Starting phenix.real_space_refine on Thu Jul 25 19:06:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7v_42012/07_2024/8u7v_42012.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7v_42012/07_2024/8u7v_42012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7v_42012/07_2024/8u7v_42012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7v_42012/07_2024/8u7v_42012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7v_42012/07_2024/8u7v_42012.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u7v_42012/07_2024/8u7v_42012.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.081 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 96 5.49 5 S 184 5.16 5 C 18456 2.51 5 N 5040 2.21 5 O 5904 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 48": "OE1" <-> "OE2" Residue "A ASP 50": "OD1" <-> "OD2" Residue "A PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 132": "OE1" <-> "OE2" Residue "A PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 477": "OD1" <-> "OD2" Residue "A TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 34": "OD1" <-> "OD2" Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 48": "OE1" <-> "OE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 132": "OE1" <-> "OE2" Residue "B PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 177": "OE1" <-> "OE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "B TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 477": "OD1" <-> "OD2" Residue "B TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 34": "OD1" <-> "OD2" Residue "C PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 48": "OE1" <-> "OE2" Residue "C ASP 50": "OD1" <-> "OD2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 132": "OE1" <-> "OE2" Residue "C PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 177": "OE1" <-> "OE2" Residue "C GLU 352": "OE1" <-> "OE2" Residue "C TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 477": "OD1" <-> "OD2" Residue "C TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 48": "OE1" <-> "OE2" Residue "D ASP 50": "OD1" <-> "OD2" Residue "D PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 132": "OE1" <-> "OE2" Residue "D PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 177": "OE1" <-> "OE2" Residue "D GLU 217": "OE1" <-> "OE2" Residue "D GLU 352": "OE1" <-> "OE2" Residue "D TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 477": "OD1" <-> "OD2" Residue "D TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 48": "OE1" <-> "OE2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 132": "OE1" <-> "OE2" Residue "E PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 177": "OE1" <-> "OE2" Residue "E GLU 217": "OE1" <-> "OE2" Residue "E GLU 352": "OE1" <-> "OE2" Residue "E TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 477": "OD1" <-> "OD2" Residue "E TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 48": "OE1" <-> "OE2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 132": "OE1" <-> "OE2" Residue "F PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "F TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 477": "OD1" <-> "OD2" Residue "F TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 34": "OD1" <-> "OD2" Residue "G PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G ASP 50": "OD1" <-> "OD2" Residue "G PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 132": "OE1" <-> "OE2" Residue "G PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 177": "OE1" <-> "OE2" Residue "G GLU 352": "OE1" <-> "OE2" Residue "G TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 477": "OD1" <-> "OD2" Residue "G TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 34": "OD1" <-> "OD2" Residue "H PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H ASP 50": "OD1" <-> "OD2" Residue "H PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 132": "OE1" <-> "OE2" Residue "H PHE 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 177": "OE1" <-> "OE2" Residue "H GLU 352": "OE1" <-> "OE2" Residue "H TYR 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 477": "OD1" <-> "OD2" Residue "H TYR 509": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 29680 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "B" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "C" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "D" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "E" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "F" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "G" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "H" Number of atoms: 3548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3548 Classifications: {'peptide': 471} Link IDs: {'PTRANS': 18, 'TRANS': 452} Chain breaks: 3 Chain: "A" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "B" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "C" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "D" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "E" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "F" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "G" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Chain: "H" Number of atoms: 162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 162 Unusual residues: {'ATP': 1, 'GTP': 2, 'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 4} Modifications used: {'rna2p': 1} Link IDs: {None: 4} Time building chain proxies: 16.26, per 1000 atoms: 0.55 Number of scatterers: 29680 At special positions: 0 Unit cell: (172.84, 172.84, 142.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 184 16.00 P 96 15.00 O 5904 8.00 N 5040 7.00 C 18456 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=0, symmetry=0 Time building additional restraints: 11.19 Conformation dependent library (CDL) restraints added in 5.6 seconds 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6784 Finding SS restraints... Secondary structure from input PDB file: 160 helices and 40 sheets defined 42.0% alpha, 11.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.06 Creating SS restraints... Processing helix chain 'A' and resid 20 through 26 removed outlier: 4.262A pdb=" N SER A 26 " --> pdb=" O GLN A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 33 No H-bonds generated for 'chain 'A' and resid 31 through 33' Processing helix chain 'A' and resid 45 through 49 Processing helix chain 'A' and resid 75 through 84 removed outlier: 3.725A pdb=" N ALA A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 126 through 137 Processing helix chain 'A' and resid 159 through 163 Processing helix chain 'A' and resid 174 through 178 Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.816A pdb=" N LEU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 267 removed outlier: 4.349A pdb=" N TYR A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 294 Processing helix chain 'A' and resid 306 through 317 removed outlier: 3.929A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 342 through 355 removed outlier: 4.146A pdb=" N TYR A 353 " --> pdb=" O LYS A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 379 Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 452 through 470 Proline residue: A 458 - end of helix removed outlier: 3.531A pdb=" N ILE A 464 " --> pdb=" O LEU A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 475 through 485 Processing helix chain 'A' and resid 494 through 499 Processing helix chain 'B' and resid 20 through 26 removed outlier: 4.257A pdb=" N SER B 26 " --> pdb=" O GLN B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 33 No H-bonds generated for 'chain 'B' and resid 31 through 33' Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 75 through 84 removed outlier: 3.724A pdb=" N ALA B 81 " --> pdb=" O ASP B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 109 Processing helix chain 'B' and resid 126 through 137 Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 174 through 178 Processing helix chain 'B' and resid 193 through 205 Processing helix chain 'B' and resid 223 through 233 removed outlier: 3.814A pdb=" N LEU B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 