Starting phenix.real_space_refine on Thu Mar 21 19:13:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8f_29848/03_2024/8g8f_29848_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8f_29848/03_2024/8g8f_29848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8f_29848/03_2024/8g8f_29848.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8f_29848/03_2024/8g8f_29848.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8f_29848/03_2024/8g8f_29848_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g8f_29848/03_2024/8g8f_29848_updated.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.280 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 168 5.16 5 C 19248 2.51 5 N 5328 2.21 5 O 6096 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 47": "OD1" <-> "OD2" Residue "A GLU 103": "OE1" <-> "OE2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 15": "OD1" <-> "OD2" Residue "B ASP 47": "OD1" <-> "OD2" Residue "B GLU 103": "OE1" <-> "OE2" Residue "B GLU 399": "OE1" <-> "OE2" Residue "B PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 470": "OD1" <-> "OD2" Residue "C ASP 15": "OD1" <-> "OD2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C GLU 177": "OE1" <-> "OE2" Residue "C GLU 352": "OE1" <-> "OE2" Residue "C ASP 470": "OD1" <-> "OD2" Residue "C TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 47": "OD1" <-> "OD2" Residue "D ASP 261": "OD1" <-> "OD2" Residue "D ASP 292": "OD1" <-> "OD2" Residue "D GLU 352": "OE1" <-> "OE2" Residue "D PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 487": "OE1" <-> "OE2" Residue "D GLU 510": "OE1" <-> "OE2" Residue "E ASP 15": "OD1" <-> "OD2" Residue "E ASP 47": "OD1" <-> "OD2" Residue "E ASP 261": "OD1" <-> "OD2" Residue "E GLU 352": "OE1" <-> "OE2" Residue "E TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 47": "OD1" <-> "OD2" Residue "F GLU 103": "OE1" <-> "OE2" Residue "F ASP 184": "OD1" <-> "OD2" Residue "F ASP 261": "OD1" <-> "OD2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 510": "OE1" <-> "OE2" Residue "G ASP 47": "OD1" <-> "OD2" Residue "G GLU 103": "OE1" <-> "OE2" Residue "G TYR 289": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 15": "OD1" <-> "OD2" Residue "H ASP 47": "OD1" <-> "OD2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "H GLU 170": "OE1" <-> "OE2" Residue "H GLU 176": "OE1" <-> "OE2" Residue "H GLU 177": "OE1" <-> "OE2" Residue "H ASP 184": "OD1" <-> "OD2" Residue "H ASP 269": "OD1" <-> "OD2" Residue "H ASP 274": "OD1" <-> "OD2" Residue "H PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 487": "OE1" <-> "OE2" Residue "H TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 510": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 30912 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "B" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "C" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "D" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "E" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "F" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "G" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "H" Number of atoms: 3735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 491, 3735 Classifications: {'peptide': 491} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 17, 'TRANS': 472} Chain breaks: 1 Chain: "A" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "B" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "D" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "F" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Chain: "H" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 129 Unusual residues: {'ATP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 3} Modifications used: {'rna3p': 1} Link IDs: {None: 3} Time building chain proxies: 16.43, per 1000 atoms: 0.53 Number of scatterers: 30912 At special positions: 0 Unit cell: (160.17, 161.856, 133.194, 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 168 16.00 P 72 15.00 O 6096 8.00 N 5328 7.00 C 19248 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 - 3.50 Amino acid : False - 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=12, symmetry=0 Number of additional bonds: simple=12, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.68 Conformation dependent library (CDL) restraints added in 5.5 seconds 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7136 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 146 helices and 48 sheets defined 33.4% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.84 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 97 through 109 Processing helix chain 'A' and resid 127 through 135 removed outlier: 5.157A pdb=" N GLU A 132 " --> pdb=" O ASP A 129 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N LYS A 134 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 204 removed outlier: 3.936A pdb=" N ARG A 203 " --> pdb=" O GLU A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 228 Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.895A pdb=" N TYR A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 343 through 357 removed outlier: 4.121A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N PHE A 357 " --> pdb=" O TYR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 417 through 420 No H-bonds generated for 'chain 'A' and resid 417 through 420' Processing helix chain 'A' and resid 453 through 471 Proline residue: A 458 - end of helix Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 495 through 501 Processing helix chain 'B' and resid 20 through 25 Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 97 through 109 Processing helix chain 'B' and resid 127 through 135 removed outlier: 4.356A pdb=" N GLU B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ALA B 133 " --> pdb=" O ASP B 129 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N LYS B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ALA B 135 " --> pdb=" O PHE B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 204 removed outlier: 3.685A pdb=" N ARG B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 228 Processing helix chain 'B' and resid 255 through 266 Processing helix chain 'B' and resid 281 through 293 Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.703A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 343 through 357 removed outlier: 4.143A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 417 through 420 No H-bonds generated for 'chain 'B' and resid 417 through 420' Processing helix chain 'B' and resid 453 through 471 Proline residue: B 458 - end of helix Processing helix chain 'B' and resid 476 through 485 Processing helix chain 'B' and resid 495 through 501 Processing helix chain 'C' and resid 20 through 24 Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 97 through 109 Processing helix chain 'C' and resid 127 through 135 removed outlier: 4.091A pdb=" N PHE C 131 " --> pdb=" O ARG C 128 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N GLU C 132 " --> pdb=" O ASP C 129 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS C 134 " --> pdb=" O PHE C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 204 removed outlier: 3.505A pdb=" N ARG C 203 " --> pdb=" O GLU C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 228 Processing helix chain 'C' and resid 255 through 266 Processing helix chain 'C' and resid 281 through 293 Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.702A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 343 through 357 removed outlier: 4.114A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N PHE C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 417 through 