Starting phenix.real_space_refine on Thu Jun 26 16:46:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7q_41989/06_2025/8u7q_41989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7q_41989/06_2025/8u7q_41989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u7q_41989/06_2025/8u7q_41989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7q_41989/06_2025/8u7q_41989.map" model { file = "/net/cci-nas-00/data/ceres_data/8u7q_41989/06_2025/8u7q_41989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7q_41989/06_2025/8u7q_41989.cif" } resolution = 3.3 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= -0.001 sd= 0.083 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 96 5.49 5 S 184 5.16 5 C 18992 2.51 5 N 5192 2.21 5 O 6056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 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: 30520 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "B" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "C" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "D" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "E" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "F" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "G" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "H" Number of atoms: 3653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 484, 3653 Classifications: {'peptide': 484} Link IDs: {'PTRANS': 18, 'TRANS': 465} Chain breaks: 1 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Time building chain proxies: 18.14, per 1000 atoms: 0.59 Number of scatterers: 30520 At special positions: 0 Unit cell: (151.96, 151.96, 112.52, 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 96 15.00 O 6056 8.00 N 5192 7.00 C 18992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.85 Conformation dependent library (CDL) restraints added in 4.0 seconds 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6976 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 48 sheets defined 40.9% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.23 Creating SS restraints... Processing helix chain 'A' and resid 19 through 25 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 Processing helix chain 'A' and resid 75 through 84 Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 126 through 138 Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 183 through 185 No H-bonds generated for 'chain 'A' and resid 183 through 185' Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 224 through 233 Processing helix chain 'A' and resid 256 through 267 Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 removed outlier: 4.136A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 355 removed outlier: 4.327A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 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 501 Processing helix chain 'B' and resid 19 through 24 Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 75 through 84 Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 183 through 185 No H-bonds generated for 'chain 'B' and resid 183 through 185' Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 224 through 233 Processing helix chain 'B' and resid 256 through 267 Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 removed outlier: 4.165A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 342 through 355 removed outlier: 4.322A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 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 501 Processing helix chain 'C' and resid 19 through 25 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 Processing helix chain 'C' and resid 75 through 84 Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 126 through 138 Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'C' and resid 183 through 185 No H-bonds generated for 'chain 'C' and resid 183 through 185' Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 256 through 267 Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 removed outlier: 4.165A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 342 through 355 removed outlier: 4.319A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 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 501 Processing helix chain 'D' and resid 19 through 24 Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 75 through 84 Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 126 through 138 Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 183 through 185 No H-bonds generated for 'chain 'D' and resid 183 through 185' Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 224 through 233 Processing helix chain 'D' and resid 256 through 267 Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 removed outlier: 4.166A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 342 through 355 removed outlier: 4.327A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 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 501 Processing helix chain 'E' and resid 19 through 25 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 Processing helix chain 'E' and resid 75 through 84 Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 126 through 138 Processing helix chain 'E' and resid 159 through 163 Processing helix chain 'E' and resid 174 through 178 Processing helix chain 'E' and resid 183 through 185 No H-bonds generated for 'chain 'E' and resid 183 through 185' Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 224 through 233 Processing helix chain 'E' and resid 256 through 267 Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 removed outlier: 4.139A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 355 removed outlier: 4.297A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 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 501 Processing helix chain 'F' and resid 19 through 25 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 Processing helix chain 'F' and resid 75 through 84 Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 126 through 138 Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 174 through 178 Processing helix chain 'F' and resid 183 through 185 No H-bonds generated for 'chain 'F' and resid 183 through 185' Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 224 through 233 Processing helix chain 'F' and resid 256 through 267 Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 removed outlier: 4.138A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 342 through 355 removed outlier: 4.296A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 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 501 Processing helix chain 'G' and resid 19 through 25 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 Processing helix chain 'G' and resid 75 through 84 Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 126 through 138 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 174 through 178 Processing helix chain 'G' and resid 183 through 185 No H-bonds generated