.11: 59 18.11 - 22.64: 45 Bond angle restraints: 41496 Sorted by residual: angle pdb=" PB ATP G 601 " pdb=" O3B ATP G 601 " pdb=" PG ATP G 601 " ideal model delta sigma weight residual 139.87 117.23 22.64 1.00e+00 1.00e+00 5.12e+02 angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 117.68 22.19 1.00e+00 1.00e+00 4.93e+02 angle pdb=" PB ATP C 602 " pdb=" O3B ATP C 602 " pdb=" PG ATP C 602 " ideal model delta sigma weight residual 139.87 117.81 22.06 1.00e+00 1.00e+00 4.87e+02 angle pdb=" PB ATP H 601 " pdb=" O3B ATP H 601 " pdb=" PG ATP H 601 " ideal model delta sigma weight residual 139.87 118.19 21.68 1.00e+00 1.00e+00 4.70e+02 angle pdb=" PB ATP F 601 " pdb=" O3B ATP F 601 " pdb=" PG ATP F 601 " ideal model delta sigma weight residual 139.87 118.27 21.60 1.00e+00 1.00e+00 4.66e+02 ... (remaining 41491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.92: 17871 32.92 - 65.84: 891 65.84 - 98.76: 133 98.76 - 131.68: 0 131.68 - 164.60: 1 Dihedral angle restraints: 18896 sinusoidal: 8040 harmonic: 10856 Sorted by residual: dihedral pdb=" C5' IMP H 603 " pdb=" O5' IMP H 603 " pdb=" P IMP H 603 " pdb=" O2P IMP H 603 " ideal model delta sinusoidal sigma weight residual -168.07 -3.47 -164.60 1 2.00e+01 2.50e-03 4.71e+01 dihedral pdb=" N THR A 10 " pdb=" C THR A 10 " pdb=" CA THR A 10 " pdb=" CB THR A 10 " ideal model delta harmonic sigma weight residual 123.40 140.08 -16.68 0 2.50e+00 1.60e-01 4.45e+01 dihedral pdb=" C THR A 10 " pdb=" N THR A 10 " pdb=" CA THR A 10 " pdb=" CB THR A 10 " ideal model delta harmonic sigma weight residual -122.00 -136.36 14.36 0 2.50e+00 1.60e-01 3.30e+01 ... (remaining 18893 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.136: 4730 0.136 - 0.273: 38 0.273 - 0.409: 30 0.409 - 0.545: 0 0.545 - 0.682: 2 Chirality restraints: 4800 Sorted by residual: chirality pdb=" CA THR A 10 " pdb=" N THR A 10 " pdb=" C THR A 10 " pdb=" CB THR A 10 " both_signs ideal model delta sigma weight residual False 2.53 1.84 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" CA TYR E 12 " pdb=" N TYR E 12 " pdb=" C TYR E 12 " pdb=" CB TYR E 12 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.61 2.00e-01 2.50e+01 9.16e+00 chirality pdb=" C3B NAD H 604 " pdb=" C2B NAD H 604 " pdb=" C4B NAD H 604 " pdb=" O3B NAD H 604 " both_signs ideal model delta sigma weight residual False -2.71 -2.34 -0.37 2.00e-01 2.50e+01 3.44e+00 ... (remaining 4797 not shown) Planarity restraints: 5160 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 12 " 0.033 2.00e-02 2.50e+03 6.47e-02 4.19e+01 pdb=" C TYR E 12 " -0.112 2.00e-02 2.50e+03 pdb=" O TYR E 12 " 0.043 2.00e-02 2.50e+03 pdb=" N VAL E 13 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 12 " -0.010 2.00e-02 2.50e+03 3.27e-02 2.14e+01 pdb=" CG TYR E 12 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR E 12 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR E 12 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR E 12 " -0.051 2.00e-02 2.50e+03 pdb=" CE2 TYR E 12 " 0.022 2.00e-02 2.50e+03 pdb=" CZ TYR E 12 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR E 12 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 8 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C GLY A 8 " 0.032 2.00e-02 2.50e+03 pdb=" O GLY A 8 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY A 9 " -0.011 2.00e-02 2.50e+03 ... (remaining 5157 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 1601 2.70 - 3.25: 30769 3.25 - 3.80: 51427 3.80 - 4.35: 68032 4.35 - 4.90: 110806 Nonbonded interactions: 262635 Sorted by model distance: nonbonded pdb=" OD1 ASP C 364 " pdb=" O3' IMP C 603 " model vdw 2.150 3.040 nonbonded pdb=" OD1 ASP F 226 " pdb=" O3' ATP F 602 " model vdw 2.188 3.040 nonbonded pdb=" O ALA D 396 " pdb=" NZ LYS D 409 " model vdw 2.188 3.120 nonbonded pdb=" O2' ATP C 601 " pdb=" O3' ATP C 601 " model vdw 2.188 2.432 nonbonded pdb=" O ALA A 396 " pdb=" NZ LYS A 409 " model vdw 2.189 3.120 ... (remaining 262630 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.040 Check model and map are aligned: 0.200 Set scattering table: 0.240 Process input model: 68.390 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.160 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 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 : 0.018 0.901 30593 Z= 1.173 Angle : 1.392 22.637 41496 Z= 0.939 Chirality : 0.060 0.682 4800 Planarity : 0.004 0.065 5160 Dihedral : 18.573 164.597 11984 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.99 % Favored : 92.96 % Rotamer: Outliers : 4.87 % Allowed : 10.42 % Favored : 84.71 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -3.02 (0.12), residues: 3792 helix: -1.31 (0.12), residues: 1416 sheet: -1.25 (0.23), residues: 352 loop : -2.74 (0.12), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 466 PHE 0.010 0.002 PHE H 99 TYR 0.051 0.002 TYR E 12 ARG 0.009 0.001 ARG D 203 Details of bonding type rmsd hydrogen bonds : bond 0.16453 ( 1090) hydrogen bonds : angle 7.36953 ( 3078) covalent geometry : bond 0.01697 (30592) covalent geometry : angle 1.39222 (41496) Misc. bond : bond 0.90091 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 603 time to evaluate : 3.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ILE cc_start: 0.9119 (OUTLIER) cc_final: 0.8634 (mm) REVERT: A 146 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.5503 (pp20) REVERT: A 224 ARG cc_start: 0.8439 (ttt90) cc_final: 0.8225 (ttt-90) REVERT: A 312 ASN cc_start: 0.9057 (m-40) cc_final: 0.8754 (m-40) REVERT: A 355 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8135 (ptt-90) REVERT: A 441 GLN cc_start: 0.8501 (mt0) cc_final: 0.8233 (mt0) REVERT: A 449 ASP cc_start: 0.7538 (t70) cc_final: 0.6824 (t70) REVERT: B 161 ARG cc_start: 0.8445 (mtt180) cc_final: 0.8207 (mtt180) REVERT: B 312 ASN cc_start: 0.9073 (m-40) cc_final: 0.8798 (m-40) REVERT: B 355 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.8178 (ptt-90) REVERT: B 395 GLU cc_start: 0.7751 (mp0) cc_final: 0.7531 (mp0) REVERT: B 441 GLN cc_start: 0.8460 (mt0) cc_final: 0.8230 (mt0) REVERT: B 448 GLN cc_start: 0.7453 (tt0) cc_final: 0.7240 (tt0) REVERT: B 449 ASP cc_start: 0.7522 (t70) cc_final: 0.7116 (t70) REVERT: C 224 ARG cc_start: 0.8353 (ttt90) cc_final: 0.8139 (ttt-90) REVERT: C 312 ASN cc_start: 0.9050 (m-40) cc_final: 0.8745 (m-40) REVERT: C 355 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8030 (ptt-90) REVERT: D 91 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8630 (mm) REVERT: D 146 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.5379 (pp20) REVERT: D 161 ARG cc_start: 0.8693 (mtt180) cc_final: 0.8485 (mtt180) REVERT: D 224 ARG cc_start: 0.8393 (ttt90) cc_final: 0.8163 (ttt-90) REVERT: D 312 ASN cc_start: 0.9101 (m-40) cc_final: 0.8760 (m-40) REVERT: D 355 ARG cc_start: 0.8608 (OUTLIER) cc_final: 0.7925 (ptt-90) REVERT: D 395 GLU cc_start: 0.7759 (mp0) cc_final: 0.7504 (mp0) REVERT: D 441 GLN cc_start: 0.8480 (mt0) cc_final: 0.8199 (mt0) REVERT: D 449 ASP cc_start: 0.7545 (t70) cc_final: 0.6855 (t70) REVERT: E 146 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.5518 (pp20) REVERT: E 179 MET cc_start: 0.5193 (mtt) cc_final: 0.4979 (mtm) REVERT: E 224 ARG cc_start: 0.8328 (ttt90) cc_final: 0.8112 (ttt-90) REVERT: E 312 ASN cc_start: 0.9057 (m-40) cc_final: 0.8757 (m-40) REVERT: E 355 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7979 (ptt-90) REVERT: E 395 GLU cc_start: 0.7778 (mp0) cc_final: 0.7555 (mp0) REVERT: E 449 ASP cc_start: 0.7523 (t70) cc_final: 0.7085 (t70) REVERT: F 91 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8617 (mm) REVERT: F 146 GLU cc_start: 0.5911 (OUTLIER) cc_final: 0.4605 (pp20) REVERT: F 161 ARG cc_start: 0.8535 (mtt180) cc_final: 0.8323 (mtt180) REVERT: F 224 ARG cc_start: 0.8332 (ttt90) cc_final: 0.8131 (ttt-90) REVERT: F 229 LYS cc_start: 0.8194 (ptpt) cc_final: 0.7964 (ptpp) REVERT: F 312 ASN cc_start: 0.9066 (m-40) cc_final: 0.8781 (m-40) REVERT: F 355 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8042 (ptt-90) REVERT: F 395 GLU cc_start: 0.7751 (mp0) cc_final: 0.7527 (mp0) REVERT: G 91 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8629 (mm) REVERT: G 146 GLU cc_start: 0.7275 (OUTLIER) cc_final: 0.6050 (pp20) REVERT: G 179 MET cc_start: 0.3655 (mtt) cc_final: 0.2840 (mpp) REVERT: G 224 ARG cc_start: 0.8371 (ttt90) cc_final: 0.8134 (ttt-90) REVERT: G 312 ASN cc_start: 0.9079 (m-40) cc_final: 0.8726 (m-40) REVERT: G 355 ARG cc_start: 0.8581 (OUTLIER) cc_final: 0.8047 (ptt-90) REVERT: G 441 GLN cc_start: 0.8431 (mt0) cc_final: 0.8154 (mt0) REVERT: G 449 ASP cc_start: 0.7506 (t70) cc_final: 0.7012 (t70) REVERT: H 91 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8616 (mm) REVERT: H 312 ASN cc_start: 0.9092 (m-40) cc_final: 0.8795 (m-40) REVERT: H 355 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.8092 (ptt-90) REVERT: H 395 GLU cc_start: 0.7789 (mp0) cc_final: 0.7570 (mp0) REVERT: H 441 GLN cc_start: 0.8484 (mt0) cc_final: 0.8207 (mt0) REVERT: H 449 ASP cc_start: 0.7528 (t70) cc_final: 0.7106 (t70) outliers start: 152 outliers final: 108 residues processed: 735 average time/residue: 0.4363 time to fit residues: 502.4017 Evaluate side-chains 689 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 563 time to evaluate : 3.