420 No H-bonds generated for 'chain 'C' and resid 417 through 420' Processing helix chain 'C' and resid 453 through 471 Proline residue: C 458 - end of helix Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 495 through 501 Processing helix chain 'D' and resid 20 through 25 Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 97 through 109 Processing helix chain 'D' and resid 127 through 129 No H-bonds generated for 'chain 'D' and resid 127 through 129' Processing helix chain 'D' and resid 131 through 135 removed outlier: 3.872A pdb=" N LYS D 134 " --> pdb=" O PHE D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 162 No H-bonds generated for 'chain 'D' and resid 160 through 162' Processing helix chain 'D' and resid 194 through 204 removed outlier: 3.685A pdb=" N ARG D 203 " --> pdb=" O GLU D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 228 Processing helix chain 'D' and resid 255 through 266 Processing helix chain 'D' and resid 281 through 293 Processing helix chain 'D' and resid 307 through 316 Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 343 through 357 removed outlier: 4.113A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE D 357 " --> pdb=" O TYR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'D' and resid 417 through 420 No H-bonds generated for 'chain 'D' and resid 417 through 420' Processing helix chain 'D' and resid 453 through 471 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 476 through 485 Processing helix chain 'D' and resid 495 through 501 Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 76 through 85 Processing helix chain 'E' and resid 97 through 109 Processing helix chain 'E' and resid 127 through 135 removed outlier: 5.099A pdb=" N GLU E 132 " --> pdb=" O ASP E 129 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N LYS E 134 " --> pdb=" O PHE E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 204 removed outlier: 3.762A pdb=" N ARG E 203 " --> pdb=" O GLU E 199 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 228 Processing helix chain 'E' and resid 255 through 266 Processing helix chain 'E' and resid 281 through 293 Processing helix chain 'E' and resid 307 through 315 removed outlier: 3.722A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 343 through 357 removed outlier: 4.089A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE E 357 " --> pdb=" O TYR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 378 Processing helix chain 'E' and resid 417 through 420 No H-bonds generated for 'chain 'E' and resid 417 through 420' Processing helix chain 'E' and resid 453 through 471 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 476 through 485 Processing helix chain 'E' and resid 495 through 501 Processing helix chain 'F' and resid 20 through 25 Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 76 through 85 Processing helix chain 'F' and resid 97 through 109 Processing helix chain 'F' and resid 127 through 135 removed outlier: 3.709A pdb=" N PHE F 131 " --> pdb=" O ARG F 128 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N GLU F 132 " --> pdb=" O ASP F 129 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS F 134 " --> pdb=" O PHE F 131 " (cutoff:3.500A) Processing helix chain 'F' and resid 194 through 204 Processing helix chain 'F' and resid 224 through 228 Processing helix chain 'F' and resid 255 through 266 Processing helix chain 'F' and resid 281 through 293 Processing helix chain 'F' and resid 307 through 316 removed outlier: 3.676A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 343 through 357 removed outlier: 4.103A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N PHE F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 378 Processing helix chain 'F' and resid 417 through 420 No H-bonds generated for 'chain 'F' and resid 417 through 420' Processing helix chain 'F' and resid 453 through 471 Proline residue: F 458 - end of helix Processing helix chain 'F' and resid 476 through 485 Processing helix chain 'F' and resid 495 through 501 Processing helix chain 'G' and resid 20 through 25 Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 76 through 85 Processing helix chain 'G' and resid 97 through 109 Processing helix chain 'G' and resid 127 through 135 removed outlier: 4.018A pdb=" N GLU G 132 " --> pdb=" O ARG G 128 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ALA G 133 " --> pdb=" O ASP G 129 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LYS G 134 " --> pdb=" O VAL G 130 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ALA G 135 " --> pdb=" O PHE G 131 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 204 removed outlier: 3.786A pdb=" N ARG G 203 " --> pdb=" O GLU G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 228 Processing helix chain 'G' and resid 255 through 266 Processing helix chain 'G' and resid 281 through 293 Processing helix chain 'G' and resid 307 through 315 removed outlier: 3.722A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 337 Processing helix chain 'G' and resid 343 through 357 removed outlier: 4.130A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE G 357 " --> pdb=" O TYR G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 378 Processing helix chain 'G' and resid 417 through 420 No H-bonds generated for 'chain 'G' and resid 417 through 420' Processing helix chain 'G' and resid 453 through 471 Proline residue: G 458 - end of helix Processing helix chain 'G' and resid 476 through 485 Processing helix chain 'G' and resid 495 through 501 Processing helix chain 'H' and resid 20 through 25 Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 76 through 85 Processing helix chain 'H' and resid 97 through 109 Processing helix chain 'H' and resid 127 through 135 removed outlier: 5.156A pdb=" N GLU H 132 " --> pdb=" O ASP H 129 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS H 134 " --> pdb=" O PHE H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 194 through 204 removed outlier: 3.638A pdb=" N ARG H 203 " --> pdb=" O GLU H 199 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 228 Processing helix chain 'H' and resid 255 through 266 Processing helix chain 'H' and resid 281 through 293 Processing helix chain 'H' and resid 307 through 316 Processing helix chain 'H' and resid 333 through 337 Processing helix chain 'H' and resid 343 through 357 removed outlier: 4.124A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE H 357 " --> pdb=" O TYR H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 378 Processing helix chain 'H' and resid 417 through 420 No H-bonds generated for 'chain 'H' and resid 417 through 420' Processing helix chain 'H' and resid 453 through 471 Proline residue: H 458 - end of helix Processing helix chain 'H' and resid 476 through 484 Processing helix chain 'H' and resid 495 through 501 Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.171A pdb=" N VAL A 384 " --> pdb=" O VAL A 66 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 208 through 211 removed outlier: 3.772A pdb=" N ALA A 220 " --> pdb=" O ILE A 211 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.443A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N VAL A 272 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLN A 298 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 401 through 403 Processing sheet with id= F, first strand: chain 'A' and resid 143 through 145 removed outlier: 3.548A pdb=" N GLY A 156 " --> pdb=" O ILE A 144 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= H, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.122A pdb=" N VAL B 384 " --> pdb=" O VAL B 66 