for 'chain 'G' and resid 183 through 185' Processing helix chain 'G' and resid 193 through 205 Processing helix chain 'G' and resid 224 through 233 Processing helix chain 'G' and resid 256 through 267 Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 removed outlier: 4.168A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'G' and resid 342 through 355 removed outlier: 4.296A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 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 501 Processing helix chain 'H' and resid 19 through 25 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 Processing helix chain 'H' and resid 75 through 84 Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 126 through 138 Processing helix chain 'H' and resid 159 through 163 Processing helix chain 'H' and resid 174 through 178 Processing helix chain 'H' and resid 183 through 185 No H-bonds generated for 'chain 'H' and resid 183 through 185' Processing helix chain 'H' and resid 193 through 205 Processing helix chain 'H' and resid 224 through 233 Processing helix chain 'H' and resid 256 through 267 Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 removed outlier: 4.168A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 337 Processing helix chain 'H' and resid 342 through 355 removed outlier: 4.341A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 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 501 Processing sheet with id=AA1, first strand: chain 'A' and resid 35 through 37 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 removed outlier: 6.595A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.678A pdb=" N ILE A 88 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 320 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.554A pdb=" N GLY A 156 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 157 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 212 removed outlier: 6.806A pdb=" N LEU A 209 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE A 221 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE A 211 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 401 through 402 removed outlier: 3.626A pdb=" N SER A 444 " --> pdb=" O THR B 510 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 509 through 510 removed outlier: 3.626A pdb=" N SER D 444 " --> pdb=" O THR A 510 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 37 Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 56 removed outlier: 6.596A pdb=" N ILE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.677A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 320 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ARG B 322 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.554A pdb=" N GLY B 156 " --> pdb=" O ILE B 144 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE B 157 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 208 through 212 removed outlier: 6.806A pdb=" N LEU B 209 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE B 221 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE B 211 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 401 through 402 removed outlier: 3.626A pdb=" N SER B 444 " --> pdb=" O THR C 510 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 37 Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.596A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.677A pdb=" N ILE C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY C 320 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG C 322 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.153A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 142 through 145 removed outlier: 3.566A pdb=" N GLY C 156 " --> pdb=" O ILE C 144 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE C 157 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 208 through 212 removed outlier: 6.806A pdb=" N LEU C 209 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE C 221 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ILE C 211 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 401 through 402 removed outlier: 3.632A pdb=" N SER C 444 " --> pdb=" O THR D 510 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 35 through 37 Processing sheet with id=AC3, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.596A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.677A pdb=" N ILE D 88 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY D 320 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG D 322 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.554A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE D 157 " --> pdb=" O THR D 180 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 208 through 212 removed outlier: 6.806A pdb=" N LEU D 209 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ILE D 221 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE D 211 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 35 through 37 Processing sheet with id=AC8, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.609A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 65 through 67 removed outlier: 3.696A pdb=" N ILE E 88 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE E 90 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY E 320 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG E 322 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.557A pdb=" N GLY E 156 " --> pdb=" O ILE E 144 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE E 157 " --> pdb=" O THR E 180 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 208 through 212 removed outlier: 6.697A pdb=" N LEU E 209 " --> pdb=" O ILE E 221 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE E 221 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE E 211 " --> pdb=" O VAL E 219 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 401 through 402 removed outlier: 3.616A pdb=" N SER E 444 " --> pdb=" O THR F 510 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 509 through 510 removed outlier: 3.616A pdb=" N SER H 444 " --> pdb=" O THR E 510 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 35 through 37 Processing sheet with id=AD6, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.609A pdb=" N ILE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.696A pdb=" N ILE F 88 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY F 320 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG F 322 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.255A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 142 through 145 removed outlier: 3.557A pdb=" N GLY F 156 " --> pdb=" O ILE F 144 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE F 157 " --> pdb=" O THR F 180 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 208 through 212 removed outlier: 6.697A pdb=" N LEU F 209 " --> pdb=" O ILE F 221 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ILE F 221 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ILE