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 91 ILE Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 147 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 452 SER Chi-restraints excluded: chain B residue 53 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 355 ARG Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 452 SER Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 146 GLU Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 91 ILE Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 146 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 355 ARG Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 452 SER Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 146 GLU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 355 ARG Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 452 SER Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 91 ILE Chi-restraints excluded: chain F residue 146 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 355 ARG Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 53 SER Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 91 ILE Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 146 GLU Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 187 VAL Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 283 GLN Chi-restraints excluded: chain G residue 355 ARG Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 452 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 91 ILE Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 146 GLU Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 187 VAL Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 355 ARG Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 452 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.7980 chunk 291 optimal weight: 1.9990 chunk 161 optimal weight: 0.2980 chunk 99 optimal weight: 1.9990 chunk 196 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 300 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 183 optimal weight: 0.8980 chunk 224 optimal weight: 0.6980 chunk 348 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 277 GLN A 303 ASN A 454 GLN A 498 GLN B 112 GLN B 277 GLN B 303 ASN B 498 GLN C 112 GLN C 277 GLN C 303 ASN C 498 GLN D 112 GLN D 277 GLN D 303 ASN D 454 GLN D 498 GLN ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN E 277 GLN E 303 ASN E 498 GLN F 277 GLN F 303 ASN F 454 GLN F 498 GLN G 112 GLN G 277 GLN G 303 ASN G 498 GLN H 277 GLN H 303 ASN H 454 GLN H 498 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.152576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.106265 restraints weight = 33705.489| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 1.95 r_work: 0.2856 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 30593 Z= 0.146 Angle : 0.562 6.564 41496 Z= 0.296 Chirality : 0.043 0.143 4800 Planarity : 0.004 0.082 5160 Dihedral : 15.750 164.361 5407 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.08 % Allowed : 15.54 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -1.59 (0.13), residues: 3792 helix: 0.21 (0.14), residues: 1424 sheet: -0.74 (0.26), residues: 272 loop : -2.09 (0.12), residues: 2096 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 93 PHE 0.015 0.001 PHE E 401 TYR 0.015 0.001 TYR G 400 ARG 0.004 0.000 ARG H 203 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 1090) hydrogen bonds : angle 5.37489 ( 3078) covalent geometry : bond 0.00327 (30592) covalent geometry : angle 0.56229 (41496) Misc. bond : bond 0.00266 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 652 time to evaluate : 3.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LYS cc_start: 0.7853 (tptt) cc_final: 0.7576 (tppt) REVERT: A 229 LYS cc_start: 0.8082 (ptpp) cc_final: 0.7861 (ptpp) REVERT: A 243 GLN cc_start: 0.8107 (mp10) cc_final: 0.7745 (mp10) REVERT: A 312 ASN cc_start: 0.9253 (m-40) cc_final: 0.9005 (m-40) REVERT: A 449 ASP cc_start: 0.7813 (t70) cc_final: 0.7305 (t70) REVERT: B 91 ILE cc_start: 0.8951 (mm) cc_final: 0.8526 (mm) REVERT: B 134 LYS cc_start: 0.7888 (tptt) cc_final: 0.7562 (tppt) REVERT: B 202 GLN cc_start: 0.8403 (tt0) cc_final: 0.8095 (mm-40) REVERT: B 312 ASN cc_start: 0.9250 (m-40) cc_final: 0.9003 (m-40) REVERT: B 395 GLU cc_start: 0.8128 (mp0) cc_final: 0.7880 (mp0) REVERT: B 411 TYR cc_start: 0.8907 (t80) cc_final: 0.8696 (t80) REVERT: B 449 ASP cc_start: 0.7889 (t70) cc_final: 0.7235 (t70) REVERT: B 455 LYS cc_start: 0.8148 (ptpp) cc_final: 0.7908 (ptpp) REVERT: C 135 MET cc_start: 0.8259 (mpp) cc_final: 0.7707 (mpp) REVERT: C 202 GLN cc_start: 0.8434 (tt0) cc_final: 0.8044 (mt0) REVERT: C 312 ASN cc_start: 0.9233 (m-40) cc_final: 0.8966 (m-40) REVERT: C 400 TYR cc_start: 0.7700 (m-80) cc_final: 0.7196 (m-80) REVERT: C 449 ASP cc_start: 0.7973 (t0) cc_final: 0.7718 (t70) REVERT: D 134 LYS cc_start: 0.7929 (tptt) cc_final: 0.7663 (tppt) REVERT: D 202 GLN cc_start: 0.8436 (tt0) cc_final: 0.8045 (mt0) REVERT: D 312 ASN cc_start: 0.9275 (m-40) cc_final: 0.8990 (m-40) REVERT: D 395 GLU cc_start: 0.8149 (mp0) cc_final: 0.7856 (mp0) REVERT: D 411 TYR cc_start: 0.8868 (t80) cc_final: 0.8565 (t80) REVERT: D 412 ARG cc_start: 0.8232 (ptt180) cc_final: 0.8020 (ptt180) REVERT: D 449 ASP cc_start: 0.7754 (t70) cc_final: 0.7374 (t70) REVERT: E 91 ILE cc_start: 0.8959 (mm) cc_final: 0.8545 (mm) REVERT: E 134 LYS cc_start: 0.7974 (tptt) cc_final: 0.7681 (tppt) REVERT: E 312 ASN cc_start: 0.9242 (m-40) cc_final: 0.8981 (m-40) REVERT: E 395 GLU cc_start: 0.8072 (mp0) cc_final: 0.7838 (mp0) REVERT: E 449 ASP cc_start: 0.7816 (t70) cc_final: 0.7149 (t70) REVERT: F 206 LYS cc_start: 0.8279 (OUTLIER) cc_final: 0.6886 (mtmm) REVERT: F 231 ARG cc_start: 0.8595 (ptp90) cc_final: 0.8393 (mtm110) REVERT: F 243 GLN cc_start: 0.8115 (mp10) cc_final: 0.7228 (mp-120) REVERT: F 312 ASN cc_start: 0.9229 (m-40) cc_final: 0.8972 (m-40) REVERT: F 395 GLU cc_start: 0.8057 (mp0) cc_final: 0.7793 (mp0) REVERT: G 179 MET cc_start: 0.3961 (mtt) cc_final: 0.3227 (mpp) REVERT: G 231 ARG cc_start: 0.8598 (ptp90) cc_final: 0.8363 (mtm110) REVERT: G 312 ASN cc_start: 0.9268 (m-40) cc_final: 0.8955 (m-40) REVERT: G 395 GLU cc_start: 0.8147 (mp0) cc_final: 0.7862 (mp0) REVERT: G 412 ARG cc_start: 0.8252 (ptt180) cc_final: 0.8018 (ptt180) REVERT: H 231 ARG cc_start: 0.8715 (ptp90) cc_final: 0.8477 (mtm180) REVERT: H 312 ASN cc_start: 0.9276 (m-40) cc_final: 0.9034 (m-40) REVERT: H 395 GLU cc_start: 0.8043 (mp0) cc_final: 0.7788 (mp0) REVERT: H 411 TYR cc_start: 0.8861 (t80) cc_final: 0.8555 (t80) REVERT: H 441 GLN cc_start: 0.8492 (mt0) cc_final: 0.8287 (mt0) outliers start: 96 outliers final: 67 residues processed: 727 average time/residue: 0.4772 time to fit residues: 545.8126 Evaluate side-chains 679 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 611 time to evaluate : 3.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 GLU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 383 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 322 optimal weight: 3.9990 chunk 105 optimal weight: 0.9980 chunk 339 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 313 optimal weight: 0.6980 chunk 157 optimal weight: 0.0470 chunk 79 optimal weight: 0.5980 chunk 72 optimal weight: 0.0970 chunk 57 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 334 GLN B 334 GLN C 334 GLN D 334 GLN ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN F 112 GLN F 334 GLN G 334 GLN H 112 GLN H 334 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.156276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.109300 restraints weight = 33860.754| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.97 r_work: 0.2903 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 30593 Z= 0.110 Angle : 0.499 6.824 41496 Z= 0.263 Chirality : 0.041 0.135 4800 Planarity : 0.004 0.033 5160 Dihedral : 14.206 164.293 5274 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 2.85 % Allowed : 17.02 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.77 (0.14), residues: 3792 helix: 0.94 (0.14), residues: 1424 sheet: -0.20 (0.26), residues: 288 loop : -1.68 (0.13), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 93 PHE 0.015 0.001 PHE C 401 TYR 0.013 0.001 TYR H 400 ARG 0.004 0.000 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03056 ( 1090) hydrogen bonds : angle 4.88320 ( 3078) covalent geometry : bond 0.00236 (30592) covalent geometry : angle 0.49873 (41496) Misc. bond : bond 0.00115 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 728 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 639 time to evaluate : 3.