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.749A pdb=" N ALA B 220 " --> pdb=" O ILE B 211 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.624A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N ILE B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N VAL B 272 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLN B 298 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'B' and resid 401 through 403 Processing sheet with id= L, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.709A pdb=" N GLY B 156 " --> pdb=" O ILE B 144 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.185A pdb=" N VAL C 384 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'C' and resid 187 through 189 removed outlier: 8.007A pdb=" N ALA C 188 " --> pdb=" O LYS C 208 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ALA C 220 " --> pdb=" O ILE C 211 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.502A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N ILE C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL C 272 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N GLN C 298 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'C' and resid 401 through 403 Processing sheet with id= R, first strand: chain 'C' and resid 142 through 145 removed outlier: 3.641A pdb=" N GLY C 156 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= T, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.161A pdb=" N VAL D 384 " --> pdb=" O VAL D 66 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 187 through 189 removed outlier: 8.096A pdb=" N ALA D 188 " --> pdb=" O LYS D 208 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA D 220 " --> pdb=" O ILE D 211 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.422A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.608A pdb=" N ILE D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VAL D 272 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N GLN D 298 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'D' and resid 401 through 403 Processing sheet with id= X, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.672A pdb=" N GLY D 156 " --> pdb=" O ILE D 144 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= Z, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.169A pdb=" N VAL E 384 " --> pdb=" O VAL E 66 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 187 through 189 removed outlier: 8.075A pdb=" N ALA E 188 " --> pdb=" O LYS E 208 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALA E 220 " --> pdb=" O ILE E 211 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.504A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.676A pdb=" N ILE E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N VAL E 272 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN E 298 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'E' and resid 401 through 403 Processing sheet with id= AD, first strand: chain 'E' and resid 142 through 145 Processing sheet with id= AE, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= AF, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.146A pdb=" N VAL F 384 " --> pdb=" O VAL F 66 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'F' and resid 187 through 189 removed outlier: 8.081A pdb=" N ALA F 188 " --> pdb=" O LYS F 208 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA F 220 " --> pdb=" O ILE F 211 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.456A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ILE F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL F 272 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN F 298 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'F' and resid 401 through 403 Processing sheet with id= AJ, first strand: chain 'F' and resid 142 through 145 removed outlier: 3.667A pdb=" N GLY F 156 " --> pdb=" O ILE F 144 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= AL, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.166A pdb=" N VAL G 384 " --> pdb=" O VAL G 66 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'G' and resid 187 through 189 removed outlier: 8.172A pdb=" N ALA G 188 " --> pdb=" O LYS G 208 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA G 220 " --> pdb=" O ILE G 211 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.676A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N ILE G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL G 272 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N GLN G 298 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'G' and resid 401 through 403 Processing sheet with id= AP, first strand: chain 'G' and resid 142 through 145 Processing sheet with id= AQ, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AR, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.143A pdb=" N VAL H 384 " --> pdb=" O VAL H 66 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'H' and resid 208 through 211 removed outlier: 3.765A pdb=" N ALA H 220 " --> pdb=" O ILE H 211 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.462A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N ILE H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N VAL H 272 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLN H 298 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'H' and resid 401 through 403 Processing sheet with id= AV, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.520A pdb=" N GLY H 156 " --> pdb=" O ILE H 144 " (cutoff:3.500A) 855 hydrogen bonds defined for protein. 2415 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.15 Time building geometry restraints manager: 13.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 5168 1.31 - 1.44: 7697 1.44 - 1.57: 18191 1.57 - 1.70: 120 1.70 - 1.82: 272 Bond restraints: 31448 Sorted by residual: bond pdb=" C4 ATP A 602 " pdb=" C5 ATP A 602 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 6.98e+01 bond pdb=" C4 ATP D 602 " pdb=" C5 ATP D 602 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.94e+01 bond pdb=" C4 ATP G 602 " pdb=" C5 ATP G 602 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.93e+01 bond pdb=" C4 ATP E 602 " pdb=" C5 ATP E 602 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.93e+01 bond pdb=" C4 ATP H 602 " pdb=" C5 ATP H 602 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.91e+01 ... (remaining 31443 not shown) Histogram of bond angle deviations from ideal: 91.08 - 100.10: 13 100.10 - 109.12: 2367 109.12 - 118.14: 22047 118.14 - 127.16: 17938 127.16 - 136.18: 267 Bond angle restraints: 42632 Sorted by residual: angle pdb=" PB ATP A 601 " pdb=" O3B ATP A 601 " pdb=" PG ATP A 601 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PB ATP F 602 " pdb=" O3B ATP F 602 " pdb=" PG ATP F 602 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PB ATP D 601 " pdb=" O3B ATP D 601 " pdb=" PG ATP D 601 " ideal model delta sigma weight residual 139.87 120.41 19.46 1.00e+00 1.00e+00 3.79e+02 angle pdb=" PB ATP E 602 " pdb=" O3B ATP E 602 " pdb=" PG ATP E 602 " ideal model delta sigma weight residual 139.87 120.43 19.44 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 120.44 19.43 1.00e+00 1.00e+00 3.78e+02 ... (remaining 42627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.33: 18646 35.33 - 70.67: 824 70.67 - 106.00: 70 106.00 - 141.34: 3 141.34 - 176.67: 1 Dihedral angle restraints: 19544 sinusoidal: 8376 harmonic: 11168 Sorted by residual: dihedral pdb=" C5' IMP A 603 " pdb=" O5' IMP A 603 " pdb=" P IMP A 603 " pdb=" O2P IMP A 603 " ideal model delta sinusoidal sigma weight residual -168.07 8.61 -176.67 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' IMP H 603 " pdb=" O5' IMP