Starting phenix.real_space_refine on Mon Dec 30 22:25:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cad_16524/12_2024/8cad_16524_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cad_16524/12_2024/8cad_16524.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cad_16524/12_2024/8cad_16524.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cad_16524/12_2024/8cad_16524.map" model { file = "/net/cci-nas-00/data/ceres_data/8cad_16524/12_2024/8cad_16524_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cad_16524/12_2024/8cad_16524_trim.cif" } resolution = 2.85 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= 0.005 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: 6 Type Number sf(0) Gaussians Cu 12 5.60 5 S 84 5.16 5 C 20820 2.51 5 N 5310 2.21 5 O 6796 1.98 5 H 31062 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 64084 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 10418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 10418 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 603} Chain breaks: 3 Chain: "B" Number of atoms: 10418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 10418 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 603} Chain breaks: 3 Chain: "C" Number of atoms: 10418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 10418 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 603} Chain breaks: 3 Chain: "D" Number of atoms: 10418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 10418 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 603} Chain breaks: 3 Chain: "E" Number of atoms: 10418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 10418 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 603} Chain breaks: 3 Chain: "F" Number of atoms: 10418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 636, 10418 Classifications: {'peptide': 636} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 603} Chain breaks: 3 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CU': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 122 Classifications: {'water': 122} Link IDs: {None: 121} Chain: "B" Number of atoms: 130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 130 Classifications: {'water': 130} Link IDs: {None: 129} Chain: "C" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Chain: "D" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 123 Classifications: {'water': 123} Link IDs: {None: 122} Chain: "E" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 128 Classifications: {'water': 128} Link IDs: {None: 127} Chain: "F" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 131 Classifications: {'water': 131} Link IDs: {None: 130} Time building chain proxies: 23.95, per 1000 atoms: 0.37 Number of scatterers: 64084 At special positions: 0 Unit cell: (139.527, 139.527, 108.521, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 12 28.99 S 84 16.00 O 6796 8.00 N 5310 7.00 C 20820 6.00 H 31062 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-2 " MAN H 4 " - " MAN H 5 " " MAN H 5 " - " MAN H 6 " " MAN J 4 " - " MAN J 5 " " MAN J 5 " - " MAN J 6 " " MAN L 4 " - " MAN L 5 " " MAN L 5 " - " MAN L 6 " " MAN N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN P 4 " - " MAN P 5 " " MAN P 5 " - " MAN P 6 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " ALPHA1-3 " BMA H 3 " - " MAN H 4 " " MAN H 7 " - " MAN H 8 " " BMA J 3 " - " MAN J 4 " " MAN J 7 " - " MAN J 8 " " BMA L 3 " - " MAN L 4 " " MAN L 7 " - " MAN L 8 " " BMA N 3 " - " MAN N 4 " " MAN N 7 " - " MAN N 8 " " BMA P 3 " - " MAN P 4 " " MAN P 7 " - " MAN P 8 " " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " ALPHA1-6 " BMA H 3 " - " MAN H 7 " " MAN H 7 " - " MAN H 9 " " BMA J 3 " - " MAN J 7 " " MAN J 7 " - " MAN J 9 " " BMA L 3 " - " MAN L 7 " " MAN L 7 " - " MAN L 9 " " BMA N 3 " - " MAN N 7 " " MAN N 7 " - " MAN N 9 " " BMA P 3 " - " MAN P 7 " " MAN P 7 " - " MAN P 9 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 9 " BETA1-4 " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG L 2 " - " BMA L 3 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " BMA R 3 " NAG-ASN " NAG G 1 " - " ASN A 477 " " NAG H 1 " - " ASN A 73 " " NAG I 1 " - " ASN B 477 " " NAG J 1 " - " ASN B 73 " " NAG K 1 " - " ASN C 477 " " NAG L 1 " - " ASN C 73 " " NAG M 1 " - " ASN D 477 " " NAG N 1 " - " ASN D 73 " " NAG O 1 " - " ASN E 477 " " NAG P 1 " - " ASN E 73 " " NAG Q 1 " - " ASN F 477 " " NAG R 1 " - " ASN F 73 " Time building additional restraints: 15.69 Conformation dependent library (CDL) restraints added in 3.8 seconds 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7344 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 36 sheets defined 44.4% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.85 Creating SS restraints... Processing helix chain 'A' and resid 31 through 42 Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 67 through 71 removed outlier: 3.519A pdb=" N LEU A 70 " --> pdb=" O ASN A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 Processing helix chain 'A' and resid 100 through 116 Processing helix chain 'A' and resid 119 through 133 Processing helix chain 'A' and resid 135 through 149 Processing helix chain 'A' and resid 150 through 154 Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 166 through 169 Processing helix chain 'A' and resid 171 through 184 Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 228 through 242 removed outlier: 3.542A pdb=" N ASN A 232 " --> pdb=" O ASP A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 254 Processing helix chain 'A' and resid 256 through 279 Processing helix chain 'A' and resid 321 through 344 removed outlier: 3.954A pdb=" N GLU A 325 " --> pdb=" O THR A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 371 Processing helix chain 'A' and resid 383 through 394 removed outlier: 3.866A pdb=" N ILE A 387 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN A 394 " --> pdb=" O LYS A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 416 Processing helix chain 'A' and resid 419 through 422 Processing helix chain 'A' and resid 423 through 443 removed outlier: 4.018A pdb=" N TYR A 427 " --> pdb=" O ASP A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 547 Processing helix chain 'A' and resid 548 through 550 No H-bonds generated for 'chain 'A' and resid 548 through 550' Processing helix chain 'A' and resid 572 through 574 No H-bonds generated for 'chain 'A' and resid 572 through 574' Processing helix chain 'A' and resid 583 through 594 removed outlier: 3.808A pdb=" N ALA A 594 " --> pdb=" O LYS A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 617 No H-bonds generated for 'chain 'A' and resid 615 through 617' Processing helix chain 'A' and resid 673 through 678 removed outlier: 3.995A pdb=" N THR A 678 " --> pdb=" O TRP A 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 32 through 42 Processing helix