F 211 " --> pdb=" O VAL F 219 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'F' and resid 401 through 402 removed outlier: 3.616A pdb=" N SER F 444 " --> pdb=" O THR G 510 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 35 through 37 Processing sheet with id=AE3, first strand: chain 'G' and resid 53 through 56 removed outlier: 6.611A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 65 through 67 removed outlier: 3.695A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY G 320 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG G 322 " --> pdb=" O GLY G 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N MET G 385 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.557A pdb=" N GLY G 156 " --> pdb=" O ILE G 144 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE G 157 " --> pdb=" O THR G 180 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'G' and resid 208 through 212 removed outlier: 6.696A pdb=" N LEU G 209 " --> pdb=" O ILE G 221 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE G 221 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE G 211 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 401 through 402 removed outlier: 3.616A pdb=" N SER G 444 " --> pdb=" O THR H 510 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 35 through 37 Processing sheet with id=AE9, first strand: chain 'H' and resid 53 through 56 removed outlier: 6.611A pdb=" N ILE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.695A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY H 320 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG H 322 " --> pdb=" O GLY H 301 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N ILE H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N MET H 385 " --> pdb=" O ILE H 361 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.557A pdb=" N GLY H 156 " --> pdb=" O ILE H 144 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE H 157 " --> pdb=" O THR H 180 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 208 through 212 removed outlier: 6.696A pdb=" N LEU H 209 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N ILE H 221 " --> pdb=" O LEU H 209 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ILE H 211 " --> pdb=" O VAL H 219 " (cutoff:3.500A) 1168 hydrogen bonds defined for protein. 3222 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: 12.28 Time building geometry restraints manager: 9.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9523 1.34 - 1.45: 3862 1.45 - 1.57: 17231 1.57 - 1.69: 152 1.69 - 1.81: 312 Bond restraints: 31080 Sorted by residual: bond pdb=" N VAL C 350 " pdb=" CA VAL C 350 " ideal model delta sigma weight residual 1.452 1.503 -0.051 1.18e-02 7.18e+03 1.85e+01 bond pdb=" N VAL B 350 " pdb=" CA VAL B 350 " ideal model delta sigma weight residual 1.452 1.503 -0.051 1.18e-02 7.18e+03 1.83e+01 bond pdb=" N VAL A 350 " pdb=" CA VAL A 350 " ideal model delta sigma weight residual 1.452 1.498 -0.046 1.18e-02 7.18e+03 1.53e+01 bond pdb=" C2 IMP F 603 " pdb=" N3 IMP F 603 " ideal model delta sigma weight residual 1.380 1.305 0.075 2.00e-02 2.50e+03 1.41e+01 bond pdb=" C2 IMP G 603 " pdb=" N3 IMP G 603 " ideal model delta sigma weight residual 1.380 1.305 0.075 2.00e-02 2.50e+03 1.41e+01 ... (remaining 31075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 41300 3.13 - 6.26: 775 6.26 - 9.39: 143 9.39 - 12.52: 54 12.52 - 15.65: 16 Bond angle restraints: 42288 Sorted by residual: angle pdb=" PA ATP H 604 " pdb=" O3A ATP H 604 " pdb=" PB ATP H 604 " ideal model delta sigma weight residual 136.83 121.18 15.65 1.00e+00 1.00e+00 2.45e+02 angle pdb=" PA ATP E 604 " pdb=" O3A ATP E 604 " pdb=" PB ATP E 604 " ideal model delta sigma weight residual 136.83 121.20 15.63 1.00e+00 1.00e+00 2.44e+02 angle pdb=" PA ATP F 604 " pdb=" O3A ATP F 604 " pdb=" PB ATP F 604 " ideal model delta sigma weight residual 136.83 121.23 15.60 1.00e+00 1.00e+00 2.43e+02 angle pdb=" PA ATP G 604 " pdb=" O3A ATP G 604 " pdb=" PB ATP G 604 " ideal model delta sigma weight residual 136.83 121.25 15.58 1.00e+00 1.00e+00 2.43e+02 angle pdb=" PA ATP B 604 " pdb=" O3A ATP B 604 " pdb=" PB ATP B 604 " ideal model delta sigma weight residual 136.83 121.65 15.18 1.00e+00 1.00e+00 2.30e+02 ... (remaining 42283 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.95: 17840 33.95 - 67.89: 911 67.89 - 101.84: 169 101.84 - 135.79: 6 135.79 - 169.73: 26 Dihedral angle restraints: 18952 sinusoidal: 8008 harmonic: 10944 Sorted by residual: dihedral pdb=" O3B GTP F 601 " pdb=" O3A GTP F 601 " pdb=" PB GTP F 601 " pdb=" PA GTP F 601 " ideal model delta sinusoidal sigma weight residual -68.92 100.81 -169.73 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O3B GTP G 601 " pdb=" O3A GTP G 601 " pdb=" PB GTP G 601 " pdb=" PA GTP G 601 " ideal model delta sinusoidal sigma weight residual -68.92 100.59 -169.51 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" C8 GTP B 601 " pdb=" C1' GTP B 601 " pdb=" N9 GTP B 601 " pdb=" O4' GTP B 601 " ideal model delta sinusoidal sigma weight residual 104.59 -59.17 163.76 1 2.00e+01 2.50e-03 4.70e+01 ... (remaining 18949 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 4308 0.077 - 0.154: 476 0.154 - 0.231: 37 0.231 - 0.308: 15 0.308 - 0.385: 60 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CA PHE B 24 " pdb=" N PHE B 24 " pdb=" C PHE B 24 " pdb=" CB PHE B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA PHE A 24 " pdb=" N PHE A 24 " pdb=" C PHE A 24 " pdb=" CB PHE A 24 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.67e+00 chirality pdb=" CA PHE H 24 " pdb=" N PHE H 24 " pdb=" C PHE H 24 " pdb=" CB PHE H 24 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.66e+00 ... (remaining 4893 not shown) Planarity restraints: 5208 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER D 122 " -0.049 5.00e-02 4.00e+02 7.34e-02 8.61e+00 pdb=" N PRO D 123 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO D 123 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 123 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 122 " 0.049 5.00e-02 4.00e+02 7.33e-02 8.61e+00 pdb=" N PRO C 123 " -0.127 5.00e-02 4.00e+02 pdb=" CA PRO C 123 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO C 123 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 122 " -0.049 5.00e-02 4.00e+02 7.31e-02 8.55e+00 pdb=" N PRO A 123 " 0.126 5.00e-02 4.00e+02 pdb=" CA PRO A 123 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO A 123 " -0.041 5.00e-02 4.00e+02 ... (remaining 5205 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 10241 2.84 - 3.36: 29431 3.36 - 3.87: 49355 3.87 - 4.39: 60214 4.39 - 4.90: 104744 Nonbonded interactions: 253985 Sorted by model distance: nonbonded pdb=" O ASP E 170 " pdb=" OG1 THR E 173 " model vdw 2.325 3.040 nonbonded pdb=" O ASP G 170 " pdb=" OG1 THR G 173 " model vdw 2.326 3.040 nonbonded pdb=" O ASP F 170 " pdb=" OG1 THR F 173 " model vdw 2.326 3.040 nonbonded pdb=" O ASP H 170 " pdb=" OG1 THR H 173 " model vdw 2.326 3.040 nonbonded pdb=" O VAL G 73 " pdb=" OG1 THR G 74 " model vdw 2.345 3.040 ... (remaining 253980 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.210 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: 0.040 Extract box with map and model: 1.140 Check model and map are aligned: 0.240 Set scattering table: 0.280 Process input model: 72.820 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.210 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:3.