H 603 " pdb=" P IMP H 603 " pdb=" O2P IMP H 603 " ideal model delta sinusoidal sigma weight residual -168.07 -30.70 -137.37 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" C5' IMP G 603 " pdb=" O5' IMP G 603 " pdb=" P IMP G 603 " pdb=" O2P IMP G 603 " ideal model delta sinusoidal sigma weight residual -168.07 -43.27 -124.80 1 2.00e+01 2.50e-03 3.77e+01 ... (remaining 19541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 3909 0.057 - 0.113: 823 0.113 - 0.170: 90 0.170 - 0.227: 33 0.227 - 0.284: 1 Chirality restraints: 4856 Sorted by residual: chirality pdb=" CA MET G 179 " pdb=" N MET G 179 " pdb=" C MET G 179 " pdb=" CB MET G 179 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA ILE B 178 " pdb=" N ILE B 178 " pdb=" C ILE B 178 " pdb=" CB ILE B 178 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.58e-01 chirality pdb=" C3D NAD H 604 " pdb=" C2D NAD H 604 " pdb=" C4D NAD H 604 " pdb=" O3D NAD H 604 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.94e-01 ... (remaining 4853 not shown) Planarity restraints: 5352 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL C 13 " -0.010 2.00e-02 2.50e+03 2.07e-02 4.29e+00 pdb=" C VAL C 13 " 0.036 2.00e-02 2.50e+03 pdb=" O VAL C 13 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO C 14 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 170 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.12e+00 pdb=" CD GLU H 170 " -0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU H 170 " 0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU H 170 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 13 " 0.010 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C VAL E 13 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL E 13 " 0.012 2.00e-02 2.50e+03 pdb=" N PRO E 14 " 0.011 2.00e-02 2.50e+03 ... (remaining 5349 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1302 2.72 - 3.26: 31354 3.26 - 3.81: 52028 3.81 - 4.35: 66645 4.35 - 4.90: 108329 Nonbonded interactions: 259658 Sorted by model distance: nonbonded pdb=" O ARG F 182 " pdb=" NH1 ARG F 182 " model vdw 2.173 2.520 nonbonded pdb=" OD2 ASP A 364 " pdb=" O2' IMP A 603 " model vdw 2.178 2.440 nonbonded pdb=" OD2 ASP C 364 " pdb=" O2' IMP C 603 " model vdw 2.194 2.440 nonbonded pdb=" OD2 ASP B 364 " pdb=" O2' IMP B 603 " model vdw 2.198 2.440 nonbonded pdb=" OD2 ASP E 364 " pdb=" O2' IMP E 603 " model vdw 2.198 2.440 ... (remaining 259653 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 5.860 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: 18.290 Check model and map are aligned: 0.000 Set scattering table: 0.070 Process input model: 82.260 Find NCS groups from input model: 2.210 Set up NCS constraints: 0.240 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:12.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 121.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.143 31448 Z= 0.489 Angle : 1.025 21.396 42632 Z= 0.704 Chirality : 0.048 0.284 4856 Planarity : 0.004 0.050 5352 Dihedral : 18.177 176.675 12408 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.98 % Favored : 93.61 % Rotamer: Outliers : 1.87 % Allowed : 17.36 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -0.22 (0.14), residues: 3896 helix: 0.74 (0.14), residues: 1488 sheet: 0.15 (0.22), residues: 472 loop : -0.91 (0.14), residues: 1936 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 454 PHE 0.017 0.001 PHE G 165 TYR 0.012 0.001 TYR E 348 ARG 0.011 0.000 ARG E 182 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 368 time to evaluate : 3.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 269 ASP cc_start: 0.7411 (m-30) cc_final: 0.7093 (m-30) REVERT: B 277 GLN cc_start: 0.9207 (OUTLIER) cc_final: 0.6811 (tm-30) REVERT: D 303 ASN cc_start: 0.9095 (m110) cc_final: 0.8894 (m-40) REVERT: E 179 MET cc_start: 0.5510 (tmm) cc_final: 0.4750 (tmm) REVERT: F 438 LYS cc_start: 0.7332 (mttm) cc_final: 0.7032 (mtmt) outliers start: 60 outliers final: 49 residues processed: 424 average time/residue: 1.2632 time to fit residues: 642.0198 Evaluate side-chains 411 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 361 time to evaluate : 3.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 181 LYS Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 361 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 318 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 331 optimal weight: 5.9990 chunk 297 optimal weight: 2.9990 chunk 164 optimal weight: 20.0000 chunk 101 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 158 optimal weight: 20.0000 chunk 307 optimal weight: 10.0000 chunk 118 optimal weight: 0.4980 chunk 186 optimal weight: 0.9990 chunk 228 optimal weight: 0.9980 chunk 355 optimal weight: 2.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 HIS A 277 GLN A 343 GLN A 441 GLN A 466 HIS A 478 GLN B 21 GLN B 93 HIS B 253 HIS B 343 GLN B 478 GLN C 93 HIS C 343 GLN C 441 GLN C 466 HIS C 478 GLN D 93 HIS D 303 ASN D 343 GLN D 441 GLN D 466 HIS D 478 GLN E 93 HIS E 343 GLN E 478 GLN F 93 HIS F 343 GLN F 466 HIS F 478 GLN G 93 HIS G 343 GLN G 466 HIS G 469 GLN G 478 GLN H 93 HIS H 343 GLN H 441 GLN H 466 HIS H 478 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 31448 Z= 0.312 Angle : 0.633 13.111 42632 Z= 0.328 Chirality : 0.047 0.203 4856 Planarity : 0.005 0.043 5352 Dihedral : 14.328 167.676 5371 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.60 % Favored : 93.97 % Rotamer: Outliers : 3.99 % Allowed : 15.21 % Favored : 80.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -0.50 (0.13), residues: 3896 helix: 0.50 (0.14), residues: 1480 sheet: 0.03 (0.22), residues: 472 loop : -1.05 (0.14), residues: 1944 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 454 PHE 0.014 0.002 PHE H 456 TYR 0.016 0.002 TYR G 348 ARG 0.006 0.001 ARG A 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 382 time to evaluate : 3.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 399 GLU cc_start: 0.7036 (pp20) cc_final: 0.6833 (pp20) REVERT: E 179 MET cc_start: 0.5886 (mmm) cc_final: 0.5095 (tmm) REVERT: F 438 LYS cc_start: 0.7386 (OUTLIER) cc_final: 0.7139 (mttm) REVERT: G 277 GLN cc_start: 0.9280 (OUTLIER) cc_final: 0.6983 (tm-30) REVERT: G 438 LYS cc_start: 0.7308 (mtmt) cc_final: 0.6836 (mmmt) REVERT: G 441 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8636 (mt0) outliers start: 128 outliers final: 78 residues processed: 485 average time/residue: 1.2519 time to fit residues: 728.8482 Evaluate side-chains 454 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 373 time to evaluate : 3.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 277 GLN Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 420 MET Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 420 MET Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 183 GLU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 438 LYS Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 441 GLN Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 175 LEU Chi-restraints excluded: chain H residue 178 ILE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 197 optimal weight: 0.8980 chunk 110 optimal weight: 0.0980 chunk 296 optimal weight: 0.7980 chunk 242 optimal weight: 0.6980 chunk 98 optimal weight: 2.9990 chunk 356 optimal weight: 10.0000 chunk 385 optimal weight: 2.9990 chunk 317 optimal weight: 1.9990 chunk 353 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 286 optimal weight: 9.