chain 'B' and resid 52 through 62 Processing helix chain 'B' and resid 67 through 71 removed outlier: 3.519A pdb=" N LEU B 70 " --> pdb=" O ASN B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 87 Processing helix chain 'B' and resid 100 through 116 Processing helix chain 'B' and resid 119 through 133 Processing helix chain 'B' and resid 135 through 149 Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'B' and resid 160 through 165 Processing helix chain 'B' and resid 166 through 169 Processing helix chain 'B' and resid 171 through 184 Processing helix chain 'B' and resid 222 through 227 Processing helix chain 'B' and resid 228 through 242 removed outlier: 3.542A pdb=" N ASN B 232 " --> pdb=" O ASP B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 254 Processing helix chain 'B' and resid 256 through 279 Processing helix chain 'B' and resid 321 through 344 removed outlier: 3.954A pdb=" N GLU B 325 " --> pdb=" O THR B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 361 through 371 Processing helix chain 'B' and resid 383 through 394 removed outlier: 3.866A pdb=" N ILE B 387 " --> pdb=" O ASP B 383 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN B 394 " --> pdb=" O LYS B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 416 Processing helix chain 'B' and resid 419 through 422 Processing helix chain 'B' and resid 423 through 444 removed outlier: 4.018A pdb=" N TYR B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU B 444 " --> pdb=" O TRP B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 547 Processing helix chain 'B' and resid 548 through 550 No H-bonds generated for 'chain 'B' and resid 548 through 550' Processing helix chain 'B' and resid 572 through 574 No H-bonds generated for 'chain 'B' and resid 572 through 574' Processing helix chain 'B' and resid 583 through 594 removed outlier: 3.808A pdb=" N ALA B 594 " --> pdb=" O LYS B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 617 No H-bonds generated for 'chain 'B' and resid 615 through 617' Processing helix chain 'B' and resid 673 through 678 removed outlier: 3.994A pdb=" N THR B 678 " --> pdb=" O TRP B 675 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 42 Processing helix chain 'C' and resid 52 through 62 Processing helix chain 'C' and resid 67 through 71 removed outlier: 3.519A pdb=" N LEU C 70 " --> pdb=" O ASN C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 87 Processing helix chain 'C' and resid 100 through 116 Processing helix chain 'C' and resid 119 through 133 Processing helix chain 'C' and resid 135 through 149 Processing helix chain 'C' and resid 150 through 154 Processing helix chain 'C' and resid 160 through 165 Processing helix chain 'C' and resid 166 through 169 Processing helix chain 'C' and resid 171 through 184 Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 228 through 242 removed outlier: 3.542A pdb=" N ASN C 232 " --> pdb=" O ASP C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 256 through 279 Processing helix chain 'C' and resid 321 through 344 removed outlier: 3.953A pdb=" N GLU C 325 " --> pdb=" O THR C 321 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 360 No H-bonds generated for 'chain 'C' and resid 358 through 360' Processing helix chain 'C' and resid 361 through 371 Processing helix chain 'C' and resid 383 through 394 removed outlier: 3.866A pdb=" N ILE C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN C 394 " --> pdb=" O LYS C 390 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 416 Processing helix chain 'C' and resid 419 through 422 Processing helix chain 'C' and resid 423 through 443 removed outlier: 4.018A pdb=" N TYR C 427 " --> pdb=" O ASP C 423 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 547 Processing helix chain 'C' and resid 548 through 550 No H-bonds generated for 'chain 'C' and resid 548 through 550' Processing helix chain 'C' and resid 572 through 574 No H-bonds generated for 'chain 'C' and resid 572 through 574' Processing helix chain 'C' and resid 583 through 594 removed outlier: 3.809A pdb=" N ALA C 594 " --> pdb=" O LYS C 590 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 617 No H-bonds generated for 'chain 'C' and resid 615 through 617' Processing helix chain 'C' and resid 673 through 678 removed outlier: 3.996A pdb=" N THR C 678 " --> pdb=" O TRP C 675 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 42 Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 67 through 71 removed outlier: 3.520A pdb=" N LEU D 70 " --> pdb=" O ASN D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 87 Processing helix chain 'D' and resid 100 through 116 Processing helix chain 'D' and resid 119 through 133 Processing helix chain 'D' and resid 135 through 149 Processing helix chain 'D' and resid 150 through 154 Processing helix chain 'D' and resid 160 through 165 Processing helix chain 'D' and resid 166 through 169 Processing helix chain 'D' and resid 171 through 184 Processing helix chain 'D' and resid 222 through 227 Processing helix chain 'D' and resid 228 through 242 removed outlier: 3.541A pdb=" N ASN D 232 " --> pdb=" O ASP D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 256 through 279 Processing helix chain 'D' and resid 321 through 344 removed outlier: 3.954A pdb=" N GLU D 325 " --> pdb=" O THR D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 360 No H-bonds generated for 'chain 'D' and resid 358 through 360' Processing helix chain 'D' and resid 361 through 371 Processing helix chain 'D' and resid 383 through 394 removed outlier: 3.865A pdb=" N ILE D 387 " --> pdb=" O ASP D 383 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN D 394 " --> pdb=" O LYS D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 416 Processing helix chain 'D' and resid 419 through 422 Processing helix chain 'D' and resid 423 through 443 removed outlier: 4.019A pdb=" N TYR D 427 " --> pdb=" O ASP D 423 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 547 Processing helix chain 'D' and resid 548 through 550 No H-bonds generated for 'chain 'D' and resid 548 through 550' Processing helix chain 'D' and resid 572 through 574 No H-bonds generated for 'chain 'D' and resid 572 through 574' Processing helix chain 'D' and resid 583 through 594 removed outlier: 3.809A pdb=" N ALA D 594 " --> pdb=" O LYS D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 617 No H-bonds generated for 'chain 'D' and resid 615 through 617' Processing helix chain 'D' and resid 673 through 678 removed outlier: 3.996A pdb=" N THR D 678 " --> pdb=" O TRP D 675 " (cutoff:3.500A) Processing helix chain 'E' and resid 32 through 42 Processing helix chain 'E' and resid 52 through 62 Processing helix chain 'E' and resid 67 through 71 removed outlier: 3.519A pdb=" N LEU E 70 " --> pdb=" O ASN E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 87 Processing helix chain 'E' and resid 100 through 