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLN cc_start: 0.8390 (tt0) cc_final: 0.8132 (mm-40) REVERT: A 225 THR cc_start: 0.8303 (m) cc_final: 0.8033 (m) REVERT: A 229 LYS cc_start: 0.8044 (ptpp) cc_final: 0.7812 (ptpp) REVERT: A 243 GLN cc_start: 0.8052 (mp10) cc_final: 0.7811 (mp-120) REVERT: A 277 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.7413 (tm-30) REVERT: A 312 ASN cc_start: 0.9199 (m-40) cc_final: 0.8951 (m-40) REVERT: B 134 LYS cc_start: 0.7830 (tptt) cc_final: 0.7491 (tppt) REVERT: B 243 GLN cc_start: 0.7783 (mp-120) cc_final: 0.7490 (mp10) REVERT: B 312 ASN cc_start: 0.9214 (m-40) cc_final: 0.8978 (m-40) REVERT: B 395 GLU cc_start: 0.8152 (mp0) cc_final: 0.7936 (mp0) REVERT: B 441 GLN cc_start: 0.8492 (mt0) cc_final: 0.8204 (mt0) REVERT: C 202 GLN cc_start: 0.8448 (tt0) cc_final: 0.8058 (mt0) REVERT: C 225 THR cc_start: 0.8289 (m) cc_final: 0.8047 (m) REVERT: C 243 GLN cc_start: 0.7851 (mp-120) cc_final: 0.7231 (mp10) REVERT: C 265 GLN cc_start: 0.8268 (mm-40) cc_final: 0.8024 (mm-40) REVERT: C 286 MET cc_start: 0.8855 (tpp) cc_final: 0.8611 (tpp) REVERT: C 312 ASN cc_start: 0.9172 (m-40) cc_final: 0.8917 (m-40) REVERT: C 400 TYR cc_start: 0.7562 (m-80) cc_final: 0.7320 (m-80) REVERT: D 103 GLU cc_start: 0.8612 (tp30) cc_final: 0.8405 (mm-30) REVERT: D 184 GLU cc_start: 0.1926 (OUTLIER) cc_final: 0.0210 (tp30) REVERT: D 243 GLN cc_start: 0.7838 (mp-120) cc_final: 0.7198 (mp10) REVERT: D 312 ASN cc_start: 0.9239 (m-40) cc_final: 0.8964 (m-40) REVERT: D 395 GLU cc_start: 0.8158 (mp0) cc_final: 0.7889 (mp0) REVERT: D 412 ARG cc_start: 0.8080 (ptt180) cc_final: 0.7867 (ptt180) REVERT: D 438 LYS cc_start: 0.8466 (mmmt) cc_final: 0.8113 (mmmm) REVERT: D 449 ASP cc_start: 0.7670 (t70) cc_final: 0.7319 (t70) REVERT: D 455 LYS cc_start: 0.7975 (ptpp) cc_final: 0.7719 (ptpp) REVERT: E 91 ILE cc_start: 0.8926 (mm) cc_final: 0.8483 (mm) REVERT: E 134 LYS cc_start: 0.7891 (tptt) cc_final: 0.7571 (tppt) REVERT: E 243 GLN cc_start: 0.7990 (mp-120) cc_final: 0.7674 (mp10) REVERT: E 265 GLN cc_start: 0.8286 (mm-40) cc_final: 0.8029 (mm-40) REVERT: E 312 ASN cc_start: 0.9189 (m-40) cc_final: 0.8931 (m-40) REVERT: E 395 GLU cc_start: 0.8091 (mp0) cc_final: 0.7845 (mp0) REVERT: F 206 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7038 (mtmm) REVERT: F 243 GLN cc_start: 0.8124 (mp10) cc_final: 0.7842 (mp-120) REVERT: F 312 ASN cc_start: 0.9201 (m-40) cc_final: 0.8925 (m-40) REVERT: F 395 GLU cc_start: 0.8092 (mp0) cc_final: 0.7833 (mp0) REVERT: G 135 MET cc_start: 0.8190 (mpp) cc_final: 0.7876 (mpp) REVERT: G 179 MET cc_start: 0.3415 (mtt) cc_final: 0.2922 (mpp) REVERT: G 231 ARG cc_start: 0.8607 (ptp90) cc_final: 0.8383 (mtm110) REVERT: G 277 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8026 (tm-30) REVERT: G 286 MET cc_start: 0.8892 (tpp) cc_final: 0.8650 (tpp) REVERT: G 312 ASN cc_start: 0.9205 (m-40) cc_final: 0.8913 (m-40) REVERT: G 395 GLU cc_start: 0.8129 (mp0) cc_final: 0.7850 (mp0) REVERT: G 412 ARG cc_start: 0.8156 (ptt180) cc_final: 0.7933 (ptt180) REVERT: G 455 LYS cc_start: 0.7983 (ptpp) cc_final: 0.7707 (ptpp) REVERT: H 202 GLN cc_start: 0.8395 (tt0) cc_final: 0.8085 (mm-40) REVERT: H 225 THR cc_start: 0.8290 (m) cc_final: 0.7818 (p) REVERT: H 231 ARG cc_start: 0.8745 (ptp90) cc_final: 0.8502 (mtm180) REVERT: H 243 GLN cc_start: 0.7826 (mp-120) cc_final: 0.7567 (mp10) REVERT: H 312 ASN cc_start: 0.9220 (m-40) cc_final: 0.8996 (m-40) REVERT: H 395 GLU cc_start: 0.8111 (mp0) cc_final: 0.7865 (mp0) outliers start: 89 outliers final: 74 residues processed: 695 average time/residue: 0.4460 time to fit residues: 483.4184 Evaluate side-chains 685 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 607 time to evaluate : 3.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 144 optimal weight: 0.6980 chunk 159 optimal weight: 0.9990 chunk 19 optimal weight: 0.5980 chunk 229 optimal weight: 3.9990 chunk 308 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 360 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 330 optimal weight: 0.0000 overall best weight: 1.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 243 GLN ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.153384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.105197 restraints weight = 33827.085| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.00 r_work: 0.2866 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 30593 Z= 0.157 Angle : 0.511 6.046 41496 Z= 0.269 Chirality : 0.042 0.134 4800 Planarity : 0.004 0.039 5160 Dihedral : 13.903 165.916 5261 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.20 % Allowed : 16.70 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.54 (0.14), residues: 3792 helix: 1.12 (0.14), residues: 1432 sheet: -0.11 (0.26), residues: 288 loop : -1.53 (0.13), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 93 PHE 0.012 0.001 PHE A 401 TYR 0.012 0.001 TYR F 348 ARG 0.009 0.000 ARG C 231 Details of bonding type rmsd hydrogen bonds : bond 0.03250 ( 1090) hydrogen bonds : angle 4.84865 ( 3078) covalent geometry : bond 0.00357 (30592) covalent geometry : angle 0.51098 (41496) Misc. bond : bond 0.00133 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 614 time to evaluate : 3.205 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 134 LYS cc_start: 0.7819 (tptt) cc_final: 0.7595 (tppt) REVERT: A 225 THR cc_start: 0.8298 (m) cc_final: 0.8005 (m) REVERT: A 229 LYS cc_start: 0.8097 (ptpp) cc_final: 0.7837 (ptpp) REVERT: A 243 GLN cc_start: 0.8050 (mp10) cc_final: 0.7759 (mp10) REVERT: A 312 ASN cc_start: 0.9244 (m-40) cc_final: 0.8938 (m-40) REVERT: A 441 GLN cc_start: 0.8434 (mt0) cc_final: 0.8230 (mt0) REVERT: A 455 LYS cc_start: 0.7988 (ptpp) cc_final: 0.7702 (ptpp) REVERT: B 78 MET cc_start: 0.8976 (tpp) cc_final: 0.8649 (tpp) REVERT: B 91 ILE cc_start: 0.8888 (mm) cc_final: 0.8446 (mm) REVERT: B 243 GLN cc_start: 0.7838 (mp-120) cc_final: 0.7110 (mp-120) REVERT: B 312 ASN cc_start: 0.9226 (m-40) cc_final: 0.8968 (m-40) REVERT: B 395 GLU cc_start: 0.8152 (mp0) cc_final: 0.7833 (mp0) REVERT: B 441 GLN cc_start: 0.8447 (mt0) cc_final: 0.8181 (mt0) REVERT: C 135 MET cc_start: 0.8324 (mpp) cc_final: 0.7892 (mpp) REVERT: C 225 THR cc_start: 0.8168 (m) cc_final: 0.7921 (m) REVERT: C 265 GLN cc_start: 0.8326 (mm-40) cc_final: 0.8054 (mm-40) REVERT: C 286 MET cc_start: 0.8888 (tpp) cc_final: 0.8672 (tpp) REVERT: C 312 ASN cc_start: 0.9214 (m-40) cc_final: 0.8928 (m-40) REVERT: C 441 GLN cc_start: 0.8402 (mt0) cc_final: 0.8154 (mt0) REVERT: C 449 ASP cc_start: 0.7611 (t0) cc_final: 0.7252 (t70) REVERT: D 134 LYS cc_start: 0.7871 (tptt) cc_final: 0.7608 (tppt) REVERT: D 184 GLU cc_start: 0.1826 (OUTLIER) cc_final: 0.0040 (tp30) REVERT: D 202 GLN cc_start: 0.8400 (tt0) cc_final: 0.8019 (mt0) REVERT: D 243 GLN cc_start: 0.7838 (mp-120) cc_final: 0.7127 (mp-120) REVERT: D 286 MET cc_start: 0.8937 (tpp) cc_final: 0.8720 (tpp) REVERT: D 312 ASN cc_start: 0.9242 (m-40) cc_final: 0.8966 (m-40) REVERT: D 395 GLU cc_start: 0.8142 (mp0) cc_final: 0.7805 (mp0) REVERT: D 412 ARG cc_start: 0.8126 (ptt180) cc_final: 0.7914 (ptt180) REVERT: D 441 GLN cc_start: 0.8465 (mt0) cc_final: 0.8224 (mt0) REVERT: D 449 ASP cc_start: 0.7813 (t70) cc_final: 0.7414 (t70) REVERT: E 78 MET cc_start: 0.8968 (tpp) cc_final: 0.8638 (tpp) REVERT: E 134 LYS cc_start: 0.7863 (tptt) cc_final: 0.7534 (tppt) REVERT: E 205 LYS cc_start: 0.8755 (mmtp) cc_final: 0.8281 (mmtp) REVERT: E 243 GLN cc_start: 0.8042 (mp10) cc_final: 0.7836 (mp-120) REVERT: E 312 ASN cc_start: 0.9240 (m-40) cc_final: 0.8986 (m-40) REVERT: E 330 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8832 (pp) REVERT: E 395 GLU cc_start: 0.8128 (mp0) cc_final: 0.7789 (mp0) REVERT: E 448 GLN cc_start: 0.7608 (tt0) cc_final: 0.7346 (tt0) REVERT: E 455 LYS cc_start: 0.7996 (ptpp) cc_final: 0.7708 (ptpp) REVERT: F 184 GLU cc_start: 0.4993 (OUTLIER) cc_final: 0.4172 (tp30) REVERT: F 206 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7132 (mtmm) REVERT: F 243 GLN cc_start: 0.8132 (mp10) cc_final: 0.7830 (mp10) REVERT: F 312 ASN cc_start: 0.9229 (m-40) cc_final: 0.8936 (m-40) REVERT: F 330 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8822 (pp) REVERT: F 395 GLU cc_start: 0.8115 (mp0) cc_final: 0.7771 (mp0) REVERT: F 412 ARG cc_start: 0.8093 (ptt180) cc_final: 0.7828 (ptt180) REVERT: F 441 GLN cc_start: 0.8453 (mt0) cc_final: 0.8186 (mt0) REVERT: G 135 MET cc_start: 0.8199 (mpp) cc_final: 0.7585 (mpp) REVERT: G 179 MET cc_start: 0.3670 (mtt) cc_final: 0.3034 (mpp) REVERT: G 243 GLN cc_start: 0.7864 (mp10) cc_final: 0.7402 (mp-120) REVERT: G 286 MET cc_start: 0.8901 (tpp) cc_final: 0.8670 (tpp) REVERT: G 312 ASN cc_start: 0.9234 (m-40) cc_final: 0.8895 (m-40) REVERT: G 330 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8835 (pp) REVERT: G 395 GLU cc_start: 0.8144 (mp0) cc_final: 0.7830 (mp0) REVERT: G 412 ARG cc_start: 0.8166 (ptt180) cc_final: 0.7957 (ptt180) REVERT: G 449 ASP cc_start: 0.7689 (t70) cc_final: 0.7352 (t70) REVERT: H 134 LYS cc_start: 0.7895 (tptt) cc_final: 0.7565 (tppt) REVERT: H 231 ARG cc_start: 0.8782 (ptp90) cc_final: 0.8524 (mtm180) REVERT: H 243 GLN cc_start: 0.7863 (mp-120) cc_final: 0.7118 (mp-120) REVERT: H 312 ASN cc_start: 0.9254 (m-40) cc_final: 0.8971 (m-40) REVERT: H 395 GLU cc_start: 0.8100 (mp0) cc_final: 0.7802 (mp0) outliers start: 131 outliers final: 103 residues processed: 704 average time/residue: 0.4340 time to fit residues: 480.2052 Evaluate side-chains 716 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 607 time to evaluate : 3.