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN B 368 GLN B 478 GLN C 466 HIS C 478 GLN D 478 GLN E 368 GLN E 478 GLN F 466 HIS F 478 GLN G 466 HIS G 469 GLN G 478 GLN H 478 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 31448 Z= 0.191 Angle : 0.547 12.626 42632 Z= 0.281 Chirality : 0.044 0.195 4856 Planarity : 0.004 0.037 5352 Dihedral : 13.631 135.584 5366 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.29 % Favored : 94.28 % Rotamer: Outliers : 4.36 % Allowed : 15.74 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -0.24 (0.13), residues: 3896 helix: 0.70 (0.14), residues: 1480 sheet: 0.68 (0.24), residues: 376 loop : -0.96 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 466 PHE 0.011 0.001 PHE H 456 TYR 0.012 0.001 TYR D 353 ARG 0.002 0.000 ARG B 412 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 397 time to evaluate : 3.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.6841 (m-30) cc_final: 0.6498 (m-30) REVERT: A 455 LYS cc_start: 0.7324 (mtpp) cc_final: 0.7023 (ptpt) REVERT: B 206 LYS cc_start: 0.6957 (OUTLIER) cc_final: 0.6580 (ptpp) REVERT: B 438 LYS cc_start: 0.7378 (mmtt) cc_final: 0.7073 (mtmt) REVERT: C 277 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.7102 (tm-30) REVERT: C 399 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6618 (pp20) REVERT: D 277 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.6761 (tm-30) REVERT: D 399 GLU cc_start: 0.7038 (OUTLIER) cc_final: 0.6661 (pp20) REVERT: E 179 MET cc_start: 0.5923 (mmm) cc_final: 0.5400 (tmm) REVERT: E 277 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.7355 (tm-30) REVERT: F 206 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6937 (pmmt) REVERT: F 277 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.7123 (tm-30) REVERT: F 438 LYS cc_start: 0.7376 (mttm) cc_final: 0.7107 (mttm) REVERT: G 277 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.6970 (tm-30) REVERT: H 162 ASP cc_start: 0.7420 (m-30) cc_final: 0.7177 (m-30) REVERT: H 277 GLN cc_start: 0.9173 (OUTLIER) cc_final: 0.6771 (tm-30) outliers start: 140 outliers final: 75 residues processed: 496 average time/residue: 1.2237 time to fit residues: 731.7603 Evaluate side-chains 465 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 380 time to evaluate : 3.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 496 SER Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 185 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 183 GLU Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 352 optimal weight: 1.9990 chunk 268 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 170 optimal weight: 6.9990 chunk 239 optimal weight: 2.9990 chunk 357 optimal weight: 5.9990 chunk 378 optimal weight: 3.9990 chunk 186 optimal weight: 0.9990 chunk 339 optimal weight: 0.8980 chunk 102 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 GLN A 368 GLN A 478 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 478 GLN E 368 GLN E 478 GLN F 298 GLN F 368 GLN F 466 HIS F 478 GLN G 466 HIS G 478 GLN H 368 GLN H 478 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 31448 Z= 0.343 Angle : 0.617 12.549 42632 Z= 0.320 Chirality : 0.047 0.192 4856 Planarity : 0.005 0.043 5352 Dihedral : 13.346 96.311 5351 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.44 % Favored : 94.12 % Rotamer: Outliers : 5.08 % Allowed : 16.15 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -0.38 (0.13), residues: 3896 helix: 0.54 (0.14), residues: 1464 sheet: 0.68 (0.24), residues: 392 loop : -1.02 (0.14), residues: 2040 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 466 PHE 0.013 0.002 PHE C 24 TYR 0.017 0.002 TYR E 348 ARG 0.004 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 549 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 386 time to evaluate : 3.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.6987 (m-30) cc_final: 0.6631 (m-30) REVERT: A 399 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6587 (pp20) REVERT: B 206 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6438 (ptpp) REVERT: B 399 GLU cc_start: 0.7054 (pp20) cc_final: 0.6810 (pp20) REVERT: B 438 LYS cc_start: 0.7365 (mmtt) cc_final: 0.6980 (mtmt) REVERT: C 162 ASP cc_start: 0.7097 (m-30) cc_final: 0.6893 (m-30) REVERT: C 399 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6658 (pp20) REVERT: D 182 ARG cc_start: 0.6638 (OUTLIER) cc_final: 0.6322 (tpt90) REVERT: D 277 GLN cc_start: 0.9201 (OUTLIER) cc_final: 0.6948 (tm-30) REVERT: D 399 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6808 (pp20) REVERT: E 179 MET cc_start: 0.6433 (mmm) cc_final: 0.5699 (tmm) REVERT: F 206 LYS cc_start: 0.7442 (OUTLIER) cc_final: 0.7181 (pmmt) REVERT: F 260 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7858 (tp) REVERT: F 277 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.7201 (tm-30) REVERT: F 438 LYS cc_start: 0.7436 (mttm) cc_final: 0.7213 (mttm) REVERT: G 277 GLN cc_start: 0.9291 (OUTLIER) cc_final: 0.6911 (tm-30) REVERT: H 162 ASP cc_start: 0.7489 (m-30) cc_final: 0.7156 (m-30) outliers start: 163 outliers final: 98 residues processed: 506 average time/residue: 1.2426 time to fit residues: 762.7089 Evaluate side-chains 484 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 376 time to evaluate : 3.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 182 ARG Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 180 THR Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 333 THR Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 447 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 333 THR Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 165 PHE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 312 ASN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 315 optimal weight: 0.9990 chunk 215 optimal weight: 6.9990 chunk 5 optimal weight: 0.7980 chunk 282 optimal weight: 0.6980 chunk 156 optimal weight: 3.9990 chunk 323 optimal weight: 0.6980 chunk 261 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 193 optimal weight: 0.2980 chunk 340 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 478 GLN B 466 HIS B 478 GLN C 466 HIS C 478 GLN D 478 GLN E 478 GLN F 466 HIS F 478 GLN G 478 GLN H 478 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 31448 Z= 0.163 Angle : 0.533 11.342 42632 Z= 0.275 Chirality : 0.043 0.169 4856 Planarity : 0.004 0.036 5352 Dihedral : 12.764 89.831 5346 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.80 % Favored : 94.76 % Rotamer: Outliers : 4.61 % Allowed : 16.86 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -0.12 (0.14), residues: 3896 helix: 0.80 (0.14), residues: 1464 sheet: 0.23 (0.23), residues: 472 loop : -0.81 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 466 PHE 0.010 0.001 PHE H 456 TYR 0.012 0.001 TYR H 353 ARG 0.003 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 407 time to evaluate : 3.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 ASP cc_start: 0.6915 (m-30) cc_final: 0.6632 (m-30) REVERT: A 399 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.6569 (pp20) REVERT: A 438 LYS cc_start: 0.7190 (mmpt) cc_final: 0.6711 (mtmt) REVERT: A 455 LYS cc_start: 0.7327 (mtpp) cc_final: 0.7043 (ptpt) REVERT: B 206 LYS cc_start: 0.6884 (OUTLIER) cc_final: 0.6488 (ptpp) REVERT: B 399 GLU cc_start: 0.7070 (pp20) cc_final: 0.6858 (pp20) REVERT: B 438 LYS cc_start: 0.7370 (mmtt) cc_final: 0.6975 (mtmt) REVERT: C 170 GLU cc_start: 0.5780 (OUTLIER) cc_final: 0.5320 (tm-30) REVERT: C 277 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.7033 (tm-30) REVERT: C 399 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6627 (pp20) REVERT: D 243 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7558 (mt0) REVERT: D 277 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.6865 (tm-30) REVERT: D 399 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6653 (pp20) REVERT: E 162 ASP cc_start: 0.7153 (m-30) cc_final: 0.6897 (m-30) REVERT: E 179 MET cc_start: 0.6480 (mmm) cc_final: 0.5789 (tmm) REVERT: E 277 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.7224 (tm-30) REVERT: F 277 GLN cc_start: 0.9217 (OUTLIER) cc_final: 0.7104 (tm-30) REVERT: F 291 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.8196 (mmtt) REVERT: F 438 LYS cc_start: 0.7415 (mttm) cc_final: 0.7019 (mtmp) REVERT: G 277 GLN cc_start: 0.9251 (OUTLIER) cc_final: 0.6979 (tm-30) REVERT: H 277 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: H 399 GLU cc_start: 0.7050 (OUTLIER) cc_final: 0.6648 (pp20) outliers start: 148 outliers final: 89 residues processed: 514 average time/residue: 1.2365 time to fit residues: 764.2904 Evaluate side-chains 491 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 388 time to evaluate : 3.