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 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 : 0.006 0.075 31080 Z= 0.283 Angle : 1.092 15.647 42288 Z= 0.583 Chirality : 0.063 0.385 4896 Planarity : 0.005 0.073 5208 Dihedral : 20.740 169.733 11976 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.28 % Favored : 96.51 % Rotamer: Outliers : 0.73 % Allowed : 15.98 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: -0.67 (0.14), residues: 3840 helix: -0.24 (0.14), residues: 1392 sheet: -1.25 (0.26), residues: 368 loop : -0.31 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 507 PHE 0.008 0.001 PHE G 41 TYR 0.010 0.001 TYR G 348 ARG 0.003 0.000 ARG A 412 Details of bonding type rmsd hydrogen bonds : bond 0.15891 ( 1168) hydrogen bonds : angle 6.94131 ( 3222) covalent geometry : bond 0.00563 (31080) covalent geometry : angle 1.09187 (42288) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 381 time to evaluate : 3.085 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 outliers start: 23 outliers final: 1 residues processed: 399 average time/residue: 0.4145 time to fit residues: 266.2641 Evaluate side-chains 347 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 346 time to evaluate : 3.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 324 optimal weight: 0.9980 chunk 291 optimal weight: 3.9990 chunk 161 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 196 optimal weight: 0.0270 chunk 155 optimal weight: 5.9990 chunk 300 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 183 optimal weight: 8.9990 chunk 224 optimal weight: 0.9990 chunk 348 optimal weight: 0.9990 overall best weight: 0.8042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 368 GLN B 368 GLN C 368 GLN D 368 GLN E 94 ASN E 368 GLN E 498 GLN F 94 ASN F 368 GLN G 94 ASN G 368 GLN H 94 ASN H 368 GLN H 498 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.158123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.138714 restraints weight = 34019.598| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.12 r_work: 0.3171 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 31080 Z= 0.140 Angle : 0.640 6.078 42288 Z= 0.319 Chirality : 0.046 0.169 4896 Planarity : 0.004 0.051 5208 Dihedral : 17.567 149.416 5138 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.88 % Favored : 95.91 % Rotamer: Outliers : 2.37 % Allowed : 17.15 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.14), residues: 3840 helix: 0.33 (0.14), residues: 1416 sheet: -1.76 (0.24), residues: 424 loop : 0.05 (0.15), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 507 PHE 0.008 0.001 PHE G 35 TYR 0.007 0.001 TYR D 459 ARG 0.002 0.000 ARG H 253 Details of bonding type rmsd hydrogen bonds : bond 0.03366 ( 1168) hydrogen bonds : angle 5.16054 ( 3222) covalent geometry : bond 0.00338 (31080) covalent geometry : angle 0.63960 (42288) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 415 time to evaluate : 3.666 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: C 337 MET cc_start: 0.7736 (mpp) cc_final: 0.7072 (ptp) outliers start: 75 outliers final: 46 residues processed: 452 average time/residue: 0.4602 time to fit residues: 348.4231 Evaluate side-chains 365 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 319 time to evaluate : 4.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 225 THR Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 225 THR Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 225 THR Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 337 MET Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 225 THR Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 417 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 117 optimal weight: 1.9990 chunk 233 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 153 optimal weight: 0.7980 chunk 320 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 87 optimal weight: 7.9990 chunk 376 optimal weight: 7.9990 chunk 305 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 52 optimal weight: 0.7980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS A 230 ASN A 303 ASN B 94 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 171 HIS B 230 ASN B 303 ASN B 368 GLN C 94 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 171 HIS C 230 ASN C 303 ASN C 368 GLN D 94 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 HIS D 230 ASN D 303 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 HIS E 230 ASN E 303 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS F 230 ASN F 303 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 HIS G 230 ASN G 303 ASN G 368 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 171 HIS H 230 ASN H 303 ASN H 368 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.152247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.132029 restraints weight = 34440.055| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.17 r_work: 0.3441 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3319 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 31080 Z= 0.195 Angle : 0.647 5.688 42288 Z= 0.329 Chirality : 0.047 0.158 4896 Planarity : 0.004 0.039 5208 Dihedral : 16.634 147.853 5136 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.21 % Allowed : 4.09 % Favored : 95.70 % Rotamer: Outliers : 4.02 % Allowed : 18.10 % Favored : 77.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 3840 helix: 0.23 (0.14), residues: 1424 sheet: -1.52 (0.26), residues: 312 loop : -0.10 (0.15), residues: 2104 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 507 PHE 0.012 0.002 PHE E 35 TYR 0.009 0.001 TYR D 459 ARG 0.002 0.000 ARG C 341 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 1168) hydrogen bonds : angle 5.07246 ( 3222) covalent geometry : bond 0.00487 (31080) covalent geometry : angle 0.64722 (42288) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 324 time to evaluate : 3.146 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: C 337 MET cc_start: 0.8053 (mpp) cc_final: 0.7378 (ptp) REVERT: D 337 MET cc_start: 0.8128 (mpp) cc_final: 0.7730 (ptp) REVERT: E 337 MET cc_start: 0.8178 (mpp) cc_final: 0.7700 (ptp) REVERT: F 337 MET cc_start: 0.8181 (mpp) cc_final: 0.7703 (ptp) REVERT: H 337 MET cc_start: 0.8178 (mpp) cc_final: 0.7695 (ptp) outliers start: 127 outliers final: 76 residues processed: 409 average time/residue: 0.3772 time to fit residues: 258.2948 Evaluate side-chains 357 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 281 time to evaluate : 3.