267 removed outlier: 4.351A pdb=" N TYR B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 294 Processing helix chain 'B' and resid 306 through 317 removed outlier: 3.927A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 337 Processing helix chain 'B' and resid 342 through 355 removed outlier: 4.145A pdb=" N TYR B 353 " --> pdb=" O LYS B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 379 Processing helix chain 'B' and resid 387 through 391 Processing helix chain 'B' and resid 452 through 470 Proline residue: B 458 - end of helix removed outlier: 3.551A pdb=" N ILE B 464 " --> pdb=" O LEU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 475 through 485 Processing helix chain 'B' and resid 494 through 499 Processing helix chain 'C' and resid 20 through 26 removed outlier: 4.256A pdb=" N SER C 26 " --> pdb=" O GLN C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 33 No H-bonds generated for 'chain 'C' and resid 31 through 33' Processing helix chain 'C' and resid 45 through 49 Processing helix chain 'C' and resid 75 through 84 removed outlier: 3.719A pdb=" N ALA C 81 " --> pdb=" O ASP C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 109 Processing helix chain 'C' and resid 126 through 137 Processing helix chain 'C' and resid 159 through 163 Processing helix chain 'C' and resid 174 through 178 Processing helix chain 'C' and resid 193 through 205 Processing helix chain 'C' and resid 224 through 233 Processing helix chain 'C' and resid 254 through 267 removed outlier: 4.350A pdb=" N TYR C 258 " --> pdb=" O GLU C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 294 Processing helix chain 'C' and resid 306 through 317 removed outlier: 3.925A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 332 through 337 Processing helix chain 'C' and resid 342 through 355 removed outlier: 4.150A pdb=" N TYR C 353 " --> pdb=" O LYS C 349 " (cutoff:3.500A) Processing helix chain 'C' and resid 369 through 379 Processing helix chain 'C' and resid 387 through 391 Processing helix chain 'C' and resid 452 through 470 Proline residue: C 458 - end of helix removed outlier: 3.534A pdb=" N ILE C 464 " --> pdb=" O LEU C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 486 Processing helix chain 'C' and resid 494 through 499 Processing helix chain 'D' and resid 20 through 26 removed outlier: 4.262A pdb=" N SER D 26 " --> pdb=" O GLN D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 33 No H-bonds generated for 'chain 'D' and resid 31 through 33' Processing helix chain 'D' and resid 45 through 49 Processing helix chain 'D' and resid 75 through 84 removed outlier: 3.742A pdb=" N ALA D 81 " --> pdb=" O ASP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 109 Processing helix chain 'D' and resid 126 through 137 Processing helix chain 'D' and resid 159 through 163 Processing helix chain 'D' and resid 174 through 178 Processing helix chain 'D' and resid 193 through 205 Processing helix chain 'D' and resid 223 through 233 removed outlier: 3.813A pdb=" N LEU D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 267 Processing helix chain 'D' and resid 280 through 294 Processing helix chain 'D' and resid 306 through 317 removed outlier: 3.926A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 337 Processing helix chain 'D' and resid 342 through 355 removed outlier: 4.124A pdb=" N TYR D 353 " --> pdb=" O LYS D 349 " (cutoff:3.500A) Processing helix chain 'D' and resid 369 through 379 Processing helix chain 'D' and resid 387 through 391 Processing helix chain 'D' and resid 452 through 470 Proline residue: D 458 - end of helix Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 494 through 499 Processing helix chain 'E' and resid 20 through 26 removed outlier: 4.262A pdb=" N SER E 26 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 33 No H-bonds generated for 'chain 'E' and resid 31 through 33' Processing helix chain 'E' and resid 45 through 49 Processing helix chain 'E' and resid 75 through 84 removed outlier: 3.742A pdb=" N ALA E 81 " --> pdb=" O ASP E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 109 Processing helix chain 'E' and resid 126 through 137 Processing helix chain 'E' and resid 159 through 163 Processing helix chain 'E' and resid 174 through 178 Processing helix chain 'E' and resid 193 through 205 Processing helix chain 'E' and resid 223 through 233 removed outlier: 3.813A pdb=" N LEU E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 267 Processing helix chain 'E' and resid 280 through 294 Processing helix chain 'E' and resid 306 through 317 removed outlier: 3.926A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 332 through 337 Processing helix chain 'E' and resid 342 through 355 removed outlier: 4.124A pdb=" N TYR E 353 " --> pdb=" O LYS E 349 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 379 Processing helix chain 'E' and resid 387 through 391 Processing helix chain 'E' and resid 452 through 470 Proline residue: E 458 - end of helix Processing helix chain 'E' and resid 475 through 485 Processing helix chain 'E' and resid 494 through 499 Processing helix chain 'F' and resid 20 through 26 removed outlier: 4.262A pdb=" N SER F 26 " --> pdb=" O GLN F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 33 No H-bonds generated for 'chain 'F' and resid 31 through 33' Processing helix chain 'F' and resid 45 through 49 Processing helix chain 'F' and resid 75 through 84 removed outlier: 3.725A pdb=" N ALA F 81 " --> pdb=" O ASP F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 109 Processing helix chain 'F' and resid 126 through 137 Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 174 through 178 Processing helix chain 'F' and resid 193 through 205 Processing helix chain 'F' and resid 223 through 233 removed outlier: 3.816A pdb=" N LEU F 227 " --> pdb=" O ALA F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 267 removed outlier: 4.349A pdb=" N TYR F 258 " --> pdb=" O GLU F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 294 Processing helix chain 'F' and resid 306 through 317 removed outlier: 3.928A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 332 through 337 Processing helix chain 'F' and resid 342 through 355 removed outlier: 4.145A pdb=" N TYR F 353 " --> pdb=" O LYS F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 369 through 379 Processing helix chain 'F' and resid 387 through 391 Processing helix chain 'F' and resid 452 through 470 Proline residue: F 458 - end of helix removed outlier: 3.526A pdb=" N ILE F 464 " --> pdb=" O LEU F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 475 through 485 Processing helix chain 'F' and resid 494 through 499 Processing helix chain 'G' and resid 20 through 26 removed outlier: 4.258A pdb=" N SER G 26 " --> pdb=" O GLN G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 33 No H-bonds generated for 'chain 'G' and resid 31 through 33' Processing helix chain 'G' and resid 45 through 49 Processing helix chain 'G' and resid 75 through 84 removed outlier: 3.724A pdb=" N ALA G 81 " --> pdb=" O ASP G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 126 through 137 Processing helix chain 'G' and resid 159 through 163 Processing helix chain 'G' and resid 174 through 178 Processing helix chain 'G' and resid 193 through 205 Processing helix chain 'G' and resid 223 through 233 removed outlier: 3.813A pdb=" N LEU G 227 " --> pdb=" O ALA G 223 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 267 removed outlier: 4.351A pdb=" N TYR G 258 " --> pdb=" O GLU G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 280 through 294 Processing helix chain 'G' and resid 306 through 317 removed outlier: 3.927A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 332 through 337 Processing helix chain 'G' and resid 342 through 355 removed outlier: 4.145A pdb=" N TYR G 353 " --> pdb=" O LYS G 349 " (cutoff:3.500A) Processing helix chain 'G' and resid 369 through 379 Processing helix chain 'G' and resid 387 through 391 Processing helix chain 'G' and resid 452 through 470 Proline residue: G 458 - end of helix removed