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain D residue 496 SER Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 291 LYS Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 420 MET Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 447 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 165 PHE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 127 optimal weight: 3.9990 chunk 341 optimal weight: 3.9990 chunk 74 optimal weight: 0.0980 chunk 222 optimal weight: 0.7980 chunk 93 optimal weight: 0.2980 chunk 379 optimal weight: 1.9990 chunk 314 optimal weight: 0.6980 chunk 175 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 125 optimal weight: 1.9990 chunk 199 optimal weight: 4.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 368 GLN A 478 GLN B 466 HIS B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 478 GLN E 368 GLN E 478 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 368 GLN H 478 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 31448 Z= 0.144 Angle : 0.512 9.486 42632 Z= 0.262 Chirality : 0.043 0.171 4856 Planarity : 0.004 0.037 5352 Dihedral : 12.194 88.162 5341 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.72 % Favored : 94.84 % Rotamer: Outliers : 4.40 % Allowed : 17.74 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.14), residues: 3896 helix: 1.02 (0.14), residues: 1464 sheet: 0.34 (0.23), residues: 472 loop : -0.70 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS E 454 PHE 0.011 0.001 PHE H 456 TYR 0.011 0.001 TYR D 353 ARG 0.002 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 396 time to evaluate : 3.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 399 GLU cc_start: 0.6942 (OUTLIER) cc_final: 0.6569 (pp20) REVERT: A 438 LYS cc_start: 0.7126 (mmpt) cc_final: 0.6838 (mmmt) REVERT: A 455 LYS cc_start: 0.7312 (mtpp) cc_final: 0.7089 (ptpt) REVERT: B 206 LYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6551 (ptpp) REVERT: B 399 GLU cc_start: 0.7063 (pp20) cc_final: 0.6832 (pp20) REVERT: C 170 GLU cc_start: 0.5659 (OUTLIER) cc_final: 0.5250 (mm-30) REVERT: C 277 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.6974 (tm-30) REVERT: C 399 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6619 (pp20) REVERT: D 182 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6460 (tpt90) REVERT: D 243 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7578 (mt0) REVERT: D 277 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.6716 (tm-30) REVERT: D 399 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6621 (pp20) REVERT: D 455 LYS cc_start: 0.7203 (mtpp) cc_final: 0.6956 (ptpt) REVERT: E 162 ASP cc_start: 0.7144 (m-30) cc_final: 0.6894 (m-30) REVERT: E 179 MET cc_start: 0.6598 (mmm) cc_final: 0.5863 (tmm) REVERT: F 277 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.7085 (tm-30) REVERT: F 455 LYS cc_start: 0.7143 (mtpp) cc_final: 0.6877 (ttmm) REVERT: G 277 GLN cc_start: 0.9237 (OUTLIER) cc_final: 0.7050 (tm-30) REVERT: G 455 LYS cc_start: 0.7146 (mtpp) cc_final: 0.6806 (ptpt) REVERT: H 399 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6557 (pp20) outliers start: 141 outliers final: 84 residues processed: 496 average time/residue: 1.2366 time to fit residues: 741.0077 Evaluate side-chains 483 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 387 time to evaluate : 3.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 448 GLN Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 165 PHE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 312 ASN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 365 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 216 optimal weight: 0.6980 chunk 276 optimal weight: 4.9990 chunk 214 optimal weight: 9.9990 chunk 319 optimal weight: 0.9990 chunk 211 optimal weight: 9.9990 chunk 377 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 230 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 368 GLN A 478 GLN B 368 GLN B 466 HIS B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 466 HIS D 478 GLN E 368 GLN E 466 HIS E 478 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 368 GLN H 478 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 31448 Z= 0.208 Angle : 0.540 9.526 42632 Z= 0.278 Chirality : 0.044 0.175 4856 Planarity : 0.004 0.033 5352 Dihedral : 12.183 89.390 5340 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.06 % Favored : 94.51 % Rotamer: Outliers : 4.05 % Allowed : 18.42 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3896 helix: 0.95 (0.14), residues: 1464 sheet: 0.28 (0.23), residues: 472 loop : -0.74 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 454 PHE 0.012 0.001 PHE E 456 TYR 0.013 0.001 TYR B 348 ARG 0.002 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 382 time to evaluate : 3.094 Fit side-chains revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7827 (tp30) cc_final: 0.6933 (mp0) REVERT: A 399 GLU cc_start: 0.6941 (OUTLIER) cc_final: 0.6555 (pp20) REVERT: A 438 LYS cc_start: 0.7215 (mmpt) cc_final: 0.7007 (mmmt) REVERT: A 455 LYS cc_start: 0.7340 (mtpp) cc_final: 0.7112 (ptpt) REVERT: B 206 LYS cc_start: 0.6948 (OUTLIER) cc_final: 0.6561 (ptpp) REVERT: B 260 LEU cc_start: 0.8360 (OUTLIER) cc_final: 0.7870 (tp) REVERT: B 399 GLU cc_start: 0.7073 (pp20) cc_final: 0.6817 (pp20) REVERT: B 438 LYS cc_start: 0.7337 (mmtt) cc_final: 0.7096 (mmtp) REVERT: C 170 GLU cc_start: 0.5486 (OUTLIER) cc_final: 0.5120 (mm-30) REVERT: C 277 GLN cc_start: 0.9183 (OUTLIER) cc_final: 0.7164 (tm-30) REVERT: C 399 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6589 (pp20) REVERT: D 182 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6453 (tpt90) REVERT: D 243 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7570 (mt0) REVERT: D 277 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.6776 (tm-30) REVERT: D 399 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6623 (pp20) REVERT: D 455 LYS cc_start: 0.7365 (mtpp) cc_final: 0.7125 (ptpt) REVERT: E 162 ASP cc_start: 0.7197 (m-30) cc_final: 0.6911 (m-30) REVERT: E 179 MET cc_start: 0.6686 (mmm) cc_final: 0.5916 (tmm) REVERT: E 277 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.6986 (tm-30) REVERT: F 277 GLN cc_start: 0.9226 (OUTLIER) cc_final: 0.7173 (tm-30) REVERT: F 438 LYS cc_start: 0.7380 (OUTLIER) cc_final: 0.7033 (mtmt) REVERT: F 455 LYS cc_start: 0.7374 (mtpp) cc_final: 0.7146 (ttmm) REVERT: G 111 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6701 (tp30) REVERT: G 277 GLN cc_start: 0.9249 (OUTLIER) cc_final: 0.6981 (tm-30) REVERT: G 455 LYS cc_start: 0.7259 (mtpp) cc_final: 0.6918 (ptpt) REVERT: H 277 GLN cc_start: 0.9136 (OUTLIER) cc_final: 0.6931 (tm-30) REVERT: H 399 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6584 (pp20) outliers start: 130 