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 116 THR Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 116 THR Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 305 VAL Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 417 LEU 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 109 optimal weight: 3.9990 chunk 142 optimal weight: 4.9990 chunk 276 optimal weight: 1.9990 chunk 145 optimal weight: 0.0770 chunk 99 optimal weight: 3.9990 chunk 263 optimal weight: 0.9990 chunk 237 optimal weight: 1.9990 chunk 21 optimal weight: 0.0030 chunk 133 optimal weight: 3.9990 chunk 223 optimal weight: 0.9980 chunk 306 optimal weight: 0.9980 overall best weight: 0.6150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 368 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 368 GLN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN E 368 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN F 368 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN H 112 GLN H 303 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.156539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.136180 restraints weight = 33951.028| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.17 r_work: 0.3470 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3342 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31080 Z= 0.109 Angle : 0.559 6.601 42288 Z= 0.279 Chirality : 0.043 0.141 4896 Planarity : 0.004 0.039 5208 Dihedral : 15.556 145.192 5136 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.59 % Favored : 96.20 % Rotamer: Outliers : 3.54 % Allowed : 18.99 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: 0.06 (0.14), residues: 3840 helix: 0.51 (0.14), residues: 1440 sheet: -1.60 (0.26), residues: 360 loop : 0.16 (0.15), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 93 PHE 0.007 0.001 PHE C 35 TYR 0.006 0.001 TYR G 348 ARG 0.002 0.000 ARG F 412 Details of bonding type rmsd hydrogen bonds : bond 0.02874 ( 1168) hydrogen bonds : angle 4.70454 ( 3222) covalent geometry : bond 0.00259 (31080) covalent geometry : angle 0.55865 (42288) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 341 time to evaluate : 4.707 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 325 MET cc_start: 0.9152 (ttt) cc_final: 0.8946 (ttt) REVERT: C 337 MET cc_start: 0.7739 (mpp) cc_final: 0.7471 (ptp) REVERT: D 337 MET cc_start: 0.7817 (mpp) cc_final: 0.7506 (ptp) REVERT: E 337 MET cc_start: 0.7815 (mpp) cc_final: 0.7505 (ptp) REVERT: F 337 MET cc_start: 0.7811 (mpp) cc_final: 0.7492 (ptp) REVERT: H 337 MET cc_start: 0.7811 (mpp) cc_final: 0.7507 (ptp) outliers start: 112 outliers final: 69 residues processed: 415 average time/residue: 0.5100 time to fit residues: 359.4158 Evaluate side-chains 360 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 291 time to evaluate : 3.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 112 GLN Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 200 optimal weight: 0.8980 chunk 237 optimal weight: 2.9990 chunk 302 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 192 optimal weight: 2.9990 chunk 288 optimal weight: 0.0270 chunk 43 optimal weight: 0.9990 chunk 225 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 242 optimal weight: 0.9980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN A 507 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN B 507 HIS ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN C 507 HIS ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 507 HIS ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN E 507 HIS ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN F 507 HIS ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN G 507 HIS H 303 ASN H 507 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.155665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.135171 restraints weight = 33815.922| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.17 r_work: 0.3487 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31080 Z= 0.114 Angle : 0.551 6.921 42288 Z= 0.275 Chirality : 0.043 0.137 4896 Planarity : 0.004 0.037 5208 Dihedral : 15.197 143.552 5136 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.65 % Favored : 96.15 % Rotamer: Outliers : 4.78 % Allowed : 17.63 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.19 (0.14), residues: 3840 helix: 0.63 (0.14), residues: 1448 sheet: -1.49 (0.25), residues: 360 loop : 0.21 (0.15), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS F 507 PHE 0.008 0.001 PHE G 35 TYR 0.007 0.001 TYR B 348 ARG 0.001 0.000 ARG D 412 Details of bonding type rmsd hydrogen bonds : bond 0.02921 ( 1168) hydrogen bonds : angle 4.61121 ( 3222) covalent geometry : bond 0.00277 (31080) covalent geometry : angle 0.55120 (42288) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 353 time to evaluate : 3.192 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 272 VAL cc_start: 0.8916 (OUTLIER) cc_final: 0.8705 (p) REVERT: B 272 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8717 (p) REVERT: C 272 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8736 (p) REVERT: D 272 VAL cc_start: 0.8933 (OUTLIER) cc_final: 0.8728 (p) REVERT: D 337 MET cc_start: 0.7787 (mpp) cc_final: 0.7467 (ptp) REVERT: E 272 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8721 (p) REVERT: E 337 MET cc_start: 0.7782 (mpp) cc_final: 0.7485 (ptp) REVERT: F 272 VAL cc_start: 0.8940 (OUTLIER) cc_final: 0.8714 (p) REVERT: F 337 MET cc_start: 0.7758 (mpp) cc_final: 0.7458 (ptp) REVERT: G 272 VAL cc_start: 0.8938 (OUTLIER) cc_final: 0.8716 (p) REVERT: H 272 VAL cc_start: 0.8942 (OUTLIER) cc_final: 0.8719 (p) REVERT: H 337 MET cc_start: 0.7792 (mpp) cc_final: 0.7510 (ptp) outliers start: 151 outliers final: 103 residues processed: 455 average time/residue: 0.3929 time to fit residues: 293.0954 Evaluate side-chains 408 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 297 time to evaluate : 3.