outlier: 3.600A pdb=" N ILE G 464 " --> pdb=" O LEU G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 486 Processing helix chain 'G' and resid 494 through 499 Processing helix chain 'H' and resid 20 through 26 removed outlier: 4.256A pdb=" N SER H 26 " --> pdb=" O GLN H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 45 through 49 Processing helix chain 'H' and resid 75 through 84 removed outlier: 3.721A pdb=" N ALA H 81 " --> pdb=" O ASP H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 109 Processing helix chain 'H' and resid 126 through 137 Processing helix chain 'H' and resid 159 through 163 Processing helix chain 'H' and resid 174 through 178 Processing helix chain 'H' and resid 193 through 205 Processing helix chain 'H' and resid 224 through 233 Processing helix chain 'H' and resid 254 through 267 removed outlier: 4.350A pdb=" N TYR H 258 " --> pdb=" O GLU H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 280 through 294 Processing helix chain 'H' and resid 306 through 317 removed outlier: 3.925A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 332 through 337 Processing helix chain 'H' and resid 342 through 355 removed outlier: 4.150A pdb=" N TYR H 353 " --> pdb=" O LYS H 349 " (cutoff:3.500A) Processing helix chain 'H' and resid 369 through 379 Processing helix chain 'H' and resid 387 through 391 Processing helix chain 'H' and resid 452 through 470 Proline residue: H 458 - end of helix removed outlier: 3.534A pdb=" N ILE H 464 " --> pdb=" O LEU H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 475 through 486 Processing helix chain 'H' and resid 494 through 499 Processing sheet with id=AA1, first strand: chain 'A' and resid 18 through 19 Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 56 removed outlier: 6.600A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 65 through 67 removed outlier: 3.607A pdb=" N PHE A 90 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY A 89 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ALA A 249 " --> pdb=" O GLY A 89 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE A 91 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA A 248 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY A 302 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY A 320 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN A 303 " --> pdb=" O ARG A 322 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE A 361 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N MET A 385 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA A 363 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE A 66 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 142 through 145 removed outlier: 3.525A pdb=" N GLY A 156 " --> pdb=" O ILE A 144 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE A 157 " --> pdb=" O THR A 180 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 188 through 189 removed outlier: 6.191A pdb=" N ALA A 188 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE A 211 " --> pdb=" O VAL A 219 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 18 through 19 Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 56 removed outlier: 6.595A pdb=" N ILE B 59 " --> pdb=" O LEU B 55 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 65 through 67 removed outlier: 3.556A pdb=" N ILE B 88 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE B 90 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLY B 89 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ALA B 249 " --> pdb=" O GLY B 89 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE B 91 " --> pdb=" O ALA B 249 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA B 248 " --> pdb=" O VAL B 272 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY B 302 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY B 320 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG B 322 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN B 303 " --> pdb=" O ARG B 322 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE B 361 " --> pdb=" O THR B 383 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N MET B 385 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA B 363 " --> pdb=" O MET B 385 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE B 66 " --> pdb=" O MET B 386 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 142 through 145 removed outlier: 3.650A pdb=" N ILE B 157 " --> pdb=" O THR B 180 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 188 through 189 removed outlier: 6.209A pdb=" N ALA B 188 " --> pdb=" O VAL B 212 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE B 211 " --> pdb=" O VAL B 219 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 18 through 19 Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 56 removed outlier: 6.592A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.557A pdb=" N ILE C 88 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE C 90 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N GLY C 89 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA C 249 " --> pdb=" O GLY C 89 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE C 91 " --> pdb=" O ALA C 249 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA C 248 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY C 302 " --> pdb=" O LEU C 273 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY C 320 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ARG C 322 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN C 303 " --> pdb=" O ARG C 322 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE C 361 " --> pdb=" O THR C 383 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N MET C 385 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA C 363 " --> pdb=" O MET C 385 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE C 66 " --> pdb=" O MET C 386 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 142 through 145 removed outlier: 3.673A pdb=" N ILE C 157 " --> pdb=" O THR C 180 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 188 through 189 removed outlier: 3.697A pdb=" N ALA C 188 " --> pdb=" O PRO C 210 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL C 212 " --> pdb=" O ALA C 188 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N LEU C 209 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE C 221 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE C 211 " --> pdb=" O VAL C 219 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 18 through 19 Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 56 removed outlier: 6.597A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 65 through 67 removed outlier: 3.611A pdb=" N PHE D 90 " --> pdb=" O SER D 67 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY D 89 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA D 249 " --> pdb=" O GLY D 89 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE D 91 " --> pdb=" O ALA D 249 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA D 248 " --> pdb=" O VAL D 272 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY D 302 " --> pdb=" O LEU D 273 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY D 320 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG D 322 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN D 303 " --> pdb=" O ARG D 322 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE D 361 " --> pdb=" O THR D 383 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N MET D 385 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA D 363 " --> pdb=" O MET D 385 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N ILE D 66 " --> pdb=" O MET D 386 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 142 through 145 removed outlier: 3.669A pdb=" N ILE D 157 " --> pdb=" O THR D 180 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 188 through 189 removed outlier: 6.204A pdb=" N ALA D 188 " --> pdb=" O VAL D 212 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE D 211 " --> pdb=" O VAL D 219 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 18 through 19 Processing sheet with id=AC4, first strand: chain 'E' and