116 Processing helix chain 'E' and resid 119 through 133 Processing helix chain 'E' and resid 135 through 149 Processing helix chain 'E' and resid 150 through 154 Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'E' and resid 166 through 169 Processing helix chain 'E' and resid 171 through 184 Processing helix chain 'E' and resid 222 through 227 Processing helix chain 'E' and resid 228 through 242 removed outlier: 3.541A pdb=" N ASN E 232 " --> pdb=" O ASP E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 249 through 254 Processing helix chain 'E' and resid 256 through 279 Processing helix chain 'E' and resid 321 through 344 removed outlier: 3.954A pdb=" N GLU E 325 " --> pdb=" O THR E 321 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 360 No H-bonds generated for 'chain 'E' and resid 358 through 360' Processing helix chain 'E' and resid 361 through 371 Processing helix chain 'E' and resid 383 through 394 removed outlier: 3.865A pdb=" N ILE E 387 " --> pdb=" O ASP E 383 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN E 394 " --> pdb=" O LYS E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 416 Processing helix chain 'E' and resid 419 through 422 Processing helix chain 'E' and resid 423 through 443 removed outlier: 4.019A pdb=" N TYR E 427 " --> pdb=" O ASP E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 547 Processing helix chain 'E' and resid 548 through 550 No H-bonds generated for 'chain 'E' and resid 548 through 550' Processing helix chain 'E' and resid 572 through 574 No H-bonds generated for 'chain 'E' and resid 572 through 574' Processing helix chain 'E' and resid 583 through 594 removed outlier: 3.809A pdb=" N ALA E 594 " --> pdb=" O LYS E 590 " (cutoff:3.500A) Processing helix chain 'E' and resid 615 through 617 No H-bonds generated for 'chain 'E' and resid 615 through 617' Processing helix chain 'E' and resid 673 through 678 removed outlier: 3.995A pdb=" N THR E 678 " --> pdb=" O TRP E 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 32 through 42 Processing helix chain 'F' and resid 52 through 62 Processing helix chain 'F' and resid 67 through 71 removed outlier: 3.520A pdb=" N LEU F 70 " --> pdb=" O ASN F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 87 Processing helix chain 'F' and resid 100 through 116 Processing helix chain 'F' and resid 119 through 133 Processing helix chain 'F' and resid 135 through 149 Processing helix chain 'F' and resid 150 through 154 Processing helix chain 'F' and resid 160 through 165 Processing helix chain 'F' and resid 166 through 169 Processing helix chain 'F' and resid 171 through 184 Processing helix chain 'F' and resid 222 through 227 Processing helix chain 'F' and resid 228 through 242 removed outlier: 3.541A pdb=" N ASN F 232 " --> pdb=" O ASP F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 254 Processing helix chain 'F' and resid 256 through 279 Processing helix chain 'F' and resid 321 through 344 removed outlier: 3.954A pdb=" N GLU F 325 " --> pdb=" O THR F 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 360 No H-bonds generated for 'chain 'F' and resid 358 through 360' Processing helix chain 'F' and resid 361 through 371 Processing helix chain 'F' and resid 383 through 394 removed outlier: 3.864A pdb=" N ILE F 387 " --> pdb=" O ASP F 383 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN F 394 " --> pdb=" O LYS F 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 416 Processing helix chain 'F' and resid 419 through 422 Processing helix chain 'F' and resid 423 through 443 removed outlier: 4.019A pdb=" N TYR F 427 " --> pdb=" O ASP F 423 " (cutoff:3.500A) Processing helix chain 'F' and resid 542 through 547 Processing helix chain 'F' and resid 548 through 550 No H-bonds generated for 'chain 'F' and resid 548 through 550' Processing helix chain 'F' and resid 572 through 574 No H-bonds generated for 'chain 'F' and resid 572 through 574' Processing helix chain 'F' and resid 583 through 594 removed outlier: 3.809A pdb=" N ALA F 594 " --> pdb=" O LYS F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 615 through 617 No H-bonds generated for 'chain 'F' and resid 615 through 617' Processing helix chain 'F' and resid 673 through 678 removed outlier: 3.995A pdb=" N THR F 678 " --> pdb=" O TRP F 675 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 196 through 199 removed outlier: 3.936A pdb=" N TRP A 198 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N VAL A 202 " --> pdb=" O TRP A 198 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL A 203 " --> pdb=" O LEU A 499 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN A 501 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LYS A 522 " --> pdb=" O GLU A 559 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU A 559 " --> pdb=" O LYS A 522 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL A 524 " --> pdb=" O ASN A 557 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN A 557 " --> pdb=" O VAL A 524 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL A 526 " --> pdb=" O ILE A 555 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE A 555 " --> pdb=" O VAL A 526 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE A 528 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 291 through 292 Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 347 Processing sheet with id=AA4, first strand: chain 'A' and resid 400 through 401 removed outlier: 4.845A pdb=" N SER A 400 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 458 through 464 removed outlier: 6.726A pdb=" N ASN A 515 " --> pdb=" O GLU A 460 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL A 462 " --> pdb=" O ARG A 513 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARG A 513 " --> pdb=" O VAL A 462 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL A 464 " --> pdb=" O THR A 511 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR A 511 " --> pdb=" O VAL A 464 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 577 through 578 Processing sheet with id=AA7, first strand: chain 'B' and resid 196 through 199 removed outlier: 3.937A pdb=" N TRP B 198 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL B 202 " --> pdb=" O TRP B 198 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL B 203 " --> pdb=" O LEU B 499 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N GLN B 501 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N LYS B 522 " --> pdb=" O GLU B 559 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU B 559 " --> pdb=" O LYS B 522 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL B 524 " --> pdb=" O ASN B 557 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN B 557 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL B 526 " --> pdb=" O ILE B 555 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE B 555 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE B 528 " --> pdb=" O ILE B 553 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 291 through 292 Processing sheet with id=AA9, first strand: chain 'B' and resid 345 through 347 Processing sheet with id=AB1, first strand: chain 'B' and resid 400 through 401 removed outlier: 4.844A pdb=" N SER B 400 " --> pdb=" O LEU B 408 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 458 through 464 removed outlier: 6.726A pdb=" N ASN B 515 " --> pdb=" O GLU B 460 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N VAL B 462 " --> pdb=" O ARG B 513 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG B 513 " --> pdb=" O VAL B 462 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL B 464 " --> pdb=" O THR B 511 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR B 511 " --> pdb=" O VAL B 464 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 577 through 578 Processing sheet with id=AB4, first strand: chain 'C' and resid 196 through 199 removed outlier: 3.936A pdb=" N TRP C 198 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL C 202 " --> pdb=" O TRP C 198 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL C 203 " --> pdb=" O LEU C 499 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN C 501 " --> pdb=" O VAL C 203 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LYS C 522 " --> pdb=" O GLU C 559 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU C 559 " --> pdb=" O LYS C 522 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL C 524 " --> pdb=" O ASN C 557 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN C 557 " --> pdb=" O VAL C 524 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL C 526 " --> pdb=" O ILE C 555 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE C 555 " --> pdb=" O VAL C 526 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE C 528 " --> pdb=" O ILE C 553 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 291 through 292 Processing sheet with id=AB6, first strand: chain 'C' and resid 345 through 347 Processing sheet with id=AB7, first strand: chain 'C' and resid 400 through 401 removed outlier: 4.845A pdb=" N SER C 400 " --> pdb=" O LEU C 408 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 458 through 464 removed outlier: 6.727A pdb=" N ASN C 515 " --> pdb=" O GLU C 460 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL C 462 " --> pdb=" O ARG C 513 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARG C 513 " --> pdb=" O VAL C 462 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL C 464 " --> pdb=" O THR C 511 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR C 511 " --> pdb=" O VAL C 464 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 577 through 578 Processing sheet with id=AC1, first strand: chain 'D' and resid 196 through 199 removed outlier: 3.936A pdb=" N TRP D 198 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL D 202 " --> pdb=" O TRP D 198 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL D 203 " --> pdb=" O LEU D 499 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN D 501 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LYS D 522 " --> pdb=" O GLU D 559 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU D 559 " --> pdb=" O LYS D 522 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL D 524 " --> pdb=" O ASN D 557 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN D 557 " --> pdb=" O VAL D 524 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL D 526 " --> pdb=" O ILE D 555 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE D 555 " --> pdb=" O VAL D 526 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N PHE D 528 " --> pdb=" O ILE D 553 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 291 through 292 Processing sheet with id=AC3, first strand: chain 'D' and resid 345 through 347 Processing sheet with id=AC4, first strand: chain 'D' and resid 400 through 401 removed outlier: 4.845A pdb=" N SER D 400 " --> pdb=" O LEU D 408 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 458 through 464 removed outlier: 6.726A pdb=" N ASN D 515 " --> pdb=" O GLU D 460 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL D 462 " --> pdb=" O ARG D 513 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARG D 513 " --> pdb=" O VAL D 462 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL D 464 " --> pdb=" O THR D 511 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR D 511 " --> pdb=" O VAL D 464 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'D' and resid 577 through 578 Processing sheet with id=AC7, first strand: chain 'E' and resid 196 through 199 removed outlier: 3.936A pdb=" N TRP E 198 " --> pdb=" O VAL E 202 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL E 202 " --> pdb=" O TRP E 198 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL E 203 " --> pdb=" O LEU E 499 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN E 501 " --> pdb=" O VAL E 203 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LYS E 522 " --> pdb=" O GLU E 559 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU E 559 " --> pdb=" O LYS E 522 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL E 524 " --> pdb=" O ASN E 557 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN E 557 " --> pdb=" O VAL E 524 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL E 526 " --> pdb=" O ILE E 555 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE E 555 " --> pdb=" O VAL E 526 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE E 528 " --> pdb=" O ILE E 553 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 291 through 292 Processing sheet with id=AC9, first strand: chain 'E' and resid 345 through 347 Processing sheet with id=AD1, first strand: chain 'E' and resid 400 through 401 removed outlier: 4.845A pdb=" N SER E 400 " --> pdb=" O LEU E 408 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 458 through 464 removed outlier: 6.726A pdb=" N ASN E 515 " --> pdb=" O GLU E 460 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N VAL E 462 " --> pdb=" O ARG E 513 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ARG E 513 " --> pdb=" O VAL E 462 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N VAL E 464 " --> pdb=" O THR E 511 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR E 511 " --> pdb=" O VAL E 464 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 577 through 578 Processing sheet with id=AD4, first strand: chain 'F' and resid 196 through 199 removed outlier: 3.936A pdb=" N TRP F 198 " --> pdb=" O VAL F 202 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N VAL F 202 " --> pdb=" O TRP F 198 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL F 203 " --> pdb=" O LEU F 499 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N GLN F 501 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LYS F 522 " --> pdb=" O GLU F 559 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N