Starting phenix.real_space_refine on Wed May 28 13:06:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7q_41989/05_2025/8u7q_41989.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7q_41989/05_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_41989/05_2025/8u7q_41989.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7q_41989/05_2025/8u7q_41989.map" model { file = "/net/cci-nas-00/data/ceres_data/8u7q_41989/05_2025/8u7q_41989.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7q_41989/05_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 17.29, per 1000 atoms: 0.57 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: 8.00 Conformation dependent library (CDL) restraints added in 3.6 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: 4.12 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: 12.97 Time building geometry restraints manager: 9.19 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: 0.11 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: 5.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.170 Check model and map are aligned: 0.210 Set scattering table: 0.260 Process input model: 68.760 Find NCS groups from input model: 1.350 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.210 ------------------------------------------------------------------------------- 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 : 3.037 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: 0.4122 time to fit residues: 263.7862 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 : 3.326 ------------------------------------------------------------------------------- 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 = 34019.595| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.12 r_work: 0.3481 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 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 : 3.116 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: 0.7769 (mpp) cc_final: 0.7015 (ptp) outliers start: 75 outliers final: 46 residues processed: 452 average time/residue: 0.3852 time to fit residues: 288.3407 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 : 3.509 ------------------------------------------------------------------------------- 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: 0.6980 chunk 233 optimal weight: 9.9990 chunk 80 optimal weight: 1.9990 chunk 153 optimal weight: 0.5980 chunk 320 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 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: 0.9782 ------------------------------------------------------------------------------- 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 A 368 GLN 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 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 D 368 GLN E 112 GLN E 171 HIS E 230 ASN E 303 ASN E 368 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 HIS F 230 ASN F 303 ASN F 368 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 HIS G 230 ASN G 303 ASN G 368 GLN H 112 GLN H 171 HIS H 230 ASN H 303 ASN H 368 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.155727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.136001 restraints weight = 34192.589| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.14 r_work: 0.3453 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 31080 Z= 0.141 Angle : 0.598 5.873 42288 Z= 0.301 Chirality : 0.044 0.144 4896 Planarity : 0.004 0.039 5208 Dihedral : 16.244 147.913 5136 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.91 % Favored : 95.89 % Rotamer: Outliers : 3.67 % Allowed : 18.48 % Favored : 77.85 % 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: -0.05 (0.14), residues: 3840 helix: 0.42 (0.14), residues: 1424 sheet: -1.86 (0.26), residues: 344 loop : 0.13 (0.15), residues: 2072 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 93 PHE 0.009 0.001 PHE F 35 TYR 0.007 0.001 TYR E 32 ARG 0.002 0.000 ARG B 412 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 1168) hydrogen bonds : angle 4.91638 ( 3222) covalent geometry : bond 0.00346 (31080) covalent geometry : angle 0.59773 (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 449 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 333 time to evaluate : 3.353 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: 0.7940 (mpp) cc_final: 0.7525 (ptp) REVERT: D 337 MET cc_start: 0.8041 (mpp) cc_final: 0.7638 (ptp) REVERT: E 337 MET cc_start: 0.8093 (mpp) cc_final: 0.7639 (ptp) REVERT: F 337 MET cc_start: 0.7996 (mpp) cc_final: 0.7502 (ptp) REVERT: H 337 MET cc_start: 0.8005 (mpp) cc_final: 0.7525 (ptp) outliers start: 116 outliers final: 64 residues processed: 403 average time/residue: 0.3674 time to fit residues: 248.8287 Evaluate side-chains 357 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 293 time to evaluate : 3.176 ------------------------------------------------------------------------------- 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 183 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 370 VAL 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 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 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 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 C residue 448 GLN 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 370 VAL 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 112 GLN 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 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 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 112 GLN 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 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: 0.9980 chunk 142 optimal weight: 0.8980 chunk 276 optimal weight: 0.9980 chunk 145 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 263 optimal weight: 4.9990 chunk 237 