resid 53 through 56 removed outlier: 6.597A pdb=" N ILE E 59 " --> pdb=" O LEU E 55 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 65 through 67 removed outlier: 3.507A pdb=" N ILE E 88 " --> pdb=" O LEU E 65 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE E 90 " --> pdb=" O SER E 67 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY E 89 " --> pdb=" O GLY E 247 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA E 249 " --> pdb=" O GLY E 89 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ILE E 91 " --> pdb=" O ALA E 249 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA E 248 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLY E 302 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY E 320 " --> pdb=" O VAL E 299 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ARG E 322 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ASN E 303 " --> pdb=" O ARG E 322 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ILE E 361 " --> pdb=" O THR E 383 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N MET E 385 " --> pdb=" O ILE E 361 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA E 363 " --> pdb=" O MET E 385 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ILE E 66 " --> pdb=" O MET E 386 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 142 through 145 removed outlier: 3.669A pdb=" N ILE E 157 " --> pdb=" O THR E 180 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 188 through 189 removed outlier: 6.204A pdb=" N ALA E 188 " --> pdb=" O VAL E 212 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE E 211 " --> pdb=" O VAL E 219 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 18 through 19 Processing sheet with id=AC9, first strand: chain 'F' and resid 53 through 56 removed outlier: 6.600A pdb=" N ILE F 59 " --> pdb=" O LEU F 55 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 65 through 67 removed outlier: 3.607A pdb=" N PHE F 90 " --> pdb=" O SER F 67 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N GLY F 89 " --> pdb=" O GLY F 247 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ALA F 249 " --> pdb=" O GLY F 89 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE F 91 " --> pdb=" O ALA F 249 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA F 248 " --> pdb=" O VAL F 272 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY F 302 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY F 320 " --> pdb=" O VAL F 299 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG F 322 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN F 303 " --> pdb=" O ARG F 322 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE F 361 " --> pdb=" O THR F 383 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N MET F 385 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ALA F 363 " --> pdb=" O MET F 385 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ILE F 66 " --> pdb=" O MET F 386 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 142 through 145 removed outlier: 3.525A pdb=" N GLY F 156 " --> pdb=" O ILE F 144 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE F 157 " --> pdb=" O THR F 180 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 188 through 189 removed outlier: 6.191A pdb=" N ALA F 188 " --> pdb=" O VAL F 212 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ILE F 211 " --> pdb=" O VAL F 219 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 18 through 19 Processing sheet with id=AD5, first strand: chain 'G' and resid 53 through 56 removed outlier: 6.596A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 65 through 67 removed outlier: 3.553A pdb=" N ILE G 88 " --> pdb=" O LEU G 65 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N PHE G 90 " --> pdb=" O SER G 67 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N GLY G 89 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ALA G 249 " --> pdb=" O GLY G 89 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE G 91 " --> pdb=" O ALA G 249 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N ALA G 248 " --> pdb=" O VAL G 272 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY G 302 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLY G 320 " --> pdb=" O VAL G 299 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG G 322 " --> pdb=" O GLY G 301 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN G 303 " --> pdb=" O ARG G 322 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ILE G 361 " --> pdb=" O THR G 383 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N MET G 385 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA G 363 " --> pdb=" O MET G 385 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ILE G 66 " --> pdb=" O MET G 386 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 142 through 145 removed outlier: 3.650A pdb=" N ILE G 157 " --> pdb=" O THR G 180 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 188 through 189 removed outlier: 6.209A pdb=" N ALA G 188 " --> pdb=" O VAL G 212 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N ILE G 211 " --> pdb=" O VAL G 219 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AE1, first strand: chain 'H' and resid 53 through 56 removed outlier: 6.592A pdb=" N ILE H 59 " --> pdb=" O LEU H 55 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 65 through 67 removed outlier: 3.557A pdb=" N ILE H 88 " --> pdb=" O LEU H 65 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N PHE H 90 " --> pdb=" O SER H 67 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLY H 89 " --> pdb=" O GLY H 247 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA H 249 " --> pdb=" O GLY H 89 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILE H 91 " --> pdb=" O ALA H 249 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA H 248 " --> pdb=" O VAL H 272 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY H 302 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY H 320 " --> pdb=" O VAL H 299 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG H 322 " --> pdb=" O GLY H 301 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN H 303 " --> pdb=" O ARG H 322 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE H 361 " --> pdb=" O THR H 383 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N MET H 385 " --> pdb=" O ILE H 361 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA H 363 " --> pdb=" O MET H 385 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE H 66 " --> pdb=" O MET H 386 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 142 through 145 removed outlier: 3.674A pdb=" N ILE H 157 " --> pdb=" O THR H 180 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 188 through 189 removed outlier: 3.699A pdb=" N ALA H 188 " --> pdb=" O PRO H 210 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL H 212 " --> pdb=" O ALA H 188 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N LEU H 209 " --> pdb=" O ILE H 221 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N ILE H 221 " --> pdb=" O LEU H 209 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ILE H 211 " --> pdb=" O VAL H 219 " (cutoff:3.500A) 1046 hydrogen bonds defined for protein. 2841 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: 10.76 Time building geometry restraints manager: 12.