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 146 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 188 optimal weight: 3.9990 chunk 65 optimal weight: 8.9990 chunk 176 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 202 optimal weight: 0.0980 chunk 238 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 93 HIS ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.153710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.105693 restraints weight = 33673.806| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.98 r_work: 0.2867 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 30593 Z= 0.149 Angle : 0.502 5.593 41496 Z= 0.265 Chirality : 0.042 0.141 4800 Planarity : 0.004 0.040 5160 Dihedral : 13.616 169.668 5260 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 4.49 % Allowed : 17.34 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.49 (0.14), residues: 3792 helix: 0.99 (0.14), residues: 1480 sheet: 0.01 (0.26), residues: 288 loop : -1.43 (0.14), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 93 PHE 0.014 0.001 PHE C 401 TYR 0.012 0.001 TYR F 353 ARG 0.007 0.000 ARG C 231 Details of bonding type rmsd hydrogen bonds : bond 0.03149 ( 1090) hydrogen bonds : angle 4.78628 ( 3078) covalent geometry : bond 0.00338 (30592) covalent geometry : angle 0.50246 (41496) Misc. bond : bond 0.00118 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 608 time to evaluate : 2.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLN cc_start: 0.8344 (tt0) cc_final: 0.7995 (mm-40) REVERT: A 225 THR cc_start: 0.8299 (m) cc_final: 0.7993 (m) REVERT: A 229 LYS cc_start: 0.8118 (ptpp) cc_final: 0.7831 (ptpp) REVERT: A 243 GLN cc_start: 0.8027 (mp10) cc_final: 0.7194 (mp10) REVERT: A 286 MET cc_start: 0.8896 (tpp) cc_final: 0.8678 (tpp) REVERT: A 312 ASN cc_start: 0.9253 (m-40) cc_final: 0.8961 (m-40) REVERT: A 449 ASP cc_start: 0.7875 (t70) cc_final: 0.7319 (t70) REVERT: A 455 LYS cc_start: 0.8006 (ptpp) cc_final: 0.7739 (ptpp) REVERT: A 476 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.9023 (mt) REVERT: B 134 LYS cc_start: 0.7956 (tptt) cc_final: 0.7733 (tppt) REVERT: B 243 GLN cc_start: 0.7833 (mp-120) cc_final: 0.7117 (mp-120) REVERT: B 265 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7936 (mm-40) REVERT: B 312 ASN cc_start: 0.9238 (m-40) cc_final: 0.8966 (m-40) REVERT: B 395 GLU cc_start: 0.8140 (mp0) cc_final: 0.7837 (mp0) REVERT: B 421 GLU cc_start: 0.6940 (mt-10) cc_final: 0.6676 (mt-10) REVERT: B 441 GLN cc_start: 0.8436 (mt0) cc_final: 0.8182 (mt0) REVERT: C 91 ILE cc_start: 0.8931 (mm) cc_final: 0.8514 (mm) REVERT: C 225 THR cc_start: 0.8163 (m) cc_final: 0.7929 (m) REVERT: C 265 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8017 (mm-40) REVERT: C 286 MET cc_start: 0.8928 (tpp) cc_final: 0.8706 (tpp) REVERT: C 312 ASN cc_start: 0.9229 (m-40) cc_final: 0.8938 (m-40) REVERT: C 441 GLN cc_start: 0.8370 (mt0) cc_final: 0.8124 (mt0) REVERT: C 449 ASP cc_start: 0.7596 (t0) cc_final: 0.7310 (t70) REVERT: C 476 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8954 (mp) REVERT: D 184 GLU cc_start: 0.1766 (OUTLIER) cc_final: 0.0108 (tp30) REVERT: D 243 GLN cc_start: 0.7747 (mp-120) cc_final: 0.7068 (mp-120) REVERT: D 312 ASN cc_start: 0.9234 (m-40) cc_final: 0.8952 (m-40) REVERT: D 395 GLU cc_start: 0.8162 (mp0) cc_final: 0.7820 (mp0) REVERT: D 441 GLN cc_start: 0.8433 (mt0) cc_final: 0.8218 (mt0) REVERT: D 449 ASP cc_start: 0.7902 (t70) cc_final: 0.7453 (t70) REVERT: E 134 LYS cc_start: 0.7857 (tptt) cc_final: 0.7530 (tppt) REVERT: E 205 LYS cc_start: 0.8804 (mmtp) cc_final: 0.8333 (mmtp) REVERT: E 243 GLN cc_start: 0.8074 (mp10) cc_final: 0.7849 (mp-120) REVERT: E 312 ASN cc_start: 0.9251 (m-40) cc_final: 0.8976 (m-40) REVERT: E 330 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8845 (pp) REVERT: E 395 GLU cc_start: 0.8142 (mp0) cc_final: 0.7849 (mp0) REVERT: E 448 GLN cc_start: 0.7635 (tt0) cc_final: 0.7378 (tt0) REVERT: F 78 MET cc_start: 0.8965 (tpp) cc_final: 0.8677 (tpp) REVERT: F 184 GLU cc_start: 0.5047 (OUTLIER) cc_final: 0.4243 (tp30) REVERT: F 206 LYS cc_start: 0.8241 (OUTLIER) cc_final: 0.7158 (mtmm) REVERT: F 243 GLN cc_start: 0.8071 (mp10) cc_final: 0.7227 (mp10) REVERT: F 312 ASN cc_start: 0.9228 (m-40) cc_final: 0.8931 (m-40) REVERT: F 330 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8838 (pp) REVERT: F 395 GLU cc_start: 0.8132 (mp0) cc_final: 0.7778 (mp0) REVERT: F 412 ARG cc_start: 0.8108 (ptt180) cc_final: 0.7846 (ptt180) REVERT: F 441 GLN cc_start: 0.8417 (mt0) cc_final: 0.8172 (mt0) REVERT: F 476 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.9026 (mt) REVERT: G 135 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7805 (mpp) REVERT: G 179 MET cc_start: 0.3732 (mtt) cc_final: 0.3006 (mpp) REVERT: G 243 GLN cc_start: 0.7880 (mp10) cc_final: 0.7532 (mp10) REVERT: G 286 MET cc_start: 0.8899 (tpp) cc_final: 0.8635 (tpp) REVERT: G 312 ASN cc_start: 0.9237 (m-40) cc_final: 0.8941 (m-40) REVERT: G 330 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8850 (pp) REVERT: G 395 GLU cc_start: 0.8153 (mp0) cc_final: 0.7835 (mp0) REVERT: G 412 ARG cc_start: 0.8155 (ptt180) cc_final: 0.7880 (ptt180) REVERT: G 449 ASP cc_start: 0.7856 (t70) cc_final: 0.7402 (t70) REVERT: G 455 LYS cc_start: 0.8015 (ptpp) cc_final: 0.7780 (ptpp) REVERT: H 134 LYS cc_start: 0.7832 (tptt) cc_final: 0.7545 (tppt) REVERT: H 202 GLN cc_start: 0.8358 (tt0) cc_final: 0.8096 (mm-40) REVERT: H 229 LYS cc_start: 0.8106 (ptpt) cc_final: 0.7887 (ptpp) REVERT: H 231 ARG cc_start: 0.8785 (ptp90) cc_final: 0.8523 (mtm180) REVERT: H 243 GLN cc_start: 0.7773 (mp-120) cc_final: 0.7062 (mp-120) REVERT: H 312 ASN cc_start: 0.9262 (m-40) cc_final: 0.8976 (m-40) REVERT: H 395 GLU cc_start: 0.8109 (mp0) cc_final: 0.7814 (mp0) REVERT: H 449 ASP cc_start: 0.7926 (t70) cc_final: 0.7382 (t70) outliers start: 140 outliers final: 110 residues processed: 705 average time/residue: 0.4327 time to fit residues: 479.5411 Evaluate side-chains 721 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 601 time to evaluate : 3.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 77 ASP Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 47 optimal weight: 0.9990 chunk 281 optimal weight: 8.9990 chunk 258 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 330 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 335 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 314 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.154127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.106796 restraints weight = 33724.802| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 1.96 r_work: 0.2850 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 30593 Z= 0.191 Angle : 0.528 6.531 41496 Z= 0.278 Chirality : 0.043 0.133 4800 Planarity : 0.004 0.039 5160 Dihedral : 13.576 176.097 5260 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.23 % Allowed : 18.01 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.36 (0.14), residues: 3792 helix: 1.17 (0.14), residues: 1432 sheet: 0.15 (0.27), residues: 272 loop : -1.36 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 466 PHE 0.014 0.001 PHE G 401 TYR 0.013 0.001 TYR D 348 ARG 0.011 0.000 ARG C 231 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 1090) hydrogen bonds : angle 4.84665 ( 3078) covalent geometry : bond 0.00436 (30592) covalent geometry : angle 0.52824 (41496) Misc. bond : bond 0.00136 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 611 time to evaluate : 3.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 GLN cc_start: 0.8361 (tt0) cc_final: 0.8109 (mm-40) REVERT: A 225 THR cc_start: 0.8287 (m) cc_final: 0.7979 (m) REVERT: A 229 LYS cc_start: 0.8155 (ptpp) cc_final: 0.7893 (ptpp) REVERT: A 243 GLN cc_start: 0.8037 (mp10) cc_final: 0.7233 (mp10) REVERT: A 286 MET cc_start: 0.8931 (tpp) cc_final: 0.8677 (tpp) REVERT: A 312 ASN cc_start: 0.9264 (m-40) cc_final: 0.8940 (m-40) REVERT: A 449 ASP cc_start: 0.7866 (t70) cc_final: 0.7363 (t70) REVERT: A 455 LYS cc_start: 0.7968 (ptpp) cc_final: 0.7764 (ptpp) REVERT: A 476 LEU cc_start: 0.9251 (OUTLIER) cc_final: 0.8986 (mp) REVERT: B 134 LYS cc_start: 0.7869 (tptt) cc_final: 0.7602 (tppt) REVERT: B 206 LYS cc_start: 0.8121 (OUTLIER) cc_final: 0.7542 (mttm) REVERT: B 243 GLN cc_start: 0.7843 (mp-120) cc_final: 0.7175 (mp-120) REVERT: B 265 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7915 (mm-40) REVERT: B 312 ASN cc_start: 0.9266 (m-40) cc_final: 0.8990 (m-40) REVERT: B 395 GLU cc_start: 0.8137 (mp0) cc_final: 0.7838 (mp0) REVERT: B 421 GLU cc_start: 0.6930 (mt-10) cc_final: 0.6569 (mt-10) REVERT: B 441 GLN cc_start: 0.8402 (mt0) cc_final: 0.8175 (mt0) REVERT: C 135 MET cc_start: 0.8338 (mpp) cc_final: 0.7998 (mpp) REVERT: C 206 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7665 (mttm) REVERT: C 225 THR cc_start: 0.8274 (m) cc_final: 0.8037 (m) REVERT: C 265 GLN