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 306 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 303 ASN D 334 GLN D 507 HIS E 303 ASN E 507 HIS ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 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: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.153575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.133292 restraints weight = 34201.152| |-----------------------------------------------------------------------------| r_work (start): 0.3597 rms_B_bonded: 1.15 r_work: 0.3424 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 31080 Z= 0.153 Angle : 0.596 7.745 42288 Z= 0.299 Chirality : 0.045 0.150 4896 Planarity : 0.004 0.039 5208 Dihedral : 15.794 145.388 5136 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.93 % Favored : 95.86 % Rotamer: Outliers : 4.43 % Allowed : 17.97 % Favored : 77.59 % 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: -0.01 (0.14), residues: 3840 helix: 0.37 (0.14), residues: 1440 sheet: -1.16 (0.27), residues: 312 loop : 0.06 (0.15), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS G 507 PHE 0.011 0.001 PHE H 35 TYR 0.008 0.001 TYR D 348 ARG 0.001 0.000 ARG B 412 Details of bonding type rmsd hydrogen bonds : bond 0.03338 ( 1168) hydrogen bonds : angle 4.80794 ( 3222) covalent geometry : bond 0.00381 (31080) covalent geometry : angle 0.59581 (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 454 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 314 time to evaluate : 3.514 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: 0.7855 (mpp) cc_final: 0.7557 (ptp) REVERT: D 337 MET cc_start: 0.7816 (mpp) cc_final: 0.7599 (ptp) REVERT: E 337 MET cc_start: 0.7852 (mpp) cc_final: 0.7516 (ptp) REVERT: F 337 MET cc_start: 0.7783 (mpp) cc_final: 0.7546 (ptp) REVERT: H 337 MET cc_start: 0.7832 (mpp) cc_final: 0.7593 (ptp) outliers start: 140 outliers final: 94 residues processed: 411 average time/residue: 0.4011 time to fit residues: 274.7511 Evaluate side-chains 381 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 287 time to evaluate : 3.154 ------------------------------------------------------------------------------- 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 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 330 ILE 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 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 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 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 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 13 VAL Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 96 THR 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 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 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 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 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 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 330 ILE 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 200 optimal weight: 0.0870 chunk 237 optimal weight: 0.7980 chunk 302 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 chunk 225 optimal weight: 2.9990 chunk 15 optimal weight: 0.0370 chunk 242 optimal weight: 1.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- 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 507 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 507 HIS C 94 ASN ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 507 HIS ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 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 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.157612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.137617 restraints weight = 33613.609| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 1.13 r_work: 0.3457 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 31080 Z= 0.102 Angle : 0.542 6.822 42288 Z= 0.269 Chirality : 0.043 0.140 4896 Planarity : 0.003 0.038 5208 Dihedral : 15.064 143.424 5136 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.41 % Favored : 96.38 % Rotamer: Outliers : 4.46 % Allowed : 18.26 % Favored : 77.28 % 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: 0.37 (0.14), residues: 3840 helix: 0.66 (0.14), residues: 1448 sheet: 0.07 (0.34), residues: 232 loop : 0.10 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS C 507 PHE 0.006 0.001 PHE G 35 TYR 0.006 0.001 TYR D 411 ARG 0.002 0.000 ARG D 412 Details of bonding type rmsd hydrogen bonds : bond 0.02737 ( 1168) hydrogen bonds : angle 4.60162 ( 3222) covalent geometry : bond 0.00241 (31080) covalent geometry : angle 0.54228 (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 510 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 369 time to evaluate : 3.397 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: 0.8865 (OUTLIER) cc_final: 0.8653 (p) REVERT: A 384 VAL cc_start: 0.9045 (OUTLIER) cc_final: 0.8633 (m) REVERT: B 272 VAL cc_start: 0.8876 (OUTLIER) cc_final: 0.8661 (p) REVERT: B 384 VAL cc_start: 0.9069 (OUTLIER) cc_final: 0.8633 (m) REVERT: C 272 VAL cc_start: 0.8888 (OUTLIER) cc_final: 0.8677 (p) REVERT: C 384 VAL cc_start: 0.9077 (OUTLIER) cc_final: 0.8642 (m) REVERT: D 272 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8679 (p) REVERT: D 384 VAL cc_start: 0.9053 (OUTLIER) cc_final: 0.8637 (m) REVERT: E 272 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8680 (p) REVERT: E 337 MET cc_start: 0.7812 (mpp) cc_final: 0.7552 (ptp) REVERT: F 272 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8678 (p) REVERT: G 272 VAL cc_start: 0.8917 (OUTLIER) cc_final: 0.8684 (p) REVERT: H 272 VAL cc_start: 0.8914 (OUTLIER) cc_final: 0.8681 (p) outliers start: 141 outliers final: 86 residues processed: 467 average time/residue: 0.3745 time to fit residues: 289.9003 Evaluate side-chains 394 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 