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 507 HIS Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain C residue 507 HIS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 417 LEU 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 254 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 0.3980 chunk 158 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 157 optimal weight: 2.9990 chunk 297 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 337 optimal weight: 0.6980 chunk 17 optimal weight: 0.3980 chunk 218 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 334 GLN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 334 GLN E 94 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN F 94 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN G 94 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN H 112 GLN H 334 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.154959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.134766 restraints weight = 33922.043| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.15 r_work: 0.3443 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3316 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 31080 Z= 0.126 Angle : 0.561 7.501 42288 Z= 0.280 Chirality : 0.043 0.138 4896 Planarity : 0.004 0.034 5208 Dihedral : 15.113 142.809 5136 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.62 % Favored : 96.17 % Rotamer: Outliers : 5.06 % Allowed : 18.32 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 3840 helix: 0.67 (0.14), residues: 1448 sheet: -0.92 (0.28), residues: 312 loop : 0.11 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 507 PHE 0.009 0.001 PHE H 35 TYR 0.007 0.001 TYR C 348 ARG 0.001 0.000 ARG B 412 Details of bonding type rmsd hydrogen bonds : bond 0.02964 ( 1168) hydrogen bonds : angle 4.57736 ( 3222) covalent geometry : bond 0.00309 (31080) covalent geometry : angle 0.56086 (42288) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 477 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 160 poor density : 317 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: symmetry clash revert: symmetry clash REVERT: A 179 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8017 (ptt) REVERT: A 272 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8730 (p) REVERT: B 179 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8045 (ptt) REVERT: B 272 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8749 (p) REVERT: C 179 MET cc_start: 0.8524 (OUTLIER) cc_final: 0.8100 (ptt) REVERT: C 272 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8773 (p) REVERT: D 179 MET cc_start: 0.8507 (OUTLIER) cc_final: 0.8033 (ptt) REVERT: D 337 MET cc_start: 0.7808 (mpp) cc_final: 0.7530 (ptp) REVERT: E 206 LYS cc_start: 0.7708 (OUTLIER) cc_final: 0.7490 (mmtp) REVERT: E 272 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8732 (p) REVERT: F 206 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7490 (mmtp) REVERT: F 272 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8734 (p) REVERT: F 337 MET cc_start: 0.7772 (mpp) cc_final: 0.7572 (ptp) REVERT: G 206 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7505 (mmtp) REVERT: G 272 VAL cc_start: 0.8951 (OUTLIER) cc_final: 0.8726 (p) REVERT: H 206 LYS cc_start: 0.7722 (OUTLIER) cc_final: 0.7498 (mmtp) REVERT: H 272 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8730 (p) outliers start: 160 outliers final: 122 residues processed: 425 average time/residue: 0.4005 time to fit residues: 280.1107 Evaluate side-chains 433 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 296 time to evaluate : 3.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 444 SER Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 272 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 444 SER Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 272 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 507 HIS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR 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 227 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 507 HIS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR 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 227 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain G residue 507 HIS Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 112 GLN 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 227 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 507 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 177 optimal weight: 0.5980 chunk 280 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 chunk 291 optimal weight: 2.9990 chunk 78 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 358 optimal weight: 0.8980 chunk 226 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN E 112 GLN E 303 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN H 94 ASN H 112 GLN H 303 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.155556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.134985 restraints weight = 33729.685| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 1.19 r_work: 0.3457 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 31080 Z= 0.119 Angle : 0.554 7.544 42288 Z= 0.277 Chirality : 0.043 0.143 4896 Planarity : 0.004 0.034 5208 Dihedral : 14.953 142.176 5136 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.57 % Favored : 96.22 % Rotamer: Outliers : 5.16 % Allowed : 18.64 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.33 (0.14), residues: 3840 helix: 0.76 (0.14), residues: 1448 sheet: -0.83 (0.29), residues: 312 loop : 0.13 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 93 PHE 0.008 0.001 PHE C 35 TYR 0.007 0.001 TYR C 348 ARG 0.001 0.000 ARG H 412 Details of bonding type rmsd hydrogen bonds : bond 0.02865 ( 1168) hydrogen bonds : angle 4.52025 ( 3222) covalent geometry : bond 0.00290 (31080) covalent geometry : angle 0.55373 (42288) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 163 poor density : 308 time to evaluate : 3.143 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 179 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8002 (ptt) REVERT: A 272 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8748 (p) REVERT: B 179 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8016 (ptt) REVERT: C 179 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.8014 (ptt) REVERT: D 179 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.7981 (ptt) REVERT: E 206 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7449 (mmtp) REVERT: E 272 VAL cc_start: 0.8965 (OUTLIER) cc_final: 0.8752 (p) REVERT: F 206 LYS cc_start: 0.7663 (OUTLIER) cc_final: 0.7458 (mmtp) REVERT: F 272 VAL cc_start: 0.8964 (OUTLIER) cc_final: 0.8748 (p) REVERT: G 272 VAL cc_start: 0.8957 (OUTLIER) cc_final: 0.8747 (p) REVERT: H 206 LYS cc_start: 0.7652 (OUTLIER) cc_final: 0.7447 (mmtp) REVERT: H 272 VAL cc_start: 0.8955 (OUTLIER) cc_final: 0.8747 (p) outliers start: 163 outliers final: 131 residues processed: 419 average time/residue: 0.4014 time to fit residues: 275.4350 Evaluate side-chains 434 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 291 time to evaluate : 3.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 507 HIS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR 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 227 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 303 ASN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 507 HIS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 303 ASN Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 369 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain G residue 507 HIS Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 112 GLN 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 227 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 303 ASN Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 369 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 507 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 203 optimal weight: 4.9990 chunk 264 optimal weight: 2.9990 chunk 198 optimal weight: 1.9990 chunk 150 optimal weight: 0.9990 chunk 302 optimal weight: 5.9990 chunk 321 optimal weight: 0.0770 chunk 48 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 338 optimal weight: 0.9980 chunk 358 optimal weight: 3.