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 4848 1.29 - 1.42: 7216 1.42 - 1.55: 17679 1.55 - 1.68: 161 1.68 - 1.81: 312 Bond restraints: 30216 Sorted by residual: bond pdb=" C5 IMP G 603 " pdb=" C6 IMP G 603 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.86e+01 bond pdb=" C5 IMP C 603 " pdb=" C6 IMP C 603 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.85e+01 bond pdb=" C5 IMP D 603 " pdb=" C6 IMP D 603 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.82e+01 bond pdb=" C5 IMP H 603 " pdb=" C6 IMP H 603 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C5 IMP B 603 " pdb=" C6 IMP B 603 " ideal model delta sigma weight residual 1.390 1.529 -0.139 2.00e-02 2.50e+03 4.81e+01 ... (remaining 30211 not shown) Histogram of bond angle deviations from ideal: 94.48 - 104.11: 659 104.11 - 113.74: 17908 113.74 - 123.37: 21562 123.37 - 133.00: 967 133.00 - 142.63: 24 Bond angle restraints: 41120 Sorted by residual: angle pdb=" PA ATP A 604 " pdb=" O3A ATP A 604 " pdb=" PB ATP A 604 " ideal model delta sigma weight residual 136.83 123.59 13.24 1.00e+00 1.00e+00 1.75e+02 angle pdb=" PA ATP F 604 " pdb=" O3A ATP F 604 " pdb=" PB ATP F 604 " ideal model delta sigma weight residual 136.83 123.59 13.24 1.00e+00 1.00e+00 1.75e+02 angle pdb=" PA ATP D 604 " pdb=" O3A ATP D 604 " pdb=" PB ATP D 604 " ideal model delta sigma weight residual 136.83 124.03 12.80 1.00e+00 1.00e+00 1.64e+02 angle pdb=" PA ATP E 604 " pdb=" O3A ATP E 604 " pdb=" PB ATP E 604 " ideal model delta sigma weight residual 136.83 124.05 12.78 1.00e+00 1.00e+00 1.63e+02 angle pdb=" PA ATP B 604 " pdb=" O3A ATP B 604 " pdb=" PB ATP B 604 " ideal model delta sigma weight residual 136.83 124.09 12.74 1.00e+00 1.00e+00 1.62e+02 ... (remaining 41115 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.18: 17612 35.18 - 70.37: 631 70.37 - 105.55: 87 105.55 - 140.74: 14 140.74 - 175.92: 48 Dihedral angle restraints: 18392 sinusoidal: 7768 harmonic: 10624 Sorted by residual: dihedral pdb=" O5' GTP B 601 " pdb=" O3A GTP B 601 " pdb=" PA GTP B 601 " pdb=" PB GTP B 601 " ideal model delta sinusoidal sigma weight residual 274.12 98.20 175.92 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O5' GTP G 601 " pdb=" O3A GTP G 601 " pdb=" PA GTP G 601 " pdb=" PB GTP G 601 " ideal model delta sinusoidal sigma weight residual 274.12 98.27 175.85 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O5' GTP D 601 " pdb=" O3A GTP D 601 " pdb=" PA GTP D 601 " pdb=" PB GTP D 601 " ideal model delta sinusoidal sigma weight residual 274.12 98.51 175.61 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 18389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.203: 4664 0.203 - 0.405: 88 0.405 - 0.608: 8 0.608 - 0.810: 0 0.810 - 1.013: 16 Chirality restraints: 4776 Sorted by residual: chirality pdb=" C4' IMP F 603 " pdb=" C3' IMP F 603 " pdb=" C5' IMP F 603 " pdb=" O4' IMP F 603 " both_signs ideal model delta sigma weight residual False -2.50 -1.49 -1.01 2.00e-01 2.50e+01 2.56e+01 chirality pdb=" C4' IMP A 603 " pdb=" C3' IMP A 603 " pdb=" C5' IMP A 603 " pdb=" O4' IMP A 603 " both_signs ideal model delta sigma weight residual False -2.50 -1.49 -1.01 2.00e-01 2.50e+01 2.55e+01 chirality pdb=" C4' IMP E 603 " pdb=" C3' IMP E 603 " pdb=" C5' IMP E 603 " pdb=" O4' IMP E 603 " both_signs ideal model delta sigma weight residual False -2.50 -1.49 -1.01 2.00e-01 2.50e+01 2.53e+01 ... (remaining 4773 not shown) Planarity restraints: 5056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 180 " 0.079 5.00e-02 4.00e+02 1.08e-01 1.88e+01 pdb=" N PRO H 181 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO H 181 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO H 181 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR E 180 " -0.015 2.00e-02 2.50e+03 2.98e-02 8.86e+00 pdb=" C THR E 180 " 0.052 2.00e-02 2.50e+03 pdb=" O THR E 180 " -0.019 2.00e-02 2.50e+03 pdb=" N PRO E 181 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR G 180 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C THR G 180 " -0.051 2.00e-02 2.50e+03 pdb=" O THR G 180 " 0.019 2.00e-02 2.50e+03 pdb=" N PRO G 181 " 0.017 2.00e-02 2.50e+03 ... (remaining 5053 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 775 2.68 - 3.24: 30073 3.24 - 3.79: 44310 3.79 - 4.35: 62667 4.35 - 4.90: 105070 Nonbonded interactions: 242895 Sorted by model distance: nonbonded pdb=" O VAL E 73 " pdb=" OG1 THR E 74 " model vdw 2.127 2.440 nonbonded pdb=" O VAL H 73 " pdb=" OG1 THR H 74 " model vdw 2.128 2.440 nonbonded pdb=" O VAL C 73 " pdb=" OG1 THR C 74 " model vdw 2.128 2.440 nonbonded pdb=" O VAL D 73 " pdb=" OG1 THR D 74 " model vdw 2.130 2.440 nonbonded pdb=" O VAL G 73 " pdb=" OG1 THR G 74 " model vdw 2.133 2.440 ... (remaining 242890 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: 5.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.090 Check model and map are aligned: 0.220 Set scattering table: 0.260 Process input model: 77.410 Find NCS groups from input model: 2.260 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 0.157 30216 Z= 0.443 Angle : 1.179 22.127 41120 Z= 0.607 Chirality : 0.089 1.013 4776 Planarity : 0.005 0.108 5056 Dihedral : 20.780 175.921 11608 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.27 % Favored : 96.52 % Rotamer: Outliers : 0.85 % Allowed : 11.98 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.13), residues: 3704 helix: -0.08 (0.14), residues: 1376 sheet: -0.61 (0.32), residues: 216 loop : -0.98 (0.13), residues: 2112 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 507 PHE 0.013 0.001 PHE B 456 TYR 0.013 0.001 TYR D 509 ARG 0.003 0.000 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 349 time to evaluate : 3.015 Fit side-chains REVERT: A 327 CYS cc_start: 0.8339 (p) cc_final: 0.7988 (p) REVERT: B 327 CYS cc_start: 0.8319 (p) cc_final: 0.7987 (p) REVERT: C 327 CYS cc_start: 0.8288 (p) cc_final: 0.7961 (p) REVERT: D 327 CYS cc_start: 0.8307 (p) cc_final: 0.7969 (p) REVERT: E 327 CYS cc_start: 0.8300 (p) cc_final: 0.7970 (p) REVERT: F 327 CYS cc_start: 0.8341 (p) cc_final: 0.7993 (p) REVERT: G 327 CYS cc_start: 0.8317 (p) cc_final: 0.7988 (p) REVERT: H 327 CYS cc_start: 0.8255 (p) cc_final: 0.7954 (p) outliers start: 26 outliers final: 11 residues processed: 373 average time/residue: 0.3418 time to fit residues: 215.5953 Evaluate side-chains 317 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 306 time to evaluate : 2.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain E residue 350 VAL Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain H residue 350 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 317 optimal weight: 0.0770 chunk 284 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 97 optimal weight: 0.0050 chunk 192 optimal weight: 2.9990 chunk 152 optimal weight: 8.9990 chunk 294 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 219 optimal weight: 0.9980 chunk 341 optimal weight: 2.9990 overall best weight: 0.5552 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN B 33 ASN D 33 ASN E 33 ASN F 33 ASN G 33 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 30216 Z= 0.194 Angle : 0.651 6.779 41120 Z= 0.318 Chirality : 0.045 0.165 4776 Planarity : 0.004 0.052 5056 Dihedral : 19.970 154.903 5014 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.40 % Favored : 96.38 % Rotamer: Outliers : 1.46 % Allowed : 11.91 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3704 helix: 0.12 (0.14), residues: 1424 sheet: -0.12 (0.30), residues: 280 loop : -0.59 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 93 PHE 0.010 0.001 PHE F 456 TYR 0.007 0.001 TYR G 509 ARG 0.003 0.001 ARG E 412 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 339 time to evaluate : 3.093 Fit side-chains REVERT: A 48 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6816 (tt0) REVERT: B 48 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6813 (tt0) REVERT: B 144 ILE cc_start: 0.7647 (mm) cc_final: 0.7320 (mm) REVERT: C 48 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.6781 (tt0) REVERT: D 48 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6791 (tt0) REVERT: D 144 ILE cc_start: 0.7629 (mm) cc_final: 0.7280 (mm) REVERT: E 48 GLU cc_start: 0.7079 (OUTLIER) cc_final: 0.6801 (tt0) REVERT: E 144 ILE cc_start: 0.7620 (mm) cc_final: 0.7300 (mm) REVERT: F 48 GLU cc_start: 0.7080 (OUTLIER) cc_final: 0.6822 (tt0) REVERT: G 48 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6777 (tt0) REVERT: G 144 ILE cc_start: 0.7689 (mm) cc_final: 0.7365 (mm) REVERT: H 48 GLU cc_start: 0.7064 (OUTLIER) cc_final: 0.6782 (tt0) outliers start: 45 outliers final: 24 residues processed: 384 average time/residue: 0.3420 time to fit residues: 231.9966 Evaluate side-chains 329 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 297 time to evaluate : 3.