296 time to evaluate : 3.313 ------------------------------------------------------------------------------- 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 96 THR Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 183 ILE 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 384 VAL Chi-restraints excluded: chain A residue 448 GLN Chi-restraints excluded: chain A residue 507 HIS 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 272 VAL Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 448 GLN Chi-restraints excluded: chain B residue 507 HIS 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 272 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 384 VAL 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 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 272 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 448 GLN Chi-restraints excluded: chain D residue 507 HIS 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 270 VAL Chi-restraints excluded: chain E residue 272 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 E residue 507 HIS 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 383 THR 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 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 370 VAL 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 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 370 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 254 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 157 optimal weight: 0.6980 chunk 297 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 337 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 218 optimal weight: 3.9990 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 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 94 ASN ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 303 ASN G 94 ASN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN H 94 ASN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.155359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.134995 restraints weight = 33824.851| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.12 r_work: 0.3443 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3320 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 31080 Z= 0.127 Angle : 0.560 7.488 42288 Z= 0.279 Chirality : 0.043 0.138 4896 Planarity : 0.004 0.034 5208 Dihedral : 15.044 142.392 5136 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.46 % Favored : 96.33 % Rotamer: Outliers : 5.19 % Allowed : 17.85 % Favored : 76.96 % 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: 0.27 (0.14), residues: 3840 helix: 0.69 (0.14), residues: 1448 sheet: -0.91 (0.28), residues: 312 loop : 0.12 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.001 HIS C 507 PHE 0.009 0.001 PHE E 35 TYR 0.008 0.001 TYR C 348 ARG 0.003 0.000 ARG E 493 Details of bonding type rmsd hydrogen bonds : bond 0.02958 ( 1168) hydrogen bonds : angle 4.56578 ( 3222) covalent geometry : bond 0.00313 (31080) covalent geometry : angle 0.56031 (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 486 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 322 time to evaluate : 3.117 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: 0.8498 (OUTLIER) cc_final: 0.8025 (ptt) REVERT: B 179 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8035 (ptt) REVERT: B 325 MET cc_start: 0.9305 (ttt) cc_final: 0.9094 (ttt) REVERT: C 179 MET cc_start: 0.8516 (OUTLIER) cc_final: 0.8037 (ptt) REVERT: D 179 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8023 (ptt) REVERT: E 206 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7486 (mmtp) REVERT: E 272 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8731 (p) REVERT: E 337 MET cc_start: 0.7815 (mpp) cc_final: 0.7548 (ptp) REVERT: E 384 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8630 (m) REVERT: F 206 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7501 (mmtp) REVERT: F 272 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8725 (p) REVERT: F 384 VAL cc_start: 0.8943 (OUTLIER) cc_final: 0.8632 (m) REVERT: G 206 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.7508 (mmtp) REVERT: G 272 VAL cc_start: 0.8952 (OUTLIER) cc_final: 0.8738 (p) REVERT: H 206 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7494 (mmtp) REVERT: H 272 VAL cc_start: 0.8947 (OUTLIER) cc_final: 0.8731 (p) outliers start: 164 outliers final: 124 residues processed: 434 average time/residue: 0.4272 time to fit residues: 307.7660 Evaluate side-chains 432 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 294 time to evaluate : 3.445 ------------------------------------------------------------------------------- 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 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 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 330 ILE 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 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 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 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 384 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 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 384 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 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 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 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 330 ILE 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: 2.9990 chunk 280 optimal weight: 10.0000 chunk 167 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 307 optimal weight: 3.9990 chunk 291 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 358 optimal weight: 2.9990 chunk 226 optimal weight: 0.0670 overall best weight: 1.1924 ------------------------------------------------------------------------------- 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 