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN C 441 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN E 303 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN H 112 GLN H 303 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.153293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.132374 restraints weight = 34023.785| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.19 r_work: 0.3437 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 31080 Z= 0.152 Angle : 0.578 7.515 42288 Z= 0.290 Chirality : 0.044 0.142 4896 Planarity : 0.004 0.032 5208 Dihedral : 15.082 141.810 5136 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.62 % Favored : 96.17 % Rotamer: Outliers : 5.47 % Allowed : 18.10 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.23 (0.14), residues: 3840 helix: 0.68 (0.14), residues: 1448 sheet: -0.86 (0.29), residues: 312 loop : 0.06 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 507 PHE 0.011 0.001 PHE E 35 TYR 0.008 0.001 TYR D 348 ARG 0.008 0.000 ARG G 136 Details of bonding type rmsd hydrogen bonds : bond 0.03135 ( 1168) hydrogen bonds : angle 4.56500 ( 3222) covalent geometry : bond 0.00379 (31080) covalent geometry : angle 0.57835 (42288) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 286 time to evaluate : 3.044 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 179 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8060 (ptt) REVERT: B 179 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8063 (ptt) REVERT: C 179 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8054 (ptt) REVERT: D 179 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.8037 (ptt) REVERT: E 206 LYS cc_start: 0.7794 (OUTLIER) cc_final: 0.7585 (mmtp) REVERT: E 272 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8787 (p) REVERT: F 206 LYS cc_start: 0.7796 (OUTLIER) cc_final: 0.7589 (mmtp) REVERT: F 272 VAL cc_start: 0.8997 (OUTLIER) cc_final: 0.8776 (p) REVERT: G 136 ARG cc_start: 0.7629 (ttm110) cc_final: 0.7312 (ttm-80) REVERT: G 272 VAL cc_start: 0.9006 (OUTLIER) cc_final: 0.8803 (p) REVERT: H 136 ARG cc_start: 0.7646 (ttm110) cc_final: 0.7328 (ttm-80) REVERT: H 206 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7581 (mmtp) REVERT: H 272 VAL cc_start: 0.9000 (OUTLIER) cc_final: 0.8800 (p) outliers start: 173 outliers final: 120 residues processed: 414 average time/residue: 0.4229 time to fit residues: 291.9756 Evaluate side-chains 418 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 287 time to evaluate : 3.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 303 ASN Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 271 ILE Chi-restraints excluded: chain C residue 303 ASN Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 303 ASN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 444 SER Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR 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 227 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 303 ASN Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 303 ASN Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 303 ASN Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 369 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 112 GLN 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 227 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 303 ASN Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 369 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 386 MET 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 268 optimal weight: 3.9990 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 142 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 290 optimal weight: 0.6980 chunk 241 optimal weight: 4.9990 chunk 382 optimal weight: 0.2980 chunk 65 optimal weight: 0.9990 chunk 207 optimal weight: 0.8980 chunk 73 optimal weight: 0.7980 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.154750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.133863 restraints weight = 33694.556| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 1.18 r_work: 0.3380 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 31080 Z= 0.118 Angle : 0.559 7.965 42288 Z= 0.279 Chirality : 0.043 0.140 4896 Planarity : 0.004 0.036 5208 Dihedral : 14.898 142.199 5136 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.54 % Favored : 96.25 % Rotamer: Outliers : 4.21 % Allowed : 19.18 % Favored : 76.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.35 (0.14), residues: 3840 helix: 0.82 (0.14), residues: 1448 sheet: -0.77 (0.29), residues: 312 loop : 0.09 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 507 PHE 0.008 0.001 PHE H 35 TYR 0.007 0.001 TYR B 348 ARG 0.008 0.000 ARG F 136 Details of bonding type rmsd hydrogen bonds : bond 0.02857 ( 1168) hydrogen bonds : angle 4.50320 ( 3222) covalent geometry : bond 0.00287 (31080) covalent geometry : angle 0.55944 (42288) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 429 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 296 time to evaluate : 3.373 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 179 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7994 (ptt) REVERT: B 179 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8003 (ptt) REVERT: C 179 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.7982 (ptt) REVERT: D 179 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.7965 (ptt) REVERT: E 272 VAL cc_start: 0.8966 (OUTLIER) cc_final: 0.8741 (p) REVERT: F 272 VAL cc_start: 0.8969 (OUTLIER) cc_final: 0.8740 (p) REVERT: G 136 ARG cc_start: 0.7658 (ttm110) cc_final: 0.7341 (ttm-80) REVERT: G 272 VAL cc_start: 0.8977 (OUTLIER) cc_final: 0.8765 (p) REVERT: H 136 ARG cc_start: 0.7655 (ttm110) cc_final: 0.7341 (ttm-80) REVERT: H 272 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8767 (p) outliers start: 133 outliers final: 116 residues processed: 387 average time/residue: 0.3943 time to fit residues: 248.6681 Evaluate side-chains 421 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 297 time to evaluate : 3.