outliers final: 89 residues processed: 478 average time/residue: 1.1741 time to fit residues: 679.0715 Evaluate side-chains 483 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 377 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 165 PHE Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 243 GLN Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 438 LYS Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 165 PHE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 233 optimal weight: 1.9990 chunk 150 optimal weight: 1.9990 chunk 225 optimal weight: 2.9990 chunk 113 optimal weight: 0.0170 chunk 74 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 240 optimal weight: 4.9990 chunk 257 optimal weight: 8.9990 chunk 186 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 296 optimal weight: 1.9990 overall best weight: 1.3224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 368 GLN A 478 GLN B 368 GLN B 466 HIS B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 368 GLN D 466 HIS D 478 GLN E 368 GLN E 466 HIS E 478 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 368 GLN H 478 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 31448 Z= 0.244 Angle : 0.562 10.312 42632 Z= 0.288 Chirality : 0.045 0.191 4856 Planarity : 0.004 0.033 5352 Dihedral : 12.211 89.700 5338 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.06 % Favored : 94.51 % Rotamer: Outliers : 4.05 % Allowed : 18.52 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: -0.09 (0.14), residues: 3896 helix: 0.85 (0.14), residues: 1464 sheet: 0.24 (0.23), residues: 472 loop : -0.80 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 466 PHE 0.014 0.002 PHE E 456 TYR 0.014 0.002 TYR E 348 ARG 0.003 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 383 time to evaluate : 3.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7824 (tp30) cc_final: 0.6902 (mp0) REVERT: A 399 GLU cc_start: 0.6923 (OUTLIER) cc_final: 0.6540 (pp20) REVERT: A 455 LYS cc_start: 0.7377 (mtpp) cc_final: 0.7128 (ptpt) REVERT: B 206 LYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6610 (ptpp) REVERT: B 260 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7879 (tp) REVERT: B 399 GLU cc_start: 0.7102 (pp20) cc_final: 0.6881 (pp20) REVERT: C 170 GLU cc_start: 0.5362 (OUTLIER) cc_final: 0.4906 (mm-30) REVERT: C 399 GLU cc_start: 0.6996 (OUTLIER) cc_final: 0.6659 (pp20) REVERT: C 455 LYS cc_start: 0.7281 (mttp) cc_final: 0.7030 (ttmm) REVERT: D 182 ARG cc_start: 0.6730 (OUTLIER) cc_final: 0.6509 (tpt90) REVERT: D 277 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.6803 (tm-30) REVERT: D 399 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6629 (pp20) REVERT: D 455 LYS cc_start: 0.7406 (mtpp) cc_final: 0.7170 (ptpt) REVERT: E 162 ASP cc_start: 0.7261 (m-30) cc_final: 0.6986 (m-30) REVERT: E 179 MET cc_start: 0.6735 (mmm) cc_final: 0.5991 (tmm) REVERT: E 277 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.7003 (tm-30) REVERT: F 277 GLN cc_start: 0.9225 (OUTLIER) cc_final: 0.7143 (tm-30) REVERT: F 438 LYS cc_start: 0.7388 (mtpp) cc_final: 0.7040 (mtmt) REVERT: F 455 LYS cc_start: 0.7387 (mtpp) cc_final: 0.7145 (ttmm) REVERT: G 111 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6703 (tp30) REVERT: G 277 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.6954 (tm-30) REVERT: G 455 LYS cc_start: 0.7248 (mtpp) cc_final: 0.6998 (ptpt) REVERT: H 277 GLN cc_start: 0.9169 (OUTLIER) cc_final: 0.6951 (tm-30) REVERT: H 399 GLU cc_start: 0.7003 (OUTLIER) cc_final: 0.6632 (pp20) outliers start: 130 outliers final: 90 residues processed: 475 average time/residue: 1.2758 time to fit residues: 729.5806 Evaluate side-chains 483 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 379 time to evaluate : 3.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 111 GLU Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 165 PHE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 343 optimal weight: 0.0870 chunk 361 optimal weight: 10.0000 chunk 330 optimal weight: 0.8980 chunk 352 optimal weight: 0.8980 chunk 211 optimal weight: 8.9990 chunk 153 optimal weight: 3.9990 chunk 276 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 318 optimal weight: 0.6980 chunk 332 optimal weight: 1.9990 chunk 350 optimal weight: 3.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 368 GLN A 478 GLN B 368 GLN B 466 HIS B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 368 GLN D 478 GLN E 368 GLN E 466 HIS E 478 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 368 GLN H 478 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 31448 Z= 0.167 Angle : 0.528 11.186 42632 Z= 0.269 Chirality : 0.043 0.188 4856 Planarity : 0.004 0.034 5352 Dihedral : 11.933 89.321 5338 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.90 % Favored : 94.66 % Rotamer: Outliers : 3.74 % Allowed : 18.89 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 0.07 (0.14), residues: 3896 helix: 0.98 (0.14), residues: 1464 sheet: 0.27 (0.23), residues: 472 loop : -0.70 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 454 PHE 0.013 0.001 PHE E 456 TYR 0.012 0.001 TYR H 353 ARG 0.002 0.000 ARG A 182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 387 time to evaluate : 3.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7820 (tp30) cc_final: 0.6885 (mp0) REVERT: A 399 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6567 (pp20) REVERT: A 455 LYS cc_start: 0.7327 (mtpp) cc_final: 0.7121 (ptpt) REVERT: B 206 LYS cc_start: 0.7007 (OUTLIER) cc_final: 0.6619 (ptpp) REVERT: B 260 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.7903 (tp) REVERT: B 399 GLU cc_start: 0.7114 (pp20) cc_final: 0.6882 (pp20) REVERT: C 170 GLU cc_start: 0.5285 (OUTLIER) cc_final: 0.4880 (mm-30) REVERT: C 277 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.7015 (tm-30) REVERT: C 399 GLU cc_start: 0.6985 (OUTLIER) cc_final: 0.6611 (pp20) REVERT: C 455 LYS cc_start: 0.7162 (mttp) cc_final: 0.6920 (ttmm) REVERT: D 182 ARG cc_start: 0.6712 (OUTLIER) cc_final: 0.6483 (tpt90) REVERT: D 277 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.6777 (tm-30) REVERT: D 399 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6605 (pp20) REVERT: E 162 ASP cc_start: 0.7124 (m-30) cc_final: 0.6866 (m-30) REVERT: E 179 MET cc_start: 0.6584 (mmm) cc_final: 0.5933 (tmm) REVERT: E 277 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.6996 (tm-30) REVERT: F 277 GLN cc_start: 0.9205 (OUTLIER) cc_final: 0.7148 (tm-30) REVERT: F 438 LYS cc_start: 0.7358 (OUTLIER) cc_final: 0.7055 (mtmt) REVERT: G 277 GLN cc_start: 0.9248 (OUTLIER) cc_final: 0.7009 (tm-30) REVERT: H 277 GLN cc_start: 0.9123 (OUTLIER) cc_final: 0.6946 (tm-30) REVERT: H 399 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6619 (pp20) outliers start: 120 outliers final: 91 residues processed: 478 average time/residue: 1.2731 time to fit residues: 736.9545 Evaluate side-chains 486 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 380 time to evaluate : 3.