A 507 HIS ** B 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 GLN B 507 HIS ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 441 GLN C 507 HIS ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.152909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.131915 restraints weight = 33925.121| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 1.20 r_work: 0.3437 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 31080 Z= 0.152 Angle : 0.588 7.266 42288 Z= 0.295 Chirality : 0.045 0.148 4896 Planarity : 0.004 0.032 5208 Dihedral : 15.237 142.384 5136 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.62 % Favored : 96.17 % Rotamer: Outliers : 4.46 % Allowed : 19.37 % Favored : 76.17 % 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: 0.18 (0.14), residues: 3840 helix: 0.63 (0.14), residues: 1448 sheet: -0.90 (0.28), residues: 312 loop : 0.04 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 507 PHE 0.011 0.001 PHE H 35 TYR 0.008 0.001 TYR B 459 ARG 0.002 0.000 ARG F 493 Details of bonding type rmsd hydrogen bonds : bond 0.03248 ( 1168) hydrogen bonds : angle 4.62797 ( 3222) covalent geometry : bond 0.00379 (31080) covalent geometry : angle 0.58811 (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 436 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 295 time to evaluate : 3.655 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 136 ARG cc_start: 0.7427 (ttm-80) cc_final: 0.7210 (ttm-80) REVERT: A 179 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8080 (ptt) REVERT: B 136 ARG cc_start: 0.7409 (ttm-80) cc_final: 0.7195 (ttm-80) REVERT: B 179 MET cc_start: 0.8582 (OUTLIER) cc_final: 0.8077 (ptt) REVERT: C 179 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8111 (ptt) REVERT: C 184 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7894 (tm-30) REVERT: D 136 ARG cc_start: 0.7381 (ttm-80) cc_final: 0.7162 (ttm-80) REVERT: D 179 MET cc_start: 0.8584 (OUTLIER) cc_final: 0.8077 (ptt) REVERT: E 179 MET cc_start: 0.8565 (OUTLIER) cc_final: 0.8133 (ptt) REVERT: E 206 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7590 (mmtp) REVERT: E 384 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8687 (m) REVERT: F 206 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7572 (mmtp) REVERT: F 384 VAL cc_start: 0.8994 (OUTLIER) cc_final: 0.8687 (m) REVERT: G 206 LYS cc_start: 0.7785 (OUTLIER) cc_final: 0.7578 (mmtp) REVERT: H 206 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7592 (mmtp) outliers start: 141 outliers final: 113 residues processed: 390 average time/residue: 0.3939 time to fit residues: 250.9945 Evaluate side-chains 400 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 276 time to evaluate : 3.571 ------------------------------------------------------------------------------- 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 444 SER 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 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 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 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 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 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 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 179 MET 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 330 ILE Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 384 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 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 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 384 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 206 LYS Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 270 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 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 206 LYS Chi-restraints excluded: chain H residue 227 LEU Chi-restraints excluded: chain H residue 270 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 417 LEU Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 203 optimal weight: 3.9990 chunk 264 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 150 optimal weight: 0.5980 chunk 302 optimal weight: 0.9990 chunk 321 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 338 optimal weight: 0.6980 chunk 358 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 277 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** E 112 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 GLN H 303 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.154536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.133581 restraints weight = 33933.366| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 1.19 r_work: 0.3404 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3160 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= 0.121 Angle : 0.560 7.884 42288 Z= 0.278 Chirality : 0.043 0.140 4896 Planarity : 0.004 0.033 5208 Dihedral : 14.900 142.114 5136 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.54 % Favored : 96.25 % Rotamer: Outliers : 4.81 % Allowed : 19.02 % Favored : 76.17 % 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: 0.78 (0.14), residues: 1448 sheet: -0.79 (0.29), residues: 312 loop : 0.11 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 137 PHE 0.008 0.001 PHE H 35 TYR 0.007 0.001 TYR C 459 ARG 0.008 0.000 ARG F 136 Details of bonding type rmsd hydrogen bonds : bond 0.02864 ( 1168) hydrogen bonds : angle 4.52744 ( 3222) covalent geometry : bond 0.00298 (31080) covalent geometry : angle 0.56015 (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 451 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 299 time to evaluate : 3.344 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: 0.8542 (OUTLIER) cc_final: 0.7978 (ptt) REVERT: B 179 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7976 (ptt) REVERT: C 136 ARG cc_start: 0.7619 (ttm110) cc_final: 0.7299 (ttm-80) REVERT: C 179 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.7986 (ptt) REVERT: D 179 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.7960 (ptt) REVERT: E 136 ARG cc_start: 0.7727 (ttm110) cc_final: 0.7390 (ttm-80) REVERT: E 272 VAL cc_start: 0.8968 (OUTLIER) cc_final: 0.8756 (p) REVERT: F 136 ARG cc_start: 0.7689 (ttm110) cc_final: 0.7357 (ttm-80) REVERT: F 179 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8009 (ptt) REVERT: F 272 VAL cc_start: 0.8970 (OUTLIER) cc_final: 0.8757 (p) REVERT: G 179 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7992 (ptt) REVERT: G 272 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8762 (p) REVERT: H 136 ARG cc_start: 0.7718 (ttm110) cc_final: 0.7384 (ttm-80) REVERT: H 179 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8000 (ptt) REVERT: H 272 VAL cc_start: 0.8978 (OUTLIER) cc_final: 0.8771 (p) outliers start: 152 outliers final: 119 residues processed: 403 average time/residue: 0.4018 time to fit residues: 263.9554 Evaluate side-chains 415 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 285 time to evaluate : 3.628 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 112 GLN 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 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 179 MET 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 179 MET 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 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 179 MET 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 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 Chi-restraints excluded: chain H residue 507 HIS 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: 0.9990 chunk 58 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 231 optimal weight: 5.9990 chunk 290 optimal weight: 2.9990 chunk 241 optimal weight: 4.9990 chunk 382 optimal weight: 0.9990 chunk 65 optimal weight: 0.7980 chunk 207 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- 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** ** E 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 137 HIS ** H 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.152190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.131162 restraints weight = 33966.681| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.18 r_work: 0.3422 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 31080 Z= 0.165 Angle : 0.592 7.826 42288 Z= 0.296 Chirality : 0.045 0.145 4896 Planarity : 0.004 0.037 5208 Dihedral : 15.059 141.478 5136 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.75 % Favored : 96.04 % Rotamer: Outliers : 4.21 % Allowed : 19.08 % Favored : 76.71 % 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: 0.16 (0.14), residues: 3840 helix: 0.65 (0.14), residues: 1448 sheet: -0.87 (0.28), residues: 312 loop : -0.01 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 137 PHE 0.012 0.001 PHE F 35 TYR 0.013 0.001 TYR F 411 ARG 0.008 0.000 ARG A 136 Details of bonding type rmsd hydrogen bonds : bond 0.03224 ( 1168) hydrogen bonds : angle 4.58663 ( 3222) covalent geometry : bond 0.00415 (31080) covalent geometry : angle 0.59217 (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 420 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 287 time to evaluate : 3.470 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 136 ARG cc_start: 0.7691 (ttm110) cc_final: 0.7434 (ttm-80) REVERT: A 179 MET cc_start: 0.8575 (OUTLIER) cc_final: 0.8017 (ptt) REVERT: B 179 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8038 (ptt) REVERT: C 136 ARG cc_start: 0.7762 (ttm110) cc_final: 0.7502 (ttm-80) REVERT: C 179 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8056 (ptt) REVERT: D 136 ARG cc_start: 0.7684 (ttm110) cc_final: 0.7426 (ttm-80) REVERT: D 179 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.8016 (ptt) REVERT: E 179 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8091 (ptt) REVERT: E 272 VAL cc_start: 0.9025 (OUTLIER) cc_final: 0.8804 (p) REVERT: F 179 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8038 (ptt) REVERT: F 272 VAL cc_start: 0.9024 (OUTLIER) cc_final: 0.8798 (p) REVERT: G 179 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8037 (ptt) REVERT: G 272 VAL cc_start: 0.9029 (OUTLIER) cc_final: 0.8813 (p) REVERT: H 179 MET cc_start: 0.8630 (OUTLIER) cc_final: 0.8045 (ptt) REVERT: H 272 VAL cc_start: 0.9031 (OUTLIER) cc_final: 0.8813 (p) outliers start: 133 outliers final: 115 residues processed: 377 average time/residue: 0.3999 time to fit residues: 247.3089 Evaluate side-chains 405 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 278 time to evaluate : 3.367 ------------------------------------------------------------------------------- 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 444 SER 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 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 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 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 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 179 MET 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 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 179 MET 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 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 179 MET 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 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 179 MET 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 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=1.00 ------------------------------------------------------------------------------- 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: 0.0870 chunk 79 optimal weight: 0.5980 chunk 317 optimal weight: 0.8980 chunk 42 optimal weight: 0.0670 chunk 339 optimal weight: 0.8980 chunk 223 optimal weight: 0.8980 chunk 8 optimal weight: 0.4980 