GLU F 559 " --> pdb=" O LYS F 522 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL F 524 " --> pdb=" O ASN F 557 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ASN F 557 " --> pdb=" O VAL F 524 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N VAL F 526 " --> pdb=" O ILE F 555 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ILE F 555 " --> pdb=" O VAL F 526 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N PHE F 528 " --> pdb=" O ILE F 553 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 291 through 292 Processing sheet with id=AD6, first strand: chain 'F' and resid 345 through 347 Processing sheet with id=AD7, first strand: chain 'F' and resid 400 through 401 removed outlier: 4.845A pdb=" N SER F 400 " --> pdb=" O LEU F 408 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 458 through 464 removed outlier: 6.726A pdb=" N ASN F 515 " --> pdb=" O GLU F 460 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N VAL F 462 " --> pdb=" O ARG F 513 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG F 513 " --> pdb=" O VAL F 462 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL F 464 " --> pdb=" O THR F 511 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR F 511 " --> pdb=" O VAL F 464 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 577 through 578 1291 hydrogen bonds defined for protein. 3603 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: 22.08 Time building geometry restraints manager: 18.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 31050 1.03 - 1.23: 42 1.23 - 1.42: 13969 1.42 - 1.61: 18941 1.61 - 1.81: 156 Bond restraints: 64158 Sorted by residual: bond pdb=" ND2 ASN C 477 " pdb="HD21 ASN C 477 " ideal model delta sigma weight residual 0.860 0.920 -0.060 2.00e-02 2.50e+03 8.88e+00 bond pdb=" ND2 ASN D 477 " pdb="HD21 ASN D 477 " ideal model delta sigma weight residual 0.860 0.920 -0.060 2.00e-02 2.50e+03 8.87e+00 bond pdb=" ND2 ASN F 477 " pdb="HD21 ASN F 477 " ideal model delta sigma weight residual 0.860 0.919 -0.059 2.00e-02 2.50e+03 8.84e+00 bond pdb=" ND2 ASN B 477 " pdb="HD21 ASN B 477 " ideal model delta sigma weight residual 0.860 0.919 -0.059 2.00e-02 2.50e+03 8.68e+00 bond pdb=" ND2 ASN A 477 " pdb="HD21 ASN A 477 " ideal model delta sigma weight residual 0.860 0.919 -0.059 2.00e-02 2.50e+03 8.56e+00 ... (remaining 64153 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 111872 1.34 - 2.69: 3123 2.69 - 4.03: 439 4.03 - 5.38: 60 5.38 - 6.72: 24 Bond angle restraints: 115518 Sorted by residual: angle pdb=" CA ASN A 73 " pdb=" C ASN A 73 " pdb=" O ASN A 73 " ideal model delta sigma weight residual 121.58 118.03 3.55 1.12e+00 7.97e-01 1.01e+01 angle pdb=" CA ASN E 477 " pdb=" CB ASN E 477 " pdb=" CG ASN E 477 " ideal model delta sigma weight residual 112.60 115.00 -2.40 1.00e+00 1.00e+00 5.77e+00 angle pdb=" CA ASN F 477 " pdb=" CB ASN F 477 " pdb=" CG ASN F 477 " ideal model delta sigma weight residual 112.60 115.00 -2.40 1.00e+00 1.00e+00 5.75e+00 angle pdb=" CA ASN C 477 " pdb=" CB ASN C 477 " pdb=" CG ASN C 477 " ideal model delta sigma weight residual 112.60 114.98 -2.38 1.00e+00 1.00e+00 5.69e+00 angle pdb=" CA ASN A 477 " pdb=" CB ASN A 477 " pdb=" CG ASN A 477 " ideal model delta sigma weight residual 112.60 114.98 -2.38 1.00e+00 1.00e+00 5.65e+00 ... (remaining 115513 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.86: 29983 20.86 - 41.71: 936 41.71 - 62.57: 269 62.57 - 83.42: 48 83.42 - 104.28: 24 Dihedral angle restraints: 31260 sinusoidal: 17268 harmonic: 13992 Sorted by residual: dihedral pdb=" O4 BMA P 3 " pdb=" C4 BMA P 3 " pdb=" C5 BMA P 3 " pdb=" O5 BMA P 3 " ideal model delta sinusoidal sigma weight residual -71.29 -175.57 104.28 1 3.00e+01 1.11e-03 1.33e+01 dihedral pdb=" O4 BMA N 3 " pdb=" C4 BMA N 3 " pdb=" C5 BMA N 3 " pdb=" O5 BMA N 3 " ideal model delta sinusoidal sigma weight residual -71.29 -175.56 104.27 1 3.00e+01 1.11e-03 1.33e+01 dihedral pdb=" O4 BMA R 3 " pdb=" C4 BMA R 3 " pdb=" C5 BMA R 3 " pdb=" O5 BMA R 3 " ideal model delta sinusoidal sigma weight residual -71.29 -175.54 104.25 1 3.00e+01 1.11e-03 1.33e+01 ... (remaining 31257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 5240 0.137 - 0.273: 29 0.273 - 0.410: 0 0.410 - 0.546: 2 0.546 - 0.683: 3 Chirality restraints: 5274 Sorted by residual: chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.52 0.12 2.00e-02 2.50e+03 3.72e+01 chirality pdb=" C1 NAG H 2 " pdb=" O4 NAG H 1 " pdb=" C2 NAG H 2 " pdb=" O5 NAG H 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.52 0.12 2.00e-02 2.50e+03 3.71e+01 chirality pdb=" C1 NAG R 2 " pdb=" O4 NAG R 1 " pdb=" C2 NAG R 2 " pdb=" O5 NAG R 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.52 0.12 2.00e-02 2.50e+03 3.62e+01 ... (remaining 5271 not shown) Planarity restraints: 9222 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 73 " 0.071 2.00e-02 2.50e+03 5.81e-02 5.07e+01 pdb=" CG ASN E 73 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN E 73 " -0.040 2.00e-02 2.50e+03 pdb=" ND2 ASN E 73 " -0.062 2.00e-02 2.50e+03 pdb="HD21 ASN E 73 " -0.043 2.00e-02 2.50e+03 pdb=" C1 NAG P 1 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 73 " 0.071 2.00e-02 2.50e+03 5.80e-02 5.05e+01 pdb=" CG ASN D 73 " -0.014 2.00e-02 2.50e+03 pdb=" OD1 ASN D 73 " -0.039 2.00e-02 2.50e+03 pdb=" ND2 ASN D 73 " -0.062 2.00e-02 2.50e+03 pdb="HD21 ASN D 73 " -0.043 2.00e-02 2.50e+03 pdb=" C1 NAG N 1 " 0.088 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 73 " 0.053 2.00e-02 2.50e+03 4.32e-02 2.80e+01 pdb=" CG ASN F 73 " -0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN F 73 " -0.029 2.00e-02 2.50e+03 pdb=" ND2 ASN F 73 " -0.046 2.00e-02 2.50e+03 pdb="HD21 ASN F 73 " -0.032 2.00e-02 2.50e+03 pdb=" C1 NAG R 1 " 0.065 2.00e-02 2.50e+03 ... (remaining 9219 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 2600 2.18 - 2.79: 126520 2.79 - 3.39: 177120 3.39 - 4.00: 235459 4.00 - 4.60: 366741 Nonbonded interactions: 908440 Sorted by model distance: nonbonded pdb=" O ILE E 634 " pdb="HD22 ASN E 682 " model vdw 1.576 2.450 nonbonded pdb=" O ILE C 634 " pdb="HD22 ASN C 682 " model vdw 1.576 2.450 nonbonded pdb=" O ILE F 634 " pdb="HD22 ASN F 682 " model vdw 1.576 2.450 nonbonded pdb=" O ILE A 634 " pdb="HD22 ASN A 682 " model vdw 1.576 2.450 nonbonded pdb=" O ILE D 634 " pdb="HD22 ASN D 682 " model vdw 1.576 2.450 ... (remaining 908435 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.980 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: 0.910 Extract box with map and model: 1.790 Check model and map are aligned: 0.370 Set scattering table: 0.440 Process input model: 104.780 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.360 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: 0.020 Load rotamer database and sin/cos tables:10.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 125.