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 GLU Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain B residue 48 GLU Chi-restraints excluded: chain B residue 350 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain E residue 48 GLU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain F residue 48 GLU Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 350 VAL Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain G residue 48 GLU Chi-restraints excluded: chain G residue 350 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 189 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 284 optimal weight: 2.9990 chunk 232 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 342 optimal weight: 4.9990 chunk 369 optimal weight: 3.9990 chunk 304 optimal weight: 0.9980 chunk 339 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 274 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN B 198 ASN C 198 ASN D 198 ASN E 198 ASN F 198 ASN G 198 ASN H 198 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 30216 Z= 0.379 Angle : 0.721 7.796 41120 Z= 0.356 Chirality : 0.049 0.182 4776 Planarity : 0.005 0.046 5056 Dihedral : 19.056 161.010 5004 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.37 % Favored : 94.41 % Rotamer: Outliers : 3.29 % Allowed : 13.25 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.14), residues: 3704 helix: -0.11 (0.14), residues: 1368 sheet: 0.12 (0.34), residues: 216 loop : -0.67 (0.14), residues: 2120 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 372 PHE 0.017 0.002 PHE B 139 TYR 0.012 0.002 TYR A 294 ARG 0.003 0.001 ARG H 203 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 322 time to evaluate : 3.109 Fit side-chains REVERT: A 135 MET cc_start: 0.7925 (tmm) cc_final: 0.7496 (tmm) REVERT: A 144 ILE cc_start: 0.8196 (mm) cc_final: 0.7818 (mt) REVERT: B 135 MET cc_start: 0.7925 (tmm) cc_final: 0.7498 (tmm) REVERT: B 144 ILE cc_start: 0.8182 (mm) cc_final: 0.7808 (mm) REVERT: C 135 MET cc_start: 0.7910 (tmm) cc_final: 0.7474 (tmm) REVERT: C 144 ILE cc_start: 0.8122 (mm) cc_final: 0.7917 (mm) REVERT: D 135 MET cc_start: 0.7939 (tmm) cc_final: 0.7510 (tmm) REVERT: E 135 MET cc_start: 0.7949 (tmm) cc_final: 0.7515 (tmm) REVERT: F 135 MET cc_start: 0.7939 (tmm) cc_final: 0.7506 (tmm) REVERT: F 144 ILE cc_start: 0.8185 (mm) cc_final: 0.7806 (mt) REVERT: G 135 MET cc_start: 0.7935 (tmm) cc_final: 0.7513 (tmm) REVERT: H 135 MET cc_start: 0.7946 (tmm) cc_final: 0.7508 (tmm) REVERT: H 144 ILE cc_start: 0.8118 (mm) cc_final: 0.7906 (mm) REVERT: H 184 GLU cc_start: 0.7292 (tm-30) cc_final: 0.6819 (mt-10) outliers start: 101 outliers final: 64 residues processed: 409 average time/residue: 0.3385 time to fit residues: 236.0345 Evaluate side-chains 355 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 291 time to evaluate : 3.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 158 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 120 VAL Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 158 VAL Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 337 optimal weight: 0.0770 chunk 257 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 163 optimal weight: 3.9990 chunk 229 optimal weight: 0.7980 chunk 343 optimal weight: 0.8980 chunk 363 optimal weight: 0.6980 chunk 179 optimal weight: 7.9990 chunk 325 optimal weight: 0.7980 chunk 97 optimal weight: 0.0980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 ASN F 469 GLN H 33 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 30216 Z= 0.158 Angle : 0.571 7.492 41120 Z= 0.278 Chirality : 0.043 0.161 4776 Planarity : 0.004 0.045 5056 Dihedral : 17.899 157.388 5000 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.62 % Favored : 97.17 % Rotamer: Outliers : 2.47 % Allowed : 15.98 % Favored : 81.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3704 helix: 0.47 (0.15), residues: 1376 sheet: -0.04 (0.28), residues: 280 loop : -0.31 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 466 PHE 0.010 0.001 PHE F 456 TYR 0.008 0.001 TYR B 348 ARG 0.002 0.000 ARG D 412 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 344 time to evaluate : 3.519 Fit side-chains REVERT: A 135 MET cc_start: 0.7935 (tmm) cc_final: 0.7492 (tmm) REVERT: A 500 GLU cc_start: 0.6052 (OUTLIER) cc_final: 0.5584 (mt-10) REVERT: B 135 MET cc_start: 0.7954 (tmm) cc_final: 0.7498 (tmm) REVERT: B 500 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5455 (mt-10) REVERT: C 135 MET cc_start: 0.7925 (tmm) cc_final: 0.7481 (tmm) REVERT: C 144 ILE cc_start: 0.8136 (mm) cc_final: 0.7905 (mm) REVERT: C 500 GLU cc_start: 0.6060 (OUTLIER) cc_final: 0.5490 (mt-10) REVERT: D 135 MET cc_start: 0.7955 (tmm) cc_final: 0.7503 (tmm) REVERT: D 500 GLU cc_start: 0.6159 (OUTLIER) cc_final: 0.5536 (mt-10) REVERT: E 135 MET cc_start: 0.7953 (tmm) cc_final: 0.7498 (tmm) REVERT: E 500 GLU cc_start: 0.6042 (OUTLIER) cc_final: 0.5428 (mt-10) REVERT: F 135 MET cc_start: 0.7937 (tmm) cc_final: 0.7495 (tmm) REVERT: F 469 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8501 (tt0) REVERT: F 500 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5574 (mt-10) REVERT: G 135 MET cc_start: 0.7953 (tmm) cc_final: 0.7500 (tmm) REVERT: G 500 GLU cc_start: 0.6067 (OUTLIER) cc_final: 0.5444 (mt-10) REVERT: H 135 MET cc_start: 0.7966 (tmm) cc_final: 0.7530 (tmm) REVERT: H 144 ILE cc_start: 0.8112 (mm) cc_final: 0.7872 (mm) REVERT: H 500 GLU cc_start: 0.6044 (OUTLIER) cc_final: 0.5461 (mt-10) outliers start: 76 outliers final: 40 residues processed: 396 average time/residue: 0.3503 time to fit residues: 233.5340 Evaluate side-chains 337 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 288 time to evaluate : 3.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 469 GLN Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 302 optimal weight: 6.9990 chunk 206 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 270 optimal weight: 0.7980 chunk 149 optimal weight: 5.9990 chunk 310 optimal weight: 4.9990 chunk 251 optimal weight: 0.0870 chunk 0 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 chunk 326 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.7362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 469 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 30216 Z= 0.177 Angle : 0.576 7.365 41120 Z= 0.277 Chirality : 0.043 0.158 4776 Planarity : 0.004 0.044 5056 Dihedral : 17.537 159.261 5000 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.62 % Favored : 96.17 % Rotamer: Outliers : 2.64 % Allowed : 15.23 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.14), residues: 3704 helix: 0.62 (0.14), residues: 1368 sheet: -0.17 (0.27), residues: 280 loop : -0.24 (0.14), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS G 466 PHE 0.009 0.001 PHE F 456 TYR 0.007 0.001 TYR A 348 ARG 0.002 0.000 ARG E 203 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 338 time to evaluate : 3.006 Fit side-chains REVERT: A 135 MET cc_start: 0.7926 (tmm) cc_final: 0.7473 (tmm) REVERT: B 135 MET cc_start: 0.7953 (tmm) cc_final: 0.7421 (tmm) REVERT: B 204 SER cc_start: 0.8116 (OUTLIER) cc_final: 0.7789 (p) REVERT: B 500 GLU cc_start: 0.5772 (OUTLIER) cc_final: 0.5354 (mt-10) REVERT: C 135 MET cc_start: 0.7870 (tmm) cc_final: 0.7370 (tmm) REVERT: C 144 ILE cc_start: 0.8191 (mm) cc_final: 0.7889 (mm) REVERT: C 500 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.5577 (mt-10) REVERT: D 135 MET cc_start: 0.7948 (tmm) cc_final: 0.7421 (tmm) REVERT: D 204 SER cc_start: 0.8039 (OUTLIER) cc_final: 0.7667 (p) REVERT: D 500 GLU cc_start: 0.6283 (OUTLIER) cc_final: 0.5638 (mt-10) REVERT: E 135 MET cc_start: 0.7950 (tmm) cc_final: 0.7416 (tmm) REVERT: E 500 GLU cc_start: 0.6272 (OUTLIER) cc_final: 0.5610 (mt-10) REVERT: F 135 MET cc_start: 0.7930 (tmm) cc_final: 0.7481 (tmm) REVERT: F 500 GLU cc_start: 0.6068 (OUTLIER) cc_final: 0.5584 (mt-10) REVERT: G 135 MET cc_start: 0.7952 (tmm) cc_final: 0.7407 (tmm) REVERT: G 204 SER cc_start: 0.8116 (OUTLIER) cc_final: 0.7787 (p) REVERT: G 500 GLU cc_start: 0.5794 (OUTLIER) cc_final: 0.5366 (mt-10) REVERT: H 135 MET cc_start: 0.7978 (tmm) cc_final: 0.7435 (tmm) REVERT: H 144 ILE cc_start: 0.8167 (mm) cc_final: 0.7861 (mm) REVERT: H 500 GLU cc_start: 0.6123 (OUTLIER) cc_final: 0.5547 (mt-10) outliers start: 81 outliers final: 44 residues processed: 398 average time/residue: 0.3701 time to fit residues: 243.4870 Evaluate side-chains 346 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 292 time to evaluate : 5.