chunk 225 optimal weight: 0.5980 chunk 138 optimal weight: 0.2980 overall best weight: 0.3096 ------------------------------------------------------------------------------- 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 277 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** C 303 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN E 137 HIS ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 334 GLN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 334 GLN ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 334 GLN H 112 GLN H 137 HIS H 334 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.157287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.136469 restraints weight = 33611.059| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.17 r_work: 0.3495 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 31080 Z= 0.096 Angle : 0.546 8.529 42288 Z= 0.271 Chirality : 0.042 0.195 4896 Planarity : 0.004 0.035 5208 Dihedral : 14.533 142.160 5136 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.21 % Allowed : 2.76 % Favored : 97.03 % Rotamer: Outliers : 3.70 % Allowed : 19.94 % Favored : 76.36 % 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: 1.00 (0.15), residues: 1440 sheet: -0.73 (0.30), residues: 312 loop : 0.09 (0.15), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 93 PHE 0.005 0.001 PHE G 490 TYR 0.011 0.001 TYR G 411 ARG 0.009 0.000 ARG B 136 Details of bonding type rmsd hydrogen bonds : bond 0.02529 ( 1168) hydrogen bonds : angle 4.42448 ( 3222) covalent geometry : bond 0.00221 (31080) covalent geometry : angle 0.54623 (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 440 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 323 time to evaluate : 3.551 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 136 ARG cc_start: 0.7668 (ttm110) cc_final: 0.7403 (ttm-80) REVERT: B 136 ARG cc_start: 0.7714 (ttm110) cc_final: 0.7420 (ttm-80) REVERT: C 136 ARG cc_start: 0.7720 (ttm110) cc_final: 0.7460 (ttm-80) REVERT: C 179 MET cc_start: 0.8525 (OUTLIER) cc_final: 0.7856 (ptt) REVERT: D 136 ARG cc_start: 0.7652 (ttm110) cc_final: 0.7384 (ttm-80) REVERT: E 179 MET cc_start: 0.8562 (OUTLIER) cc_final: 0.7874 (ptt) REVERT: E 272 VAL cc_start: 0.8908 (OUTLIER) cc_final: 0.8691 (p) REVERT: F 179 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7858 (ptt) REVERT: F 272 VAL cc_start: 0.8911 (OUTLIER) cc_final: 0.8690 (p) REVERT: G 179 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.7877 (ptt) REVERT: G 272 VAL cc_start: 0.8929 (OUTLIER) cc_final: 0.8714 (p) REVERT: H 179 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.7870 (ptt) REVERT: H 272 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8698 (p) outliers start: 117 outliers final: 101 residues processed: 397 average time/residue: 0.4002 time to fit residues: 260.4037 Evaluate side-chains 396 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 286 time to evaluate : 3.325 ------------------------------------------------------------------------------- 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 227 LEU 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 96 THR Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 227 LEU 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 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 227 LEU 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 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 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 444 SER 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 179 MET 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 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 179 MET Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 272 VAL 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 414 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 179 MET 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 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 179 MET 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 384 random chunks: chunk 334 optimal weight: 2.9990 chunk 104 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 16 optimal weight: 0.0770 chunk 277 optimal weight: 5.9990 chunk 186 optimal weight: 0.6980 chunk 194 optimal weight: 2.9990 chunk 225 optimal weight: 0.7980 chunk 373 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 1 optimal weight: 1.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- 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** ** C 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 HIS ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 137 HIS ** G 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.154198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.133131 restraints weight = 33795.533| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.23 r_work: 0.3456 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3422 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= 0.127 Angle : 0.572 8.350 42288 Z= 0.282 Chirality : 0.043 0.141 4896 Planarity : 0.004 0.038 5208 Dihedral : 14.660 140.015 5136 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.21 % Allowed : 3.75 % Favored : 96.04 % Rotamer: Outliers : 3.96 % Allowed : 19.43 % 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: 0.34 (0.14), residues: 3840 helix: 0.91 (0.14), residues: 1448 sheet: -0.77 (0.29), residues: 312 loop : 0.01 (0.15), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 288 PHE 0.009 0.001 PHE G 35 TYR 0.011 0.001 TYR E 411 ARG 0.009 0.000 ARG E 136 Details of bonding type rmsd hydrogen bonds : bond 0.02920 ( 1168) hydrogen bonds : angle 4.48622 ( 3222) covalent geometry : bond 0.00315 (31080) covalent geometry : angle 0.57189 (42288) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13742.28 seconds wall clock time: 239 minutes 32.78 seconds (14372.78 seconds total)