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.003 0.031 33096 Z= 0.207 Angle : 0.593 6.725 45102 Z= 0.287 Chirality : 0.045 0.683 5274 Planarity : 0.004 0.068 5610 Dihedral : 11.538 104.276 13044 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.82 (0.14), residues: 3768 helix: 1.64 (0.14), residues: 1362 sheet: 0.12 (0.21), residues: 582 loop : -0.07 (0.15), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 440 HIS 0.002 0.000 HIS A 483 PHE 0.008 0.001 PHE E 261 TYR 0.012 0.001 TYR E 346 ARG 0.003 0.000 ARG F 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 574 time to evaluate : 3.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 461 LYS cc_start: 0.7009 (ptmt) cc_final: 0.6778 (ptpt) REVERT: B 52 ILE cc_start: 0.7618 (mt) cc_final: 0.6783 (tt) REVERT: B 89 GLN cc_start: 0.7460 (pt0) cc_final: 0.7190 (pt0) REVERT: B 124 TYR cc_start: 0.7346 (t80) cc_final: 0.7057 (t80) REVERT: C 52 ILE cc_start: 0.7475 (mt) cc_final: 0.6749 (tt) REVERT: C 78 HIS cc_start: 0.6958 (m-70) cc_final: 0.6714 (m170) REVERT: C 430 MET cc_start: 0.8132 (mmm) cc_final: 0.7915 (mmm) REVERT: D 461 LYS cc_start: 0.7005 (ptmt) cc_final: 0.6772 (ptpt) REVERT: E 52 ILE cc_start: 0.7604 (mt) cc_final: 0.6768 (tt) REVERT: E 89 GLN cc_start: 0.7448 (pt0) cc_final: 0.7177 (pt0) REVERT: E 124 TYR cc_start: 0.7355 (t80) cc_final: 0.7054 (t80) REVERT: F 52 ILE cc_start: 0.7501 (mt) cc_final: 0.6767 (tt) REVERT: F 78 HIS cc_start: 0.6930 (m-70) cc_final: 0.6690 (m170) REVERT: F 430 MET cc_start: 0.8148 (mmm) cc_final: 0.7920 (mmm) REVERT: F 573 ASP cc_start: 0.7069 (t0) cc_final: 0.6852 (t70) outliers start: 0 outliers final: 0 residues processed: 574 average time/residue: 2.2225 time to fit residues: 1557.1007 Evaluate side-chains 352 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 352 time to evaluate : 3.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 319 optimal weight: 6.9990 chunk 286 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 193 optimal weight: 6.9990 chunk 153 optimal weight: 0.4980 chunk 296 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 180 optimal weight: 0.9980 chunk 220 optimal weight: 1.9990 chunk 343 optimal weight: 5.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 89 GLN A 480 ASN A 523 HIS A 539 ASN B 480 ASN B 523 HIS B 539 ASN C 89 GLN C 480 ASN C 539 ASN D 86 ASN D 89 GLN D 480 ASN D 523 HIS D 539 ASN E 446 HIS E 480 ASN E 523 HIS E 539 ASN F 89 GLN F 480 ASN F 539 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 33096 Z= 0.203 Angle : 0.532 4.981 45102 Z= 0.273 Chirality : 0.042 0.169 5274 Planarity : 0.004 0.060 5610 Dihedral : 7.947 75.231 5490 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.22 % Allowed : 9.72 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.59 (0.14), residues: 3768 helix: 1.55 (0.14), residues: 1416 sheet: 0.04 (0.20), residues: 582 loop : -0.38 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 440 HIS 0.005 0.001 HIS C 78 PHE 0.011 0.001 PHE D 43 TYR 0.016 0.001 TYR A 214 ARG 0.005 0.001 ARG E 513 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 357 time to evaluate : 3.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 220 MET cc_start: 0.5499 (OUTLIER) cc_final: 0.5212 (mmm) REVERT: C 44 PHE cc_start: 0.6832 (OUTLIER) cc_final: 0.6559 (m-10) REVERT: C 78 HIS cc_start: 0.6926 (m-70) cc_final: 0.6659 (m170) REVERT: C 636 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6763 (mp0) REVERT: D 78 HIS cc_start: 0.7063 (OUTLIER) cc_final: 0.6671 (m-70) REVERT: E 157 ARG cc_start: 0.7120 (mmt90) cc_final: 0.6775 (mmm160) REVERT: E 180 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.6989 (mtt180) REVERT: F 44 PHE cc_start: 0.6832 (OUTLIER) cc_final: 0.6565 (m-10) REVERT: F 78 HIS cc_start: 0.6911 (m-70) cc_final: 0.6679 (m170) REVERT: F 636 GLU cc_start: 0.7018 (OUTLIER) cc_final: 0.6764 (mp0) outliers start: 43 outliers final: 16 residues processed: 371 average time/residue: 2.4239 time to fit residues: 1084.1062 Evaluate side-chains 338 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 315 time to evaluate : 3.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 MET Chi-restraints excluded: chain A residue 331 GLU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 331 GLU Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 180 ARG Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 636 GLU Chi-restraints excluded: chain F residue 663 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 190 optimal weight: 10.0000 chunk 106 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 chunk 233 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 343 optimal weight: 2.9990 chunk 371 optimal weight: 7.9990 chunk 306 optimal weight: 0.0370 chunk 341 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 275 optimal weight: 2.9990 overall best weight: 1.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 320 GLN A 480 ASN A 523 HIS A 539 ASN B 89 GLN B 154 GLN B 480 ASN B 539 ASN C 539 ASN D 320 GLN D 480 ASN D 523 HIS D 539 ASN E 89 GLN E 154 GLN E 480 ASN E 539 ASN F 539 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 33096 Z= 0.163 Angle : 0.502 4.434 45102 Z= 0.256 Chirality : 0.041 0.205 5274 Planarity : 0.004 0.057 5610 Dihedral : 6.801 59.374 5490 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.81 % Allowed : 9.95 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.50 (0.13), residues: 3768 helix: 1.61 (0.14), residues: 1422 sheet: -0.01 (0.19), residues: 588 loop : -0.57 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 198 HIS 0.007 0.001 HIS D 133 PHE 0.009 0.001 PHE E 261 TYR 0.013 0.001 TYR A 192 ARG 0.004 0.000 ARG C 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 337 time to evaluate : 3.837 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 70 LEU cc_start: 0.7902 (mp) cc_final: 0.7663 (mt) REVERT: A 78 HIS cc_start: 0.7096 (OUTLIER) cc_final: 0.6715 (m-70) REVERT: A 121 ASP cc_start: 0.6826 (OUTLIER) cc_final: 0.6618 (t0) REVERT: A 180 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.6795 (mtt180) REVERT: A 435 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7692 (mtmp) REVERT: B 44 PHE cc_start: 0.6893 (OUTLIER) cc_final: 0.6399 (m-10) REVERT: B 157 ARG cc_start: 0.7204 (mmt90) cc_final: 0.6934 (mmm160) REVERT: B 180 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.6912 (mtt180) REVERT: C 78 HIS cc_start: 0.6942 (m-70) cc_final: 0.6671 (m170) REVERT: C 180 ARG cc_start: 0.8049 (OUTLIER) cc_final: 0.6912 (mtt180) REVERT: C 606 LYS cc_start: 0.6370 (mttt) cc_final: 0.5962 (mmmt) REVERT: C 636 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6787 (mp0) REVERT: D 70 LEU cc_start: 0.7918 (mp) cc_final: 0.7678 (mt) REVERT: D 78 HIS cc_start: 0.7098 (OUTLIER) cc_final: 0.6728 (m-70) REVERT: D 121 ASP cc_start: 0.6824 (OUTLIER) cc_final: 0.6610 (t0) REVERT: D 180 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.6802 (mtt180) REVERT: D 435 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7678 (mtmp) REVERT: E 44 PHE cc_start: 0.6903 (OUTLIER) cc_final: 0.6532 (m-10) REVERT: F 78 HIS cc_start: 0.6915 (m-70) cc_final: 0.6644 (m170) REVERT: F 180 ARG cc_start: 0.8044 (OUTLIER) cc_final: 0.6930 (mtt180) REVERT: F 606 LYS cc_start: 0.6379 (mttt) cc_final: 0.5970 (mmmt) REVERT: F 636 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6783 (mp0) outliers start: 64 outliers final: 33 residues processed: 367 average time/residue: 2.5036 time to fit residues: 1100.0128 Evaluate side-chains 362 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 314 time to evaluate : 3.