cc_start: 0.8369 (mm-40) cc_final: 0.8145 (mm-40) REVERT: C 312 ASN cc_start: 0.9253 (m-40) cc_final: 0.8941 (m-40) REVERT: C 441 GLN cc_start: 0.8359 (mt0) cc_final: 0.8123 (mt0) REVERT: C 449 ASP cc_start: 0.7598 (t0) cc_final: 0.7284 (t70) REVERT: C 476 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9007 (mp) REVERT: D 184 GLU cc_start: 0.2041 (OUTLIER) cc_final: 0.0269 (tp30) REVERT: D 243 GLN cc_start: 0.7851 (mp-120) cc_final: 0.7174 (mp-120) REVERT: D 312 ASN cc_start: 0.9252 (m-40) cc_final: 0.8925 (m-40) REVERT: D 395 GLU cc_start: 0.8169 (mp0) cc_final: 0.7826 (mp0) REVERT: D 441 GLN cc_start: 0.8409 (mt0) cc_final: 0.8192 (mt0) REVERT: D 449 ASP cc_start: 0.7940 (t70) cc_final: 0.7440 (t70) REVERT: E 205 LYS cc_start: 0.8817 (mmtp) cc_final: 0.8319 (mmtp) REVERT: E 206 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7503 (mttm) REVERT: E 225 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.7892 (p) REVERT: E 243 GLN cc_start: 0.8062 (mp10) cc_final: 0.7795 (mp-120) REVERT: E 312 ASN cc_start: 0.9274 (m-40) cc_final: 0.8970 (m-40) REVERT: E 330 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8826 (pp) REVERT: E 395 GLU cc_start: 0.8129 (mp0) cc_final: 0.7836 (mp0) REVERT: E 448 GLN cc_start: 0.7635 (tt0) cc_final: 0.7389 (tt0) REVERT: F 179 MET cc_start: 0.3070 (mpp) cc_final: 0.2793 (mpp) REVERT: F 206 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7207 (mtmm) REVERT: F 231 ARG cc_start: 0.8703 (ptp90) cc_final: 0.8321 (mtm110) REVERT: F 243 GLN cc_start: 0.8073 (mp10) cc_final: 0.7823 (mp10) REVERT: F 312 ASN cc_start: 0.9243 (m-40) cc_final: 0.8917 (m-40) REVERT: F 330 ILE cc_start: 0.9058 (OUTLIER) cc_final: 0.8835 (pp) REVERT: F 395 GLU cc_start: 0.8118 (mp0) cc_final: 0.7814 (mp0) REVERT: F 412 ARG cc_start: 0.8138 (ptt180) cc_final: 0.7864 (ptt180) REVERT: F 441 GLN cc_start: 0.8405 (mt0) cc_final: 0.8166 (mt0) REVERT: F 476 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8990 (mp) REVERT: G 135 MET cc_start: 0.8277 (OUTLIER) cc_final: 0.7816 (mpp) REVERT: G 179 MET cc_start: 0.3782 (mtt) cc_final: 0.3011 (mpp) REVERT: G 243 GLN cc_start: 0.7869 (mp10) cc_final: 0.7489 (mp10) REVERT: G 286 MET cc_start: 0.8907 (tpp) cc_final: 0.8666 (tpp) REVERT: G 312 ASN cc_start: 0.9255 (m-40) cc_final: 0.8916 (m-40) REVERT: G 330 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8851 (pp) REVERT: G 395 GLU cc_start: 0.8165 (mp0) cc_final: 0.7834 (mp0) REVERT: G 412 ARG cc_start: 0.8202 (ptt180) cc_final: 0.7936 (ptt180) REVERT: G 449 ASP cc_start: 0.7933 (t70) cc_final: 0.7403 (t70) REVERT: G 455 LYS cc_start: 0.8047 (ptpp) cc_final: 0.7813 (ptpp) REVERT: H 202 GLN cc_start: 0.8379 (tt0) cc_final: 0.8060 (mm-40) REVERT: H 206 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7374 (mttm) REVERT: H 225 THR cc_start: 0.8064 (m) cc_final: 0.7588 (p) REVERT: H 231 ARG cc_start: 0.8780 (ptp90) cc_final: 0.8538 (mtm180) REVERT: H 243 GLN cc_start: 0.7783 (mp-120) cc_final: 0.7067 (mp-120) REVERT: H 312 ASN cc_start: 0.9267 (m-40) cc_final: 0.8946 (m-40) REVERT: H 395 GLU cc_start: 0.8123 (mp0) cc_final: 0.7811 (mp0) REVERT: H 449 ASP cc_start: 0.7944 (t70) cc_final: 0.7389 (t70) outliers start: 132 outliers final: 108 residues processed: 701 average time/residue: 0.4256 time to fit residues: 469.5827 Evaluate side-chains 711 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 589 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 476 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 206 LYS Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 476 LEU Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 361 ILE Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 452 SER Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 77 ASP Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 28 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 chunk 120 optimal weight: 0.3980 chunk 337 optimal weight: 0.0770 chunk 72 optimal weight: 2.9990 chunk 156 optimal weight: 9.9990 chunk 118 optimal weight: 0.6980 chunk 177 optimal weight: 0.9990 chunk 343 optimal weight: 0.6980 chunk 364 optimal weight: 0.4980 chunk 110 optimal weight: 5.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS ** C 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 ASN ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.155805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.107932 restraints weight = 33611.032| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.99 r_work: 0.2906 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 30593 Z= 0.107 Angle : 0.488 6.233 41496 Z= 0.258 Chirality : 0.041 0.135 4800 Planarity : 0.003 0.042 5160 Dihedral : 13.189 175.374 5259 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.59 % Allowed : 19.87 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.28 (0.14), residues: 3792 helix: 1.11 (0.14), residues: 1472 sheet: 0.27 (0.27), residues: 272 loop : -1.27 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS D 93 PHE 0.006 0.001 PHE H 24 TYR 0.012 0.001 TYR F 353 ARG 0.009 0.000 ARG C 231 Details of bonding type rmsd hydrogen bonds : bond 0.02848 ( 1090) hydrogen bonds : angle 4.67270 ( 3078) covalent geometry : bond 0.00234 (30592) covalent geometry : angle 0.48815 (41496) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 624 time to evaluate : 3.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.4879 (OUTLIER) cc_final: 0.4259 (mtm) REVERT: A 225 THR cc_start: 0.8243 (m) cc_final: 0.7993 (m) REVERT: A 243 GLN cc_start: 0.8047 (mp10) cc_final: 0.7254 (mp10) REVERT: A 277 GLN cc_start: 0.9211 (OUTLIER) cc_final: 0.8117 (tm-30) REVERT: A 286 MET cc_start: 0.8892 (tpp) cc_final: 0.8639 (tpp) REVERT: A 312 ASN cc_start: 0.9222 (m-40) cc_final: 0.8936 (m-40) REVERT: A 337 MET cc_start: 0.8843 (mmm) cc_final: 0.8346 (mtt) REVERT: A 420 MET cc_start: 0.6888 (mtt) cc_final: 0.6455 (mtt) REVERT: A 449 ASP cc_start: 0.7874 (t70) cc_final: 0.7323 (t70) REVERT: A 455 LYS cc_start: 0.7989 (ptpp) cc_final: 0.7788 (ptpp) REVERT: A 470 ASP cc_start: 0.8951 (m-30) cc_final: 0.8737 (m-30) REVERT: B 134 LYS cc_start: 0.7815 (tptt) cc_final: 0.7530 (tppt) REVERT: B 243 GLN cc_start: 0.7723 (mp-120) cc_final: 0.7069 (mp-120) REVERT: B 265 GLN cc_start: 0.8177 (mm-40) cc_final: 0.7882 (mm-40) REVERT: B 277 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8002 (tm-30) REVERT: B 286 MET cc_start: 0.8886 (tpp) cc_final: 0.8651 (tpp) REVERT: B 312 ASN cc_start: 0.9213 (m-40) cc_final: 0.8942 (m-40) REVERT: B 395 GLU cc_start: 0.8141 (mp0) cc_final: 0.7864 (mp0) REVERT: B 470 ASP cc_start: 0.8975 (m-30) cc_final: 0.8711 (m-30) REVERT: C 103 GLU cc_start: 0.8618 (tp30) cc_final: 0.8387 (mm-30) REVERT: C 184 GLU cc_start: 0.4910 (OUTLIER) cc_final: 0.4313 (tp30) REVERT: C 227 LEU cc_start: 0.8635 (mm) cc_final: 0.8197 (mp) REVERT: C 243 GLN cc_start: 0.7866 (mp10) cc_final: 0.7632 (mp-120) REVERT: C 265 GLN cc_start: 0.8288 (mm-40) cc_final: 0.8065 (mm-40) REVERT: C 286 MET cc_start: 0.8898 (tpp) cc_final: 0.8616 (tpp) REVERT: C 312 ASN cc_start: 0.9180 (m-40) cc_final: 0.8892 (m-40) REVERT: C 449 ASP cc_start: 0.7596 (t0) cc_final: 0.7343 (t70) REVERT: D 103 GLU cc_start: 0.8625 (tp30) cc_final: 0.8407 (mm-30) REVERT: D 184 GLU cc_start: 0.2024 (OUTLIER) cc_final: 0.0381 (tp30) REVERT: D 206 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7443 (mttm) REVERT: D 243 GLN cc_start: 0.7742 (mp-120) cc_final: 0.7081 (mp-120) REVERT: D 277 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.7781 (tm-30) REVERT: D 286 MET cc_start: 0.8959 (tpp) cc_final: 0.8709 (tpp) REVERT: D 312 ASN cc_start: 0.9180 (m-40) cc_final: 0.8887 (m-40) REVERT: D 395 GLU cc_start: 0.8177 (mp0) cc_final: 0.7850 (mp0) REVERT: D 441 GLN cc_start: 0.8395 (mt0) cc_final: 0.8180 (mt0) REVERT: D 449 ASP cc_start: 0.7903 (t70) cc_final: 0.7504 (t70) REVERT: E 134 LYS cc_start: 0.7975 (tptt) cc_final: 0.7760 (tppt) REVERT: E 205 LYS cc_start: 0.8783 (mmtp) cc_final: 0.8295 (mmtp) REVERT: E 206 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7564 (mttm) REVERT: E 225 THR cc_start: 0.8258 (m) cc_final: 0.7841 (p) REVERT: E 243 GLN cc_start: 0.8062 (mp10) cc_final: 0.7416 (mp-120) REVERT: E 277 GLN cc_start: 0.9199 (OUTLIER) cc_final: 0.7724 (tm-30) REVERT: E 286 MET cc_start: 0.8899 (tpp) cc_final: 0.8635 (tpp) REVERT: E 312 ASN cc_start: 0.9205 (m-40) cc_final: 0.8945 (m-40) REVERT: E 395 GLU cc_start: 0.8136 (mp0) cc_final: 0.7867 (mp0) REVERT: E 448 GLN cc_start: 0.7629 (tt0) cc_final: 0.7379 (tt0) REVERT: F 103 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8286 (mm-30) REVERT: F 179 MET cc_start: 0.3034 (mpp) cc_final: 0.2812 (mpp) REVERT: F 184 GLU cc_start: 0.5344 (OUTLIER) cc_final: 0.3844 (tp30) REVERT: F 202 GLN cc_start: 0.8344 (tt0) cc_final: 0.8079 (mm-40) REVERT: F 206 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7050 (mtmm) REVERT: F 231 ARG cc_start: 0.8693 (ptp90) cc_final: 0.8301 (mtm110) REVERT: F 243 GLN cc_start: 0.8058 (mp10) cc_final: 0.7795 (mp10) REVERT: F 277 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.7756 (tm-30) REVERT: F 286 MET cc_start: 0.8879 (tpp) cc_final: 0.8635 (tpp) REVERT: F 312 ASN cc_start: 0.9184 (m-40) cc_final: 0.8904 (m-40) REVERT: F 395 GLU cc_start: 0.8135 (mp0) cc_final: 0.7859 (mp0) REVERT: F 441 GLN cc_start: 0.8399 (mt0) cc_final: 0.8137 (mt0) REVERT: G 103 GLU cc_start: 0.8616 (tp30) cc_final: 0.8397 (mm-30) REVERT: G 114 PHE cc_start: 0.8170 (m-10) cc_final: 0.7949 (m-10) REVERT: G 135 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7807 (mpp) REVERT: G 179 MET cc_start: 0.3711 (mtt) cc_final: 0.3115 (mpp) REVERT: G 202 GLN cc_start: 0.8265 (tt0) cc_final: 0.8050 (mm-40) REVERT: G 206 LYS cc_start: 0.7873 (OUTLIER) cc_final: 0.7520 (mttm) REVERT: G 243 GLN cc_start: 0.7790 (mp10) cc_final: 0.7379 (mp10) REVERT: G 277 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.8083 (tm-30) REVERT: G 286 MET cc_start: 0.8879 (tpp) cc_final: 0.8546 (tpp) REVERT: G 312 ASN cc_start: 0.9179 (m-40) cc_final: 0.8879 (m-40) REVERT: G 395 GLU cc_start: 0.8167 (mp0) cc_final: 0.7867 (mp0) REVERT: G 449 ASP cc_start: 0.7782 (t70) cc_final: 0.7424 (t70) REVERT: H 47 ASP cc_start: 0.8729 (m-30) cc_final: 0.8295 (m-30) REVERT: H 202 GLN cc_start: 0.8341 (tt0) cc_final: 0.8090 (mm-40) REVERT: H 206 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7223 (mttm) REVERT: H 231 ARG cc_start: 0.8797 (ptp90) cc_final: 0.8543 (mtm180) REVERT: H 243 GLN cc_start: 0.7755 (mp-120) cc_final: 0.7176 (mp-120) REVERT: H 265 GLN cc_start: 0.8087 (mm-40) cc_final: 0.7868 (mm-40) REVERT: H 286 MET cc_start: 0.8899 (tpp) cc_final: 0.8656 (tpp) REVERT: H 312 ASN cc_start: 0.9227 (m-40) cc_final: 0.8949 (m-40) REVERT: H 395 GLU cc_start: 0.8115 (mp0) cc_final: 0.7814 (mp0) REVERT: H 400 TYR cc_start: 0.7729 (m-80) cc_final: 0.6866 (m-80) REVERT: H 449 ASP cc_start: 0.7962 (t70) cc_final: 0.7308 (t70) outliers start: 112 outliers final: 87 residues processed: 705 average time/residue: 0.4520 time to fit residues: 499.7820 Evaluate side-chains 713 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 610 time to evaluate : 3.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 93 HIS Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 77 ASP Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 93 HIS Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 382 optimal weight: 1.9990 chunk 147 optimal weight: 0.2980 chunk 155 optimal weight: 4.9990 chunk 1 optimal weight: 0.2980 chunk 95 optimal weight: 0.2980 chunk 77 optimal weight: 1.9990 chunk 285 optimal weight: 2.9990 chunk 66 optimal weight: 10.0000 chunk 84 optimal weight: 0.7980 chunk 114 optimal weight: 1.9990 chunk 150 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS ** A 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 GLN ** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 202 GLN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 HIS G 93 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.157279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.109864 restraints weight = 33639.119| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.95 r_work: 0.2914 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2776 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 30593 Z= 0.110 Angle : 0.487 6.326 41496 Z= 0.258 Chirality : 0.041 0.149 4800 Planarity : 0.003 0.031 5160 Dihedral : 12.854 153.013 5250 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.53 % Allowed : 20.22 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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 (0.14), residues: 3792 helix: 1.17 (0.14), residues: 1472 sheet: -0.46 (0.25), residues: 352 loop : -1.28 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.019 0.001 HIS G 93 PHE 0.016 0.001 PHE G 401 TYR 0.013 0.001 TYR B 400 ARG 0.007 0.000 ARG C 231 Details of bonding type rmsd hydrogen bonds : bond 0.02820 ( 1090) hydrogen bonds : angle 4.61483 ( 3078) covalent geometry : bond 0.00242 (30592) covalent geometry : angle 0.48652 (41496) Misc. bond : bond 0.00067 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 726 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 616 time to evaluate : 3.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 PHE cc_start: 0.8128 (m-10) cc_final: 0.7903 (m-10) REVERT: A 179 MET cc_start: 0.4878 (OUTLIER) cc_final: 0.4264 (mtm) REVERT: A 206 LYS cc_start: 0.8009 (OUTLIER) cc_final: 0.7460 (mttm) REVERT: A 277 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8055 (tm-30) REVERT: A 286 MET cc_start: 0.8905 (tpp) cc_final: 0.8657 (tpp) REVERT: A 312 ASN cc_start: 0.9177 (m-40) cc_final: 0.8884 (m-40) REVERT: A 337 MET cc_start: 0.8813 (mmm) cc_final: 0.8375 (mtt) REVERT: A 420 MET cc_start: 0.6878 (mtt) cc_final: 0.6416 (mtt) REVERT: A 449 ASP cc_start: 0.7870 (t70) cc_final: 0.7442 (t70) REVERT: A 455 LYS cc_start: 0.8011 (ptpp) cc_final: 0.7791 (ptpp) REVERT: B 103 GLU cc_start: 0.8644 (tp30) cc_final: 0.8436 (mm-30) REVERT: B 134 LYS cc_start: 0.7775 (tptt) cc_final: 0.7495 (tppt) REVERT: B 243 GLN cc_start: 0.7737 (mp-120) cc_final: 0.7083 (mp10) REVERT: B 265 GLN cc_start: 0.8240 (mm-40) cc_final: 0.8013 (mm-40) REVERT: B 277 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8051 (tm-30) REVERT: B 312 ASN cc_start: 0.9164 (m-40) cc_final: 0.8920 (m-40) REVERT: B 337 MET cc_start: 0.8708 (mmm) cc_final: 0.8292 (mtt) REVERT: B 395 GLU cc_start: 0.8149 (mp0) cc_final: 0.7889 (mp0) REVERT: C 184 GLU cc_start: 0.4794 (OUTLIER) cc_final: 0.4300 (tp30) REVERT: C 227 LEU cc_start: 0.8652 (mm) cc_final: 0.8229 (mp) REVERT: C 243 GLN cc_start: 0.7759 (mp10) cc_final: 0.7469 (mp10) REVERT: C 277 GLN cc_start: 0.9250 (OUTLIER) cc_final: 0.7880 (tm-30) REVERT: C 286 MET cc_start: 0.8902 (tpp) cc_final: 0.8621 (tpp) REVERT: C 312 ASN cc_start: 0.9171 (m-40) cc_final: 0.8901 (m-40) REVERT: C 449 ASP cc_start: 0.7639 (t0) cc_final: 0.7373 (t70) REVERT: D 184 GLU cc_start: 0.2014 (OUTLIER) cc_final: 0.0478 (tp30) REVERT: D 206 LYS cc_start: 0.7868 (OUTLIER) cc_final: 0.7541 (mttm) REVERT: D 243 GLN cc_start: 0.7750 (mp-120) cc_final: 0.7171 (mp-120) REVERT: D 277 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.7820 (tm-30) REVERT: D 286 MET cc_start: 0.8972 (tpp) cc_final: 0.8704 (tpp) REVERT: D 312 ASN cc_start: 0.9159 (m-40) cc_final: 0.8862 (m-40) REVERT: D 395 GLU cc_start: 0.8172 (mp0) cc_final: 0.7867 (mp0) REVERT: D 420 MET cc_start: 0.6979 (mtt) cc_final: 0.6746 (mtt) REVERT: D 438 LYS cc_start: 0.8496 (mmmt) cc_final: 0.8139 (mmmm) REVERT: D 441 GLN cc_start: 0.8394 (mt0) cc_final: 0.8189 (mt0) REVERT: D 449 ASP cc_start: 0.7921 (t70) cc_final: 0.7542 (t70) REVERT: E 205 LYS cc_start: 0.8822 (mmtp) cc_final: 0.8368 (mmtp) REVERT: E 225 THR cc_start: 0.8268 (m) cc_final: 0.7868 (p) REVERT: E 243 GLN cc_start: 0.8066 (mp10) cc_final: 0.7398 (mp10) REVERT: E 277 GLN cc_start: 0.9190 (OUTLIER) cc_final: 0.8057 (tm-30) REVERT: E 286 MET cc_start: 0.8898 (tpp) cc_final: 0.8614 (tpp) REVERT: E 312 ASN cc_start: 0.9194 (m-40) cc_final: 0.8933 (m-40) REVERT: E 395 GLU cc_start: 0.8157 (mp0) cc_final: 0.7908 (mp0) REVERT: E 448 GLN cc_start: 0.7683 (tt0) cc_final: 0.7447 (tt0) REVERT: F 103 GLU cc_start: 0.8534 (mm-30) cc_final: 0.8312 (mm-30) REVERT: F 179 MET cc_start: 0.3025 (mpp) cc_final: 0.2799 (mpp) REVERT: F 184 GLU cc_start: 0.5348 (OUTLIER) cc_final: 0.3856 (tp30) REVERT: F 206 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7081 (mtmm) REVERT: F 231 ARG cc_start: 0.8714 (ptp90) cc_final: 0.8319 (mtm110) REVERT: F 277 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8131 (tm-30) REVERT: F 286 MET cc_start: 0.8890 (tpp) cc_final: 0.8598 (tpp) REVERT: F 312 ASN cc_start: 0.9166 (m-40) cc_final: 0.8885 (m-40) REVERT: F 395 GLU cc_start: 0.8150 (mp0) cc_final: 0.7874 (mp0) REVERT: F 441 GLN cc_start: 0.8412 (mt0) cc_final: 0.8174 (mt0) REVERT: G 103 GLU cc_start: 0.8605 (tp30) cc_final: 0.8391 (mm-30) REVERT: G 135 MET cc_start: 0.8238 (OUTLIER) cc_final: 0.7776 (mpp) REVERT: G 179 MET cc_start: 0.3627 (mtt) cc_final: 0.3075 (mpp) REVERT: G 206 LYS cc_start: 0.7892 (OUTLIER) cc_final: 0.7624 (mttm) REVERT: G 243 GLN cc_start: 0.7788 (mp10) cc_final: 0.7025 (mp10) REVERT: G 277 GLN cc_start: 0.9244 (OUTLIER) cc_final: 0.8136 (tm-30) REVERT: G 286 MET cc_start: 0.8896 (tpp) cc_final: 0.8569 (tpp) REVERT: G 312 ASN cc_start: 0.9158 (m-40) cc_final: 0.8849 (m-40) REVERT: G 395 GLU cc_start: 0.8108 (mp0) cc_final: 0.7819 (mp0) REVERT: G 412 ARG cc_start: 0.7965 (ptt180) cc_final: 0.7754 (ptt180) REVERT: G 449 ASP cc_start: 0.7796 (t70) cc_final: 0.7418 (t70) REVERT: H 47 ASP cc_start: 0.8677 (m-30) cc_final: 0.8225 (m-30) REVERT: H 202 GLN cc_start: 0.8349 (tt0) cc_final: 0.8118 (mm-40) REVERT: H 206 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7258 (mttm) REVERT: H 225 THR cc_start: 0.7944 (m) cc_final: 0.7539 (p) REVERT: H 231 ARG cc_start: 0.8800 (ptp90) cc_final: 0.8571 (mtm180) REVERT: H 243 GLN cc_start: 0.7749 (mp-120) cc_final: 0.7174 (mp10) REVERT: H 265 GLN cc_start: 0.8108 (mm-40) cc_final: 0.7886 (mm-40) REVERT: H 277 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8008 (tm-30) REVERT: H 286 MET cc_start: 0.8910 (tpp) cc_final: 0.8670 (tpp) REVERT: H 312 ASN cc_start: 0.9185 (m-40) cc_final: 0.8904 (m-40) REVERT: H 395 GLU cc_start: 0.8098 (mp0) cc_final: 0.7794 (mp0) REVERT: H 400 TYR cc_start: 0.7744 (m-80) cc_final: 0.6889 (m-80) REVERT: H 449 ASP cc_start: 0.7972 (t70) cc_final: 0.7322 (t70) outliers start: 110 outliers final: 83 residues processed: 695 average time/residue: 0.4242 time to fit residues: 465.3464 Evaluate side-chains 699 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 598 time to evaluate : 3.