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 122 optimal weight: 4.9990 chunk 327 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 363 optimal weight: 2.9990 chunk 301 optimal weight: 1.9990 chunk 168 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 190 optimal weight: 2.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN B 33 ASN C 112 GLN D 112 GLN E 112 GLN G 33 ASN H 112 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 30216 Z= 0.351 Angle : 0.670 7.570 41120 Z= 0.327 Chirality : 0.048 0.199 4776 Planarity : 0.004 0.039 5056 Dihedral : 17.976 161.333 5000 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.81 % Favored : 94.98 % Rotamer: Outliers : 4.13 % Allowed : 14.26 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.14), residues: 3704 helix: 0.30 (0.14), residues: 1376 sheet: -0.37 (0.28), residues: 280 loop : -0.54 (0.14), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 372 PHE 0.018 0.002 PHE B 35 TYR 0.013 0.002 TYR A 348 ARG 0.004 0.000 ARG C 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 271 time to evaluate : 4.423 Fit side-chains REVERT: A 500 GLU cc_start: 0.6139 (OUTLIER) cc_final: 0.5631 (mt-10) REVERT: B 204 SER cc_start: 0.8184 (OUTLIER) cc_final: 0.7690 (p) REVERT: B 500 GLU cc_start: 0.6037 (OUTLIER) cc_final: 0.5536 (mt-10) REVERT: C 500 GLU cc_start: 0.6147 (OUTLIER) cc_final: 0.5611 (mt-10) REVERT: D 204 SER cc_start: 0.8171 (OUTLIER) cc_final: 0.7680 (p) REVERT: D 500 GLU cc_start: 0.6116 (OUTLIER) cc_final: 0.5593 (mt-10) REVERT: E 204 SER cc_start: 0.8166 (OUTLIER) cc_final: 0.7675 (p) REVERT: E 500 GLU cc_start: 0.6113 (OUTLIER) cc_final: 0.5588 (mt-10) REVERT: F 500 GLU cc_start: 0.6041 (OUTLIER) cc_final: 0.5585 (mt-10) REVERT: G 204 SER cc_start: 0.8176 (OUTLIER) cc_final: 0.7684 (p) REVERT: G 500 GLU cc_start: 0.6033 (OUTLIER) cc_final: 0.5538 (mt-10) REVERT: H 500 GLU cc_start: 0.6120 (OUTLIER) cc_final: 0.5595 (mt-10) outliers start: 127 outliers final: 76 residues processed: 386 average time/residue: 0.3633 time to fit residues: 238.9650 Evaluate side-chains 353 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 265 time to evaluate : 3.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 140 SER Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain F residue 140 SER Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 350 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 265 optimal weight: 0.7980 chunk 205 optimal weight: 4.9990 chunk 306 optimal weight: 0.9990 chunk 203 optimal weight: 0.9990 chunk 362 optimal weight: 0.8980 chunk 226 optimal weight: 6.9990 chunk 220 optimal weight: 0.8980 chunk 167 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN C 21 GLN C 112 GLN D 33 ASN D 112 GLN E 33 ASN E 112 GLN F 33 ASN H 21 GLN H 112 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 30216 Z= 0.180 Angle : 0.573 6.965 41120 Z= 0.277 Chirality : 0.043 0.161 4776 Planarity : 0.004 0.040 5056 Dihedral : 17.386 162.141 5000 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.89 % Favored : 96.90 % Rotamer: Outliers : 3.03 % Allowed : 15.85 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.14), residues: 3704 helix: 0.64 (0.14), residues: 1376 sheet: -0.57 (0.24), residues: 320 loop : -0.37 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 466 PHE 0.009 0.001 PHE A 456 TYR 0.008 0.001 TYR A 348 ARG 0.002 0.000 ARG A 224 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 287 time to evaluate : 3.178 Fit side-chains REVERT: A 204 SER cc_start: 0.8114 (OUTLIER) cc_final: 0.7759 (p) REVERT: A 500 GLU cc_start: 0.6061 (OUTLIER) cc_final: 0.5578 (mt-10) REVERT: B 204 SER cc_start: 0.8209 (OUTLIER) cc_final: 0.7770 (p) REVERT: B 500 GLU cc_start: 0.6203 (OUTLIER) cc_final: 0.5706 (mt-10) REVERT: D 204 SER cc_start: 0.8196 (OUTLIER) cc_final: 0.7764 (p) REVERT: E 204 SER cc_start: 0.8193 (OUTLIER) cc_final: 0.7764 (p) REVERT: E 500 GLU cc_start: 0.6102 (OUTLIER) cc_final: 0.5635 (mt-10) REVERT: F 204 SER cc_start: 0.8109 (OUTLIER) cc_final: 0.7758 (p) REVERT: G 204 SER cc_start: 0.8210 (OUTLIER) cc_final: 0.7776 (p) REVERT: G 500 GLU cc_start: 0.6203 (OUTLIER) cc_final: 0.5712 (mt-10) REVERT: H 500 GLU cc_start: 0.6056 (OUTLIER) cc_final: 0.5621 (mt-10) outliers start: 93 outliers final: 67 residues processed: 372 average time/residue: 0.3499 time to fit residues: 219.9058 Evaluate side-chains 340 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 262 time to evaluate : 2.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 186 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 186 VAL Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 186 VAL Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 186 VAL Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 224 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 109 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 246 optimal weight: 6.9990 chunk 179 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 284 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 112 GLN F 112 GLN G 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 30216 Z= 0.370 Angle : 0.668 8.287 41120 Z= 0.327 Chirality : 0.047 0.165 4776 Planarity : 0.004 0.037 5056 Dihedral : 17.811 163.136 5000 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.13 % Favored : 94.65 % Rotamer: Outliers : 3.52 % Allowed : 15.46 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.14), residues: 3704 helix: 0.33 (0.14), residues: 1376 sheet: -0.80 (0.24), residues: 320 loop : -0.62 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 372 PHE 0.016 0.002 PHE B 35 TYR 0.011 0.002 TYR G 348 ARG 0.003 0.000 ARG F 480 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 251 time to evaluate : 3.139 Fit side-chains REVERT: A 204 SER cc_start: 0.8265 (OUTLIER) cc_final: 0.7804 (p) REVERT: A 500 GLU cc_start: 0.6046 (OUTLIER) cc_final: 0.5529 (mt-10) REVERT: B 204 SER cc_start: 0.8308 (OUTLIER) cc_final: 0.7819 (p) REVERT: B 500 GLU cc_start: 0.6009 (OUTLIER) cc_final: 0.5547 (mt-10) REVERT: C 204 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.7839 (p) REVERT: D 204 SER cc_start: 0.8296 (OUTLIER) cc_final: 0.7810 (p) REVERT: E 204 SER cc_start: 0.8289 (OUTLIER) cc_final: 0.7807 (p) REVERT: E 500 GLU cc_start: 0.6103 (OUTLIER) cc_final: 0.5730 (mt-10) REVERT: F 117 ASP cc_start: 0.8044 (p0) cc_final: 0.7815 (p0) REVERT: G 117 ASP cc_start: 0.8060 (t70) cc_final: 0.7860 (t0) REVERT: G 204 SER cc_start: 0.8309 (OUTLIER) cc_final: 0.7818 (p) REVERT: G 500 GLU cc_start: 0.6030 (OUTLIER) cc_final: 0.5563 (mt-10) REVERT: H 204 SER cc_start: 0.8281 (OUTLIER) cc_final: 0.7846 (p) outliers start: 108 outliers final: 80 residues processed: 353 average time/residue: 0.3582 time to fit residues: 214.8842 Evaluate side-chains 329 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 238 time to evaluate : 3.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 327 CYS Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 327 CYS Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 383 THR Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 327 CYS Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 455 LYS Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 477 ASP Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 329 optimal weight: 0.7980 chunk 347 optimal weight: 2.9990 chunk 316 optimal weight: 0.9990 chunk 337 optimal weight: 4.9990 chunk 203 optimal weight: 8.9990 chunk 147 optimal weight: 0.7980 chunk 265 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 305 optimal weight: 0.9980 chunk 319 optimal weight: 2.9990 chunk 336 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 21 GLN B 112 GLN C 21 GLN D 21 GLN D 441 GLN E 21 GLN F 21 GLN F 112 GLN G 112 GLN H 21 GLN H 441 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30216 Z= 0.193 Angle : 0.587 8.456 41120 Z= 0.283 Chirality : 0.044 0.164 4776 Planarity : 0.004 0.037 5056 Dihedral : 17.293 164.608 5000 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.22 % Allowed : 3.08 % Favored : 96.71 % Rotamer: Outliers : 3.03 % Allowed : 16.93 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.14), residues: 3704 helix: 0.65 (0.14), residues: 1376 sheet: -0.76 (0.24), residues: 320 loop : -0.45 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS G 466 PHE 0.010 0.001 PHE C 139 TYR 0.008 0.001 TYR A 348 ARG 0.003 0.000 ARG H 224 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 273 time to evaluate : 3.