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 121 ASP Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 435 LYS Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 418 GLN Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 121 ASP Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 418 GLN Chi-restraints excluded: chain D residue 435 LYS Chi-restraints excluded: chain D residue 515 ASN Chi-restraints excluded: chain D residue 631 MET Chi-restraints excluded: chain D residue 636 GLU Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 180 ARG Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 418 GLN Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 180 ARG Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 418 GLN Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain F residue 631 MET Chi-restraints excluded: chain F residue 636 GLU Chi-restraints excluded: chain F residue 663 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 339 optimal weight: 4.9990 chunk 258 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 38 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 230 optimal weight: 7.9990 chunk 345 optimal weight: 4.9990 chunk 365 optimal weight: 4.9990 chunk 180 optimal weight: 0.0570 chunk 327 optimal weight: 5.9990 chunk 98 optimal weight: 3.9990 overall best weight: 2.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 GLN A 186 GLN A 320 GLN A 539 ASN B 36 GLN B 86 ASN B 154 GLN B 186 GLN B 539 ASN C 36 GLN C 86 ASN C 186 GLN C 206 HIS C 515 ASN C 539 ASN D 36 GLN D 186 GLN D 320 GLN D 523 HIS D 539 ASN E 36 GLN E 86 ASN E 154 GLN E 186 GLN E 480 ASN E 515 ASN E 539 ASN F 36 GLN F 86 ASN F 186 GLN F 206 HIS ** F 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 515 ASN F 539 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 33096 Z= 0.248 Angle : 0.551 4.890 45102 Z= 0.282 Chirality : 0.043 0.187 5274 Planarity : 0.004 0.083 5610 Dihedral : 6.535 56.351 5490 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.69 % Allowed : 9.44 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.29 (0.13), residues: 3768 helix: 1.51 (0.13), residues: 1416 sheet: -0.15 (0.19), residues: 594 loop : -0.74 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 62 HIS 0.006 0.001 HIS D 45 PHE 0.011 0.001 PHE C 43 TYR 0.014 0.001 TYR A 346 ARG 0.008 0.001 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 329 time to evaluate : 3.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 HIS cc_start: 0.7168 (OUTLIER) cc_final: 0.6791 (m-70) REVERT: A 180 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.6644 (mtt180) REVERT: A 540 GLU cc_start: 0.7595 (tt0) cc_final: 0.7315 (tt0) REVERT: B 180 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.6887 (mtt180) REVERT: B 264 TRP cc_start: 0.7724 (OUTLIER) cc_final: 0.7215 (m-10) REVERT: B 340 MET cc_start: 0.8886 (ttp) cc_final: 0.8667 (ttp) REVERT: B 435 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7651 (mtpm) REVERT: B 606 LYS cc_start: 0.6533 (mttt) cc_final: 0.6148 (mmmt) REVERT: C 64 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7732 (mp) REVERT: C 78 HIS cc_start: 0.7021 (m-70) cc_final: 0.6729 (m170) REVERT: C 120 TYR cc_start: 0.7983 (t80) cc_final: 0.7621 (t80) REVERT: C 180 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.6944 (mtt180) REVERT: C 558 TYR cc_start: 0.7353 (t80) cc_final: 0.6936 (t80) REVERT: C 606 LYS cc_start: 0.6436 (mttt) cc_final: 0.6017 (mmmt) REVERT: D 78 HIS cc_start: 0.7155 (OUTLIER) cc_final: 0.6798 (m-70) REVERT: D 180 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.6702 (mtt180) REVERT: D 540 GLU cc_start: 0.7578 (tt0) cc_final: 0.7313 (tt0) REVERT: E 44 PHE cc_start: 0.7003 (OUTLIER) cc_final: 0.6530 (m-10) REVERT: E 264 TRP cc_start: 0.7684 (OUTLIER) cc_final: 0.7173 (m-10) REVERT: E 435 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.7657 (mtpm) REVERT: E 606 LYS cc_start: 0.6501 (mttt) cc_final: 0.6092 (mmmt) REVERT: F 64 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7718 (mp) REVERT: F 78 HIS cc_start: 0.7003 (m-70) cc_final: 0.6747 (m170) REVERT: F 120 TYR cc_start: 0.7982 (t80) cc_final: 0.7629 (t80) REVERT: F 180 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.6967 (mtt180) REVERT: F 558 TYR cc_start: 0.7354 (t80) cc_final: 0.6933 (t80) REVERT: F 606 LYS cc_start: 0.6441 (mttt) cc_final: 0.6021 (mmmt) outliers start: 95 outliers final: 47 residues processed: 382 average time/residue: 2.4851 time to fit residues: 1139.8798 Evaluate side-chains 374 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 313 time to evaluate : 3.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 418 GLN Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 446 HIS Chi-restraints excluded: chain B residue 515 ASN Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 418 GLN Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain D residue 44 PHE Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 418 GLN Chi-restraints excluded: chain D residue 631 MET Chi-restraints excluded: chain D residue 636 GLU Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 418 GLN Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 446 HIS Chi-restraints excluded: chain E residue 515 ASN Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 180 ARG Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 418 GLN Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain F residue 631 MET Chi-restraints excluded: chain F residue 636 GLU Chi-restraints excluded: chain F residue 663 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 5 optimal weight: 10.0000 chunk 272 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 311 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 186 optimal weight: 5.9990 chunk 327 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 HIS A 320 GLN A 539 ASN ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN C 86 ASN C 206 HIS C 480 ASN C 515 ASN C 539 ASN D 320 GLN D 539 ASN E 154 GLN ** E 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 ASN F 86 ASN F 206 HIS ** F 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 515 ASN F 539 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 33096 Z= 0.442 Angle : 0.678 6.252 45102 Z= 0.354 Chirality : 0.047 0.194 5274 Planarity : 0.005 0.075 5610 Dihedral : 7.378 59.903 5490 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.20 % Allowed : 9.04 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.31 (0.13), residues: 3768 helix: 0.90 (0.13), residues: 1434 sheet: -0.39 (0.20), residues: 600 loop : -1.05 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 62 HIS 0.009 0.001 HIS D 481 PHE 0.014 0.002 PHE B 43 TYR 0.017 0.002 TYR F 196 ARG 0.007 0.001 ARG E 205 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 321 time to evaluate : 3.