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 93 HIS Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 147 THR Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 287 VAL Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 43 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 347 optimal weight: 0.0270 chunk 61 optimal weight: 0.9980 chunk 222 optimal weight: 2.9990 chunk 191 optimal weight: 0.2980 chunk 233 optimal weight: 10.0000 chunk 282 optimal weight: 0.0970 chunk 216 optimal weight: 0.9990 chunk 338 optimal weight: 0.7980 chunk 225 optimal weight: 0.9980 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS D 93 HIS D 202 GLN ** E 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 HIS G 93 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.158277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.110731 restraints weight = 33715.358| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 1.98 r_work: 0.2929 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2790 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 30593 Z= 0.100 Angle : 0.486 6.545 41496 Z= 0.256 Chirality : 0.041 0.150 4800 Planarity : 0.003 0.031 5160 Dihedral : 12.560 121.759 5250 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.30 % Allowed : 20.42 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.26 (0.14), residues: 3792 helix: 1.20 (0.14), residues: 1472 sheet: -0.20 (0.25), residues: 360 loop : -1.27 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.025 0.001 HIS F 93 PHE 0.032 0.001 PHE C 99 TYR 0.011 0.001 TYR B 400 ARG 0.004 0.000 ARG A 412 Details of bonding type rmsd hydrogen bonds : bond 0.02727 ( 1090) hydrogen bonds : angle 4.55170 ( 3078) covalent geometry : bond 0.00218 (30592) covalent geometry : angle 0.48562 (41496) Misc. bond : bond 0.00139 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 627 time to evaluate : 3.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7667 (mttm) REVERT: A 225 THR cc_start: 0.8043 (m) cc_final: 0.7674 (p) REVERT: A 243 GLN cc_start: 0.8041 (mp10) cc_final: 0.7200 (mp10) REVERT: A 277 GLN cc_start: 0.9142 (OUTLIER) cc_final: 0.8101 (tm-30) REVERT: A 286 MET cc_start: 0.8903 (tpp) cc_final: 0.8650 (tpp) REVERT: A 312 ASN cc_start: 0.9173 (m-40) cc_final: 0.8900 (m-40) REVERT: A 337 MET cc_start: 0.8821 (mmm) cc_final: 0.8396 (mtt) REVERT: A 420 MET cc_start: 0.6840 (mtt) cc_final: 0.6330 (mtt) REVERT: A 441 GLN cc_start: 0.8084 (mt0) cc_final: 0.7821 (mt0) REVERT: A 449 ASP cc_start: 0.7883 (t70) cc_final: 0.7463 (t70) REVERT: A 455 LYS cc_start: 0.7988 (ptpp) cc_final: 0.7778 (ptpp) REVERT: B 243 GLN cc_start: 0.7719 (mp-120) cc_final: 0.7101 (mp10) REVERT: B 265 GLN cc_start: 0.8269 (mm-40) cc_final: 0.8060 (mm-40) REVERT: B 277 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8036 (tm-30) REVERT: B 312 ASN cc_start: 0.9162 (m-40) cc_final: 0.8916 (m-40) REVERT: B 337 MET cc_start: 0.8750 (mmm) cc_final: 0.8221 (mtt) REVERT: B 395 GLU cc_start: 0.8156 (mp0) cc_final: 0.7899 (mp0) REVERT: C 184 GLU cc_start: 0.4911 (OUTLIER) cc_final: 0.4372 (tp30) REVERT: C 227 LEU cc_start: 0.8595 (mm) cc_final: 0.8186 (mp) REVERT: C 277 GLN cc_start: 0.9193 (OUTLIER) cc_final: 0.7968 (tm-30) REVERT: C 286 MET cc_start: 0.8890 (tpp) cc_final: 0.8606 (tpp) REVERT: C 312 ASN cc_start: 0.9158 (m-40) cc_final: 0.8879 (m-40) REVERT: C 337 MET cc_start: 0.8735 (mmm) cc_final: 0.8267 (mtt) REVERT: C 449 ASP cc_start: 0.7639 (t0) cc_final: 0.7359 (t70) REVERT: D 184 GLU cc_start: 0.1914 (OUTLIER) cc_final: 0.0541 (tp30) REVERT: D 206 LYS cc_start: 0.7855 (OUTLIER) cc_final: 0.7418 (mttm) REVERT: D 243 GLN cc_start: 0.7739 (mp-120) cc_final: 0.7165 (mp10) REVERT: D 277 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.7911 (tm-30) REVERT: D 286 MET cc_start: 0.8954 (tpp) cc_final: 0.8685 (tpp) REVERT: D 312 ASN cc_start: 0.9175 (m-40) cc_final: 0.8903 (m-40) REVERT: D 395 GLU cc_start: 0.8095 (mp0) cc_final: 0.7758 (mp0) REVERT: D 420 MET cc_start: 0.6893 (mtt) cc_final: 0.6449 (mtt) REVERT: D 438 LYS cc_start: 0.8429 (mmmt) cc_final: 0.8063 (mmmm) REVERT: D 449 ASP cc_start: 0.7888 (t70) cc_final: 0.7492 (t70) REVERT: E 103 GLU cc_start: 0.8580 (tp30) cc_final: 0.8367 (mm-30) REVERT: E 205 LYS cc_start: 0.8819 (mmtp) cc_final: 0.8313 (mmtp) REVERT: E 206 LYS cc_start: 0.8023 (OUTLIER) cc_final: 0.7636 (mttm) REVERT: E 225 THR cc_start: 0.8235 (m) cc_final: 0.7822 (p) REVERT: E 243 GLN cc_start: 0.8058 (mp10) cc_final: 0.7379 (mp10) REVERT: E 277 GLN cc_start: 0.9166 (OUTLIER) cc_final: 0.8023 (tm-30) REVERT: E 286 MET cc_start: 0.8870 (tpp) cc_final: 0.8584 (tpp) REVERT: E 312 ASN cc_start: 0.9187 (m-40) cc_final: 0.8915 (m-40) REVERT: E 395 GLU cc_start: 0.8058 (mp0) cc_final: 0.7795 (mp0) REVERT: E 448 GLN cc_start: 0.7695 (tt0) cc_final: 0.7444 (tt0) REVERT: F 179 MET cc_start: 0.2979 (mpp) cc_final: 0.2762 (mpp) REVERT: F 184 GLU cc_start: 0.5202 (OUTLIER) cc_final: 0.3791 (tp30) REVERT: F 205 LYS cc_start: 0.8962 (mmtp) cc_final: 0.8407 (mmtp) REVERT: F 277 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.7971 (tm-30) REVERT: F 286 MET cc_start: 0.8871 (tpp) cc_final: 0.8536 (tpp) REVERT: F 312 ASN cc_start: 0.9172 (m-40) cc_final: 0.8895 (m-40) REVERT: F 395 GLU cc_start: 0.8087 (mp0) cc_final: 0.7799 (mp0) REVERT: F 441 GLN cc_start: 0.8363 (mt0) cc_final: 0.8136 (mt0) REVERT: G 135 MET cc_start: 0.8243 (OUTLIER) cc_final: 0.7770 (mpp) REVERT: G 179 MET cc_start: 0.3559 (mtt) cc_final: 0.3064 (mpp) REVERT: G 206 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7299 (mttm) REVERT: G 243 GLN cc_start: 0.7769 (mp10) cc_final: 0.7049 (mp10) REVERT: G 277 GLN cc_start: 0.9186 (OUTLIER) cc_final: 0.8143 (tm-30) REVERT: G 286 MET cc_start: 0.8888 (tpp) cc_final: 0.8529 (tpp) REVERT: G 312 ASN cc_start: 0.9154 (m-40) cc_final: 0.8858 (m-40) REVERT: G 395 GLU cc_start: 0.8087 (mp0) cc_final: 0.7797 (mp0) REVERT: G 412 ARG cc_start: 0.7909 (ptt180) cc_final: 0.7667 (ptt180) REVERT: G 449 ASP cc_start: 0.7665 (t70) cc_final: 0.7337 (t70) REVERT: H 202 GLN cc_start: 0.8303 (tt0) cc_final: 0.8058 (mm-40) REVERT: H 206 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7249 (mttm) REVERT: H 225 THR cc_start: 0.7901 (m) cc_final: 0.7491 (p) REVERT: H 231 ARG cc_start: 0.8814 (ptp90) cc_final: 0.8560 (mtm180) REVERT: H 243 GLN cc_start: 0.7736 (mp-120) cc_final: 0.7198 (mp10) REVERT: H 265 GLN cc_start: 0.8116 (mm-40) cc_final: 0.7891 (mm-40) REVERT: H 277 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.8033 (tm-30) REVERT: H 286 MET cc_start: 0.8886 (tpp) cc_final: 0.8625 (tpp) REVERT: H 312 ASN cc_start: 0.9182 (m-40) cc_final: 0.8915 (m-40) REVERT: H 395 GLU cc_start: 0.8051 (mp0) cc_final: 0.7752 (mp0) REVERT: H 400 TYR cc_start: 0.7753 (m-80) cc_final: 0.6903 (m-80) REVERT: H 449 ASP cc_start: 0.7987 (t70) cc_final: 0.7359 (t70) outliers start: 103 outliers final: 80 residues processed: 701 average time/residue: 0.4209 time to fit residues: 467.5998 Evaluate side-chains 700 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 603 time to evaluate : 3.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 135 MET Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 93 HIS Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 206 LYS Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 17 optimal weight: 0.9990 chunk 133 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 161 optimal weight: 9.9990 chunk 83 optimal weight: 0.5980 chunk 232 optimal weight: 0.9990 chunk 374 optimal weight: 3.9990 chunk 376 optimal weight: 6.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 93 HIS D 202 GLN ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 HIS ** F 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.156038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.108085 restraints weight = 33707.471| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 1.98 r_work: 0.2901 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 30593 Z= 0.140 Angle : 0.506 7.448 41496 Z= 0.269 Chirality : 0.042 0.182 4800 Planarity : 0.004 0.039 5160 Dihedral : 12.487 99.929 5250 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 3.27 % Allowed : 20.42 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.25 (0.14), residues: 3792 helix: 1.30 (0.14), residues: 1432 sheet: -0.68 (0.24), residues: 392 loop : -1.19 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS D 93 PHE 0.029 0.001 PHE F 99 TYR 0.011 0.001 TYR B 400 ARG 0.007 0.000 ARG A 412 Details of bonding type rmsd hydrogen bonds : bond 0.03028 ( 1090) hydrogen bonds : angle 4.63453 ( 3078) covalent geometry : bond 0.00316 (30592) covalent geometry : angle 0.50603 (41496) Misc. bond : bond 0.00229 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7584 Ramachandran restraints generated. 