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 271 ILE Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 271 ILE Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 507 HIS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 507 HIS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 369 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain G residue 507 HIS Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 369 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 444 SER 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 265 optimal weight: 2.9990 chunk 289 optimal weight: 4.9990 chunk 186 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 317 optimal weight: 3.9990 chunk 42 optimal weight: 0.0980 chunk 339 optimal weight: 1.9990 chunk 223 optimal weight: 5.9990 chunk 8 optimal weight: 0.3980 chunk 225 optimal weight: 0.7980 chunk 138 optimal weight: 0.4980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 HIS B 94 ASN ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS B 303 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 HIS ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS E 137 HIS ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.156717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.136078 restraints weight = 33664.149| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.16 r_work: 0.3449 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 31080 Z= 0.103 Angle : 0.543 8.382 42288 Z= 0.269 Chirality : 0.042 0.262 4896 Planarity : 0.004 0.034 5208 Dihedral : 14.589 141.254 5136 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.23 % Favored : 96.56 % Rotamer: Outliers : 4.02 % Allowed : 19.40 % Favored : 76.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.45 (0.14), residues: 3840 helix: 0.97 (0.14), residues: 1448 sheet: -0.74 (0.30), residues: 312 loop : 0.10 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 507 PHE 0.007 0.001 PHE H 35 TYR 0.009 0.001 TYR E 411 ARG 0.006 0.000 ARG G 136 Details of bonding type rmsd hydrogen bonds : bond 0.02648 ( 1168) hydrogen bonds : angle 4.42803 ( 3222) covalent geometry : bond 0.00247 (31080) covalent geometry : angle 0.54263 (42288) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7680 Ramachandran restraints generated. 3840 Oldfield, 0 Emsley, 3840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 447 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 320 time to evaluate : 3.366 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 179 MET cc_start: 0.8566 (OUTLIER) cc_final: 0.7889 (ptt) REVERT: B 94 ASN cc_start: 0.9049 (OUTLIER) cc_final: 0.8844 (t0) REVERT: C 179 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.7874 (ptt) REVERT: D 179 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.7856 (ptt) REVERT: E 272 VAL cc_start: 0.8932 (OUTLIER) cc_final: 0.8713 (p) REVERT: F 272 VAL cc_start: 0.8937 (OUTLIER) cc_final: 0.8722 (p) REVERT: G 272 VAL cc_start: 0.8939 (OUTLIER) cc_final: 0.8722 (p) REVERT: H 136 ARG cc_start: 0.7667 (ttm110) cc_final: 0.7408 (ttm-80) REVERT: H 272 VAL cc_start: 0.8936 (OUTLIER) cc_final: 0.8728 (p) outliers start: 127 outliers final: 117 residues processed: 404 average time/residue: 0.4053 time to fit residues: 268.4558 Evaluate side-chains 422 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 297 time to evaluate : 3.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 VAL Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 330 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 13 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 94 ASN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 330 ILE Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain C residue 13 VAL Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 37 ILE Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 179 MET Chi-restraints excluded: chain C residue 183 ILE Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 369 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 414 MET Chi-restraints excluded: chain C residue 448 GLN Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 158 VAL Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 507 HIS Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 37 ILE Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 183 ILE Chi-restraints excluded: chain E residue 227 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 507 HIS Chi-restraints excluded: chain F residue 13 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 37 ILE Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 183 ILE Chi-restraints excluded: chain F residue 227 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 272 VAL Chi-restraints excluded: chain F residue 329 SER Chi-restraints excluded: chain F residue 330 ILE Chi-restraints excluded: chain F residue 369 THR Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain F residue 507 HIS Chi-restraints excluded: chain G residue 13 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 37 ILE Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 158 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 272 VAL Chi-restraints excluded: chain G residue 329 SER Chi-restraints excluded: chain G residue 330 ILE Chi-restraints excluded: chain G residue 369 THR Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 448 GLN Chi-restraints excluded: chain G residue 507 HIS Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 183 ILE Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 272 VAL Chi-restraints excluded: chain H residue 329 SER Chi-restraints excluded: chain H residue 330 ILE Chi-restraints excluded: chain H residue 369 THR Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 444 SER Chi-restraints excluded: chain H residue 448 GLN Chi-restraints excluded: chain H residue 507 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 334 optimal weight: 1.9990 chunk 104 optimal weight: 0.5980 chunk 56 optimal weight: 0.1980 chunk 16 optimal weight: 0.6980 chunk 277 optimal weight: 4.9990 chunk 186 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 225 optimal weight: 0.7980 chunk 373 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 ASN ** A 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 HIS ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 HIS D 94 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 137 HIS E 137 HIS ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.156484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.135528 restraints weight = 33646.505| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.17 r_work: 0.3484 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 31080 Z= 0.107 Angle : 0.550 8.429 42288 Z= 0.271 Chirality : 0.042 0.137 4896 Planarity : 0.004 0.034 5208 Dihedral : 14.462 140.140 5136 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.31 % Favored : 96.48 % Rotamer: Outliers : 4.05 % Allowed : 19.68 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.46 (0.14), residues: 3840 helix: 0.99 (0.14), residues: 1448 sheet: -0.72 (0.30), residues: 312 loop : 0.10 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 93 PHE 0.007 0.001 PHE G 35 TYR 0.012 0.001 TYR H 411 ARG 0.008 0.000 ARG G 136 Details of bonding type rmsd hydrogen bonds : bond 0.02698 ( 1168) hydrogen bonds : angle 4.41786 ( 3222) covalent geometry : bond 0.00261 (31080) covalent geometry : angle 0.54989 (42288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14570.56 seconds wall clock time: 252 minutes 16.07 seconds (15136.07 seconds total)