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 SER cc_start: 0.8188 (OUTLIER) cc_final: 0.7788 (p) REVERT: A 500 GLU cc_start: 0.6039 (OUTLIER) cc_final: 0.5570 (mt-10) REVERT: B 204 SER cc_start: 0.8205 (OUTLIER) cc_final: 0.7725 (p) REVERT: C 204 SER cc_start: 0.8159 (OUTLIER) cc_final: 0.7739 (p) REVERT: D 204 SER cc_start: 0.8177 (OUTLIER) cc_final: 0.7729 (p) REVERT: E 204 SER cc_start: 0.8180 (OUTLIER) cc_final: 0.7732 (p) REVERT: E 500 GLU cc_start: 0.5976 (OUTLIER) cc_final: 0.5579 (mt-10) REVERT: F 204 SER cc_start: 0.8188 (OUTLIER) cc_final: 0.7787 (p) REVERT: G 204 SER cc_start: 0.8208 (OUTLIER) cc_final: 0.7724 (p) REVERT: H 204 SER cc_start: 0.8142 (OUTLIER) cc_final: 0.7726 (p) outliers start: 93 outliers final: 75 residues processed: 355 average time/residue: 0.3576 time to fit residues: 213.9331 Evaluate side-chains 339 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 254 time to evaluate : 3.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 204 SER Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 204 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 204 SER Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 221 optimal weight: 4.9990 chunk 357 optimal weight: 3.9990 chunk 217 optimal weight: 0.7980 chunk 169 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 374 optimal weight: 0.6980 chunk 344 optimal weight: 5.9990 chunk 298 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 230 optimal weight: 3.9990 chunk 182 optimal weight: 0.2980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN F 112 GLN F 448 GLN G 21 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30216 Z= 0.204 Angle : 0.586 9.975 41120 Z= 0.282 Chirality : 0.043 0.159 4776 Planarity : 0.004 0.038 5056 Dihedral : 17.111 164.441 5000 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.86 % Favored : 95.95 % Rotamer: Outliers : 2.86 % Allowed : 17.55 % Favored : 79.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.14), residues: 3704 helix: 0.73 (0.14), residues: 1376 sheet: -0.71 (0.25), residues: 320 loop : -0.39 (0.14), residues: 2008 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 504 PHE 0.010 0.001 PHE G 35 TYR 0.014 0.001 TYR E 509 ARG 0.002 0.000 ARG A 224 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7408 Ramachandran restraints generated. 3704 Oldfield, 0 Emsley, 3704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 267 time to evaluate : 3.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 500 GLU cc_start: 0.6018 (OUTLIER) cc_final: 0.5612 (mt-10) REVERT: B 204 SER cc_start: 0.8209 (OUTLIER) cc_final: 0.7716 (p) REVERT: D 483 MET cc_start: 0.8870 (tmm) cc_final: 0.8618 (tmm) REVERT: E 204 SER cc_start: 0.8181 (OUTLIER) cc_final: 0.7727 (p) REVERT: E 483 MET cc_start: 0.8861 (tmm) cc_final: 0.8607 (tmm) REVERT: E 500 GLU cc_start: 0.6055 (OUTLIER) cc_final: 0.5643 (mt-10) REVERT: F 204 SER cc_start: 0.8150 (OUTLIER) cc_final: 0.7735 (p) REVERT: G 204 SER cc_start: 0.8210 (OUTLIER) cc_final: 0.7720 (p) REVERT: H 204 SER cc_start: 0.8147 (OUTLIER) cc_final: 0.7740 (p) outliers start: 88 outliers final: 74 residues processed: 348 average time/residue: 0.3520 time to fit residues: 207.0082 Evaluate side-chains 330 residues out of total 3072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 249 time to evaluate : 3.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 ASP Chi-restraints excluded: chain A residue 126 THR Chi-restraints excluded: chain A residue 157 ILE Chi-restraints excluded: chain A residue 158 VAL Chi-restraints excluded: chain A residue 193 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 299 VAL Chi-restraints excluded: chain A residue 383 THR Chi-restraints excluded: chain A residue 477 ASP Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 126 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 204 SER Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 299 VAL Chi-restraints excluded: chain B residue 383 THR Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 477 ASP Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain C residue 157 ILE Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain C residue 299 VAL Chi-restraints excluded: chain C residue 383 THR Chi-restraints excluded: chain C residue 477 ASP Chi-restraints excluded: chain D residue 71 ASP Chi-restraints excluded: chain D residue 126 THR Chi-restraints excluded: chain D residue 157 ILE Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 299 VAL Chi-restraints excluded: chain D residue 439 ILE Chi-restraints excluded: chain D residue 477 ASP Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 157 ILE Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain E residue 299 VAL Chi-restraints excluded: chain E residue 383 THR Chi-restraints excluded: chain E residue 439 ILE Chi-restraints excluded: chain E residue 477 ASP Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain F residue 126 THR Chi-restraints excluded: chain F residue 157 ILE Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 193 THR Chi-restraints excluded: chain F residue 204 SER Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 270 VAL Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 383 THR Chi-restraints excluded: chain F residue 477 ASP Chi-restraints excluded: chain G residue 71 ASP Chi-restraints excluded: chain G residue 126 THR Chi-restraints excluded: chain G residue 157 ILE Chi-restraints excluded: chain G residue 204 SER Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 270 VAL Chi-restraints excluded: chain G residue 299 VAL Chi-restraints excluded: chain G residue 383 THR Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 477 ASP Chi-restraints excluded: chain H residue 71 ASP Chi-restraints excluded: chain H residue 126 THR Chi-restraints excluded: chain H residue 157 ILE Chi-restraints excluded: chain H residue 193 THR Chi-restraints excluded: chain H residue 204 SER Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 270 VAL Chi-restraints excluded: chain H residue 299 VAL Chi-restraints excluded: chain H residue 383 THR Chi-restraints excluded: chain H residue 477 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 376 random chunks: chunk 236 optimal weight: 2.9990 chunk 317 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 275 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 298 optimal weight: 0.8980 chunk 125 optimal weight: 1.9990 chunk 306 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 448 GLN D 441 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.156458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.128522 restraints weight = 38416.003| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.54 r_work: 0.3584 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 30216 Z= 0.360 Angle : 0.666 9.605 41120 Z= 0.327 Chirality : 0.047 0.167 4776 Planarity : 0.004 0.040 5056 Dihedral : 17.518 165.200 5000 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.19 % Allowed : 4.81 % Favored : 95.01 % Rotamer: Outliers : 3.03 % Allowed : 17.55 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.13), residues: 3704 helix: 0.36 (0.14), residues: 1384 sheet: -0.80 (0.24), residues: 320 loop : -0.67 (0.14), residues: 2000 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 507 PHE 0.014 0.002 PHE A 35 TYR 0.013 0.002 TYR G 509 ARG 0.003 0.000 ARG B 480 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6136.60 seconds wall clock time: 110 minutes 55.99 seconds (6655.99 seconds total)