3792 Oldfield, 0 Emsley, 3792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 603 time to evaluate : 4.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.4790 (OUTLIER) cc_final: 0.4237 (mtm) REVERT: A 206 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7525 (mttm) REVERT: A 225 THR cc_start: 0.8119 (m) cc_final: 0.7718 (p) REVERT: A 243 GLN cc_start: 0.8014 (mp10) cc_final: 0.7219 (mp10) REVERT: A 277 GLN cc_start: 0.9192 (OUTLIER) cc_final: 0.8154 (tm-30) REVERT: A 312 ASN cc_start: 0.9234 (m-40) cc_final: 0.8934 (m-40) REVERT: A 337 MET cc_start: 0.8926 (mmm) cc_final: 0.8525 (mtt) REVERT: A 420 MET cc_start: 0.6914 (mtt) cc_final: 0.6437 (mtt) REVERT: A 441 GLN cc_start: 0.8111 (mt0) cc_final: 0.7873 (mt0) REVERT: A 449 ASP cc_start: 0.7962 (t70) cc_final: 0.7459 (t0) REVERT: A 455 LYS cc_start: 0.7997 (ptpp) cc_final: 0.7771 (ptpp) REVERT: B 134 LYS cc_start: 0.7949 (tppt) cc_final: 0.7579 (tppt) REVERT: B 205 LYS cc_start: 0.8815 (mmtp) cc_final: 0.8409 (mttm) REVERT: B 243 GLN cc_start: 0.7693 (mp-120) cc_final: 0.7221 (mp10) REVERT: B 277 GLN cc_start: 0.9218 (OUTLIER) cc_final: 0.8168 (tm-30) REVERT: B 312 ASN cc_start: 0.9167 (m-40) cc_final: 0.8878 (m-40) REVERT: B 395 GLU cc_start: 0.8139 (mp0) cc_final: 0.7852 (mp0) REVERT: C 78 MET cc_start: 0.8969 (tpp) cc_final: 0.8554 (tpp) REVERT: C 184 GLU cc_start: 0.4997 (OUTLIER) cc_final: 0.4406 (tp30) REVERT: C 205 LYS cc_start: 0.8924 (mmtp) cc_final: 0.8641 (mmtp) REVERT: C 227 LEU cc_start: 0.8594 (mm) cc_final: 0.8190 (mp) REVERT: C 277 GLN cc_start: 0.9255 (OUTLIER) cc_final: 0.8149 (tm-30) REVERT: C 286 MET cc_start: 0.8911 (tpp) cc_final: 0.8638 (tpp) REVERT: C 312 ASN cc_start: 0.9222 (m-40) cc_final: 0.8917 (m-40) REVERT: C 449 ASP cc_start: 0.7644 (t0) cc_final: 0.7397 (t70) REVERT: D 78 MET cc_start: 0.8941 (tpp) cc_final: 0.8540 (tpp) REVERT: D 114 PHE cc_start: 0.8228 (m-10) cc_final: 0.8001 (m-10) REVERT: D 184 GLU cc_start: 0.2197 (OUTLIER) cc_final: 0.0782 (tp30) REVERT: D 206 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7512 (mttm) REVERT: D 243 GLN cc_start: 0.7751 (mp-120) cc_final: 0.7175 (mp10) REVERT: D 277 GLN cc_start: 0.9163 (OUTLIER) cc_final: 0.8016 (tm-30) REVERT: D 312 ASN cc_start: 0.9219 (m-40) cc_final: 0.8919 (m-40) REVERT: D 395 GLU cc_start: 0.8122 (mp0) cc_final: 0.7825 (mp0) REVERT: D 421 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7183 (pt0) REVERT: D 438 LYS cc_start: 0.8464 (mmmt) cc_final: 0.8077 (mmmm) REVERT: D 449 ASP cc_start: 0.7944 (t70) cc_final: 0.7542 (t70) REVERT: E 114 PHE cc_start: 0.8180 (m-10) cc_final: 0.7950 (m-10) REVERT: E 225 THR cc_start: 0.8132 (m) cc_final: 0.7764 (p) REVERT: E 243 GLN cc_start: 0.8073 (mp10) cc_final: 0.7390 (mp10) REVERT: E 277 GLN cc_start: 0.9229 (OUTLIER) cc_final: 0.8131 (tm-30) REVERT: E 312 ASN cc_start: 0.9207 (m-40) cc_final: 0.8928 (m-40) REVERT: E 395 GLU cc_start: 0.8068 (mp0) cc_final: 0.7793 (mp0) REVERT: E 448 GLN cc_start: 0.7701 (tt0) cc_final: 0.7444 (tt0) REVERT: F 184 GLU cc_start: 0.5349 (OUTLIER) cc_final: 0.4335 (tp30) REVERT: F 205 LYS cc_start: 0.8947 (mmtp) cc_final: 0.8384 (mmtp) REVERT: F 206 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7192 (mtmm) REVERT: F 243 GLN cc_start: 0.8050 (mp10) cc_final: 0.7244 (mp10) REVERT: F 277 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8026 (tm-30) REVERT: F 286 MET cc_start: 0.8895 (tpp) cc_final: 0.8611 (tpp) REVERT: F 312 ASN cc_start: 0.9208 (m-40) cc_final: 0.8901 (m-40) REVERT: F 337 MET cc_start: 0.8841 (mmm) cc_final: 0.8569 (mtt) REVERT: F 395 GLU cc_start: 0.8083 (mp0) cc_final: 0.7747 (mp0) REVERT: F 441 GLN cc_start: 0.8398 (mt0) cc_final: 0.8089 (mt0) REVERT: F 476 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.9001 (mt) REVERT: G 135 MET cc_start: 0.8270 (OUTLIER) cc_final: 0.7798 (mpp) REVERT: G 179 MET cc_start: 0.3614 (mtt) cc_final: 0.3035 (mpp) REVERT: G 206 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7406 (mttm) REVERT: G 243 GLN cc_start: 0.7781 (mp10) cc_final: 0.7051 (mp10) REVERT: G 277 GLN cc_start: 0.9260 (OUTLIER) cc_final: 0.8185 (tm-30) REVERT: G 286 MET cc_start: 0.8898 (tpp) cc_final: 0.8561 (tpp) REVERT: G 312 ASN cc_start: 0.9215 (m-40) cc_final: 0.8899 (m-40) REVERT: G 395 GLU cc_start: 0.8075 (mp0) cc_final: 0.7735 (mp0) REVERT: G 449 ASP cc_start: 0.7809 (t70) cc_final: 0.7450 (t70) REVERT: H 225 THR cc_start: 0.7990 (m) cc_final: 0.7570 (p) REVERT: H 231 ARG cc_start: 0.8840 (ptp90) cc_final: 0.8584 (mtm180) REVERT: H 243 GLN cc_start: 0.7752 (mp-120) cc_final: 0.7138 (mp10) REVERT: H 265 GLN cc_start: 0.8127 (mm-40) cc_final: 0.7905 (mm-40) REVERT: H 277 GLN cc_start: 0.9240 (OUTLIER) cc_final: 0.8090 (tm-30) REVERT: H 286 MET cc_start: 0.8897 (tpp) cc_final: 0.8644 (tpp) REVERT: H 312 ASN cc_start: 0.9235 (m-40) cc_final: 0.8937 (m-40) REVERT: H 395 GLU cc_start: 0.8061 (mp0) cc_final: 0.7717 (mp0) REVERT: H 449 ASP cc_start: 0.7995 (t70) cc_final: 0.7772 (t0) outliers start: 102 outliers final: 82 residues processed: 674 average time/residue: 0.5055 time to fit residues: 542.3710 Evaluate side-chains 697 residues out of total 3120 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 597 time to evaluate : 3.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 127 VAL Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 206 LYS Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 283 GLN Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 146 GLU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 283 GLN Chi-restraints excluded: chain B residue 361 ILE Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain C residue 67 SER Chi-restraints excluded: chain C residue 93 HIS Chi-restraints excluded: chain C residue 127 VAL Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 283 GLN Chi-restraints excluded: chain C residue 361 ILE Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 127 VAL Chi-restraints excluded: chain D residue 147 THR Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 206 LYS Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 283 GLN Chi-restraints excluded: chain D residue 361 ILE Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain E residue 67 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 147 THR Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 206 LYS Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 283 GLN Chi-restraints excluded: chain E residue 361 ILE Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 127 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 184 GLU Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 283 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 476 LEU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 127 VAL Chi-restraints excluded: chain G residue 135 MET Chi-restraints excluded: chain G residue 147 THR Chi-restraints excluded: chain G residue 154 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 361 ILE Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 67 SER Chi-restraints excluded: chain H residue 127 VAL Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 160 SER Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 283 GLN Chi-restraints excluded: chain H residue 361 ILE Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 235 optimal weight: 2.9990 chunk 136 optimal weight: 4.9990 chunk 118 optimal weight: 0.5980 chunk 47 optimal weight: 0.1980 chunk 146 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 212 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 189 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 93 HIS D 202 GLN ** D 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 198 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.158073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.110357 restraints weight = 33530.155| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.97 r_work: 0.2908 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30593 Z= 0.123 Angle : 0.508 7.511 41496 Z= 0.269 Chirality : 0.042 0.274 4800 Planarity : 0.003 0.034 5160 Dihedral : 12.387 95.216 5246 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.33 % Allowed : 20.64 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.11 (0.14), residues: 3792 helix: 1.27 (0.14), residues: 1432 sheet: -0.03 (0.27), residues: 312 loop : -1.09 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.000 HIS D 93 PHE 0.027 0.001 PHE A 99 TYR 0.012 0.001 TYR H 400 ARG 0.010 0.000 ARG D 203 Details of bonding type rmsd hydrogen bonds : bond 0.02951 ( 1090) hydrogen bonds : angle 4.64137 ( 3078) covalent geometry : bond 0.00276 (30592) covalent geometry : angle 0.50784 (41496) Misc. bond : bond 0.00188 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21113.20 seconds wall clock time: 371 minutes 45.75 seconds (22305.75 seconds total)