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 438 LYS Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 165 PHE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 312 ASN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 231 optimal weight: 3.9990 chunk 372 optimal weight: 0.9980 chunk 227 optimal weight: 2.9990 chunk 176 optimal weight: 0.1980 chunk 258 optimal weight: 1.9990 chunk 390 optimal weight: 2.9990 chunk 359 optimal weight: 7.9990 chunk 310 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 240 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 368 GLN A 478 GLN B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 368 GLN D 478 GLN E 368 GLN E 466 HIS E 478 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 102 ASN H 368 GLN H 478 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 31448 Z= 0.177 Angle : 0.535 11.702 42632 Z= 0.272 Chirality : 0.043 0.180 4856 Planarity : 0.004 0.032 5352 Dihedral : 11.815 89.032 5338 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.44 % Allowed : 5.06 % Favored : 94.51 % Rotamer: Outliers : 3.74 % Allowed : 18.98 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % 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: 0.09 (0.14), residues: 3896 helix: 1.02 (0.14), residues: 1464 sheet: 0.27 (0.23), residues: 472 loop : -0.70 (0.14), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 454 PHE 0.014 0.001 PHE E 456 TYR 0.012 0.001 TYR A 353 ARG 0.003 0.000 ARG A 182 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7792 Ramachandran restraints generated. 3896 Oldfield, 0 Emsley, 3896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 384 time to evaluate : 3.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.7834 (tp30) cc_final: 0.6903 (mp0) REVERT: A 399 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.6551 (pp20) REVERT: B 260 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7876 (tp) REVERT: B 399 GLU cc_start: 0.7116 (pp20) cc_final: 0.6805 (pp20) REVERT: C 111 GLU cc_start: 0.7084 (tp30) cc_final: 0.6884 (tp30) REVERT: C 170 GLU cc_start: 0.5105 (OUTLIER) cc_final: 0.4700 (mm-30) REVERT: C 277 GLN cc_start: 0.9161 (OUTLIER) cc_final: 0.7007 (tm-30) REVERT: C 399 GLU cc_start: 0.6986 (OUTLIER) cc_final: 0.6605 (pp20) REVERT: C 455 LYS cc_start: 0.7192 (mttp) cc_final: 0.6950 (ttmm) REVERT: D 179 MET cc_start: 0.5888 (ppp) cc_final: 0.5629 (ppp) REVERT: D 182 ARG cc_start: 0.6752 (OUTLIER) cc_final: 0.6536 (tpt90) REVERT: D 277 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.6731 (tm-30) REVERT: D 399 GLU cc_start: 0.7041 (OUTLIER) cc_final: 0.6633 (pp20) REVERT: E 277 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.6997 (tm-30) REVERT: F 277 GLN cc_start: 0.9204 (OUTLIER) cc_final: 0.7161 (tm-30) REVERT: F 438 LYS cc_start: 0.7374 (OUTLIER) cc_final: 0.7091 (mtmt) REVERT: G 277 GLN cc_start: 0.9241 (OUTLIER) cc_final: 0.7010 (tm-30) REVERT: H 111 GLU cc_start: 0.7249 (tp30) cc_final: 0.7038 (tp30) REVERT: H 277 GLN cc_start: 0.9126 (OUTLIER) cc_final: 0.6939 (tm-30) REVERT: H 399 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6638 (pp20) outliers start: 120 outliers final: 94 residues processed: 475 average time/residue: 1.2608 time to fit residues: 718.6171 Evaluate side-chains 491 residues out of total 3208 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 383 time to evaluate : 3.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 178 ILE Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 318 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 410 LYS Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain A residue 447 VAL Chi-restraints excluded: chain A residue 450 LYS Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 181 LYS Chi-restraints excluded: chain B residue 206 LYS Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 277 GLN Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain C residue 154 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 181 LYS Chi-restraints excluded: chain C residue 255 ASP Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 277 GLN Chi-restraints excluded: chain C residue 318 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 410 LYS Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain C residue 450 LYS Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 154 LEU Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 255 ASP Chi-restraints excluded: chain D residue 265 GLN Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 277 GLN Chi-restraints excluded: chain D residue 312 ASN Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 333 THR Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 420 MET Chi-restraints excluded: chain D residue 439 VAL Chi-restraints excluded: chain D residue 450 LYS Chi-restraints excluded: chain E residue 154 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 165 PHE Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 277 GLN Chi-restraints excluded: chain E residue 318 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 420 MET Chi-restraints excluded: chain E residue 439 VAL Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain E residue 447 VAL Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain F residue 154 LEU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 165 PHE Chi-restraints excluded: chain F residue 181 LYS Chi-restraints excluded: chain F residue 206 LYS Chi-restraints excluded: chain F residue 243 GLN Chi-restraints excluded: chain F residue 277 GLN Chi-restraints excluded: chain F residue 318 VAL Chi-restraints excluded: chain F residue 333 THR Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 438 LYS Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain F residue 450 LYS Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 165 PHE Chi-restraints excluded: chain G residue 206 LYS Chi-restraints excluded: chain G residue 255 ASP Chi-restraints excluded: chain G residue 277 GLN Chi-restraints excluded: chain G residue 318 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 420 MET Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain G residue 450 LYS Chi-restraints excluded: chain H residue 154 LEU Chi-restraints excluded: chain H residue 165 PHE Chi-restraints excluded: chain H residue 181 LYS Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 277 GLN Chi-restraints excluded: chain H residue 312 ASN Chi-restraints excluded: chain H residue 318 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 399 GLU Chi-restraints excluded: chain H residue 420 MET Chi-restraints excluded: chain H residue 439 VAL Chi-restraints excluded: chain H residue 447 VAL Chi-restraints excluded: chain H residue 448 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 392 random chunks: chunk 247 optimal weight: 1.9990 chunk 331 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 286 optimal weight: 8.9990 chunk 45 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 311 optimal weight: 0.0370 chunk 130 optimal weight: 0.3980 chunk 319 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 GLN A 368 GLN A 478 GLN B 368 GLN B 478 GLN C 368 GLN C 466 HIS C 478 GLN D 478 GLN E 368 GLN E 466 HIS E 478 GLN F 368 GLN F 466 HIS F 478 GLN G 368 GLN G 466 HIS G 478 GLN H 478 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.190588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.137961 restraints weight = 32891.506| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.82 r_work: 0.3259 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 31448 Z= 0.155 Angle : 0.523 11.670 42632 Z= 0.264 Chirality : 0.042 0.167 4856 Planarity : 0.004 0.032 5352 Dihedral : 11.624 88.774 5338 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.44 % Allowed : 4.75 % Favored : 94.82 % Rotamer: Outliers : 3.65 % Allowed : 19.11 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.21 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.14), residues: 3896 helix: 1.08 (0.14), residues: 1464 sheet: -0.03 (0.22), residues: 512 loop : -0.65 (0.15), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 454 PHE 0.015 0.001 PHE E 456 TYR 0.012 0.001 TYR H 353 ARG 0.003 0.000 ARG G 149 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11929.25 seconds wall clock time: 211 minutes 33.97 seconds (12693.97 seconds total)