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 HIS cc_start: 0.7241 (OUTLIER) cc_final: 0.6923 (m-70) REVERT: A 180 ARG cc_start: 0.8023 (OUTLIER) cc_final: 0.6864 (mtt180) REVERT: A 264 TRP cc_start: 0.7726 (OUTLIER) cc_final: 0.7404 (m-10) REVERT: A 540 GLU cc_start: 0.7608 (tt0) cc_final: 0.7324 (tt0) REVERT: A 606 LYS cc_start: 0.6565 (mttt) cc_final: 0.6078 (mmmt) REVERT: B 44 PHE cc_start: 0.7168 (OUTLIER) cc_final: 0.6578 (m-10) REVERT: B 180 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.6914 (mtt180) REVERT: B 264 TRP cc_start: 0.7681 (OUTLIER) cc_final: 0.7293 (m-10) REVERT: B 435 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.7813 (mtpm) REVERT: B 558 TYR cc_start: 0.7305 (t80) cc_final: 0.7022 (t80) REVERT: B 606 LYS cc_start: 0.6683 (mttt) cc_final: 0.6143 (mmmt) REVERT: C 64 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7768 (mp) REVERT: C 78 HIS cc_start: 0.7183 (m-70) cc_final: 0.6778 (m-70) REVERT: C 120 TYR cc_start: 0.8085 (t80) cc_final: 0.7739 (t80) REVERT: C 180 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7046 (mtt180) REVERT: C 264 TRP cc_start: 0.7756 (OUTLIER) cc_final: 0.7400 (m-10) REVERT: C 558 TYR cc_start: 0.7397 (t80) cc_final: 0.7062 (t80) REVERT: D 78 HIS cc_start: 0.7275 (OUTLIER) cc_final: 0.6938 (m-70) REVERT: D 180 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.6811 (mtt180) REVERT: D 264 TRP cc_start: 0.7723 (OUTLIER) cc_final: 0.7400 (m-10) REVERT: D 540 GLU cc_start: 0.7594 (tt0) cc_final: 0.7319 (tt0) REVERT: D 606 LYS cc_start: 0.6564 (mttt) cc_final: 0.6076 (mmmt) REVERT: E 44 PHE cc_start: 0.7200 (OUTLIER) cc_final: 0.6703 (m-10) REVERT: E 264 TRP cc_start: 0.7669 (OUTLIER) cc_final: 0.7282 (m-10) REVERT: E 435 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.7803 (mtpm) REVERT: E 452 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8680 (mp) REVERT: E 558 TYR cc_start: 0.7327 (t80) cc_final: 0.6982 (t80) REVERT: E 606 LYS cc_start: 0.6684 (mttt) cc_final: 0.6140 (mmmt) REVERT: F 64 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7729 (mp) REVERT: F 78 HIS cc_start: 0.7171 (m-70) cc_final: 0.6769 (m-70) REVERT: F 120 TYR cc_start: 0.8086 (t80) cc_final: 0.7739 (t80) REVERT: F 180 ARG cc_start: 0.8140 (OUTLIER) cc_final: 0.7009 (mtt180) REVERT: F 264 TRP cc_start: 0.7749 (OUTLIER) cc_final: 0.7384 (m-10) REVERT: F 558 TYR cc_start: 0.7407 (t80) cc_final: 0.7068 (t80) outliers start: 113 outliers final: 60 residues processed: 392 average time/residue: 2.4519 time to fit residues: 1155.1621 Evaluate side-chains 393 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 313 time to evaluate : 3.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 480 ASN Chi-restraints excluded: chain B residue 515 ASN Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 264 TRP Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 418 GLN Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 515 ASN Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 636 GLU Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain D residue 44 PHE Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 153 THR Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 264 TRP Chi-restraints excluded: chain D residue 418 GLN Chi-restraints excluded: chain D residue 631 MET Chi-restraints excluded: chain D residue 636 GLU Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 452 LEU Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 568 THR Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 180 ARG Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 418 GLN Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 515 ASN Chi-restraints excluded: chain F residue 568 THR Chi-restraints excluded: chain F residue 631 MET Chi-restraints excluded: chain F residue 636 GLU Chi-restraints excluded: chain F residue 663 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 122 optimal weight: 8.9990 chunk 329 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 365 optimal weight: 0.0980 chunk 303 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 192 optimal weight: 9.9990 overall best weight: 2.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 320 GLN B 86 ASN ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN C 86 ASN C 206 HIS C 480 ASN ** C 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 539 ASN D 86 ASN D 320 GLN E 86 ASN E 154 GLN E 480 ASN ** E 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 ASN F 86 ASN ** F 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 539 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 33096 Z= 0.240 Angle : 0.573 5.383 45102 Z= 0.297 Chirality : 0.043 0.162 5274 Planarity : 0.004 0.078 5610 Dihedral : 6.684 56.040 5490 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.78 % Allowed : 9.75 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.13), residues: 3768 helix: 1.21 (0.13), residues: 1416 sheet: -0.20 (0.20), residues: 594 loop : -0.99 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 675 HIS 0.004 0.001 HIS E 483 PHE 0.011 0.001 PHE A 43 TYR 0.019 0.001 TYR F 196 ARG 0.010 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 321 time to evaluate : 4.041 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.6733 (mtt180) REVERT: A 264 TRP cc_start: 0.7714 (OUTLIER) cc_final: 0.7341 (m-10) REVERT: A 540 GLU cc_start: 0.7593 (tt0) cc_final: 0.7339 (tt0) REVERT: A 606 LYS cc_start: 0.6525 (mttt) cc_final: 0.6033 (mmmt) REVERT: B 264 TRP cc_start: 0.7649 (OUTLIER) cc_final: 0.7258 (m-10) REVERT: B 435 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.7693 (mtpm) REVERT: B 558 TYR cc_start: 0.7305 (t80) cc_final: 0.6981 (t80) REVERT: B 606 LYS cc_start: 0.6670 (mttt) cc_final: 0.6159 (mmmt) REVERT: C 64 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7783 (mp) REVERT: C 120 TYR cc_start: 0.8042 (t80) cc_final: 0.7689 (t80) REVERT: C 180 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7005 (mtt180) REVERT: C 264 TRP cc_start: 0.7756 (OUTLIER) cc_final: 0.7371 (m-10) REVERT: C 558 TYR cc_start: 0.7380 (t80) cc_final: 0.7062 (t80) REVERT: D 78 HIS cc_start: 0.7233 (OUTLIER) cc_final: 0.6897 (m-70) REVERT: D 180 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.6759 (mtt180) REVERT: D 264 TRP cc_start: 0.7713 (OUTLIER) cc_final: 0.7340 (m-10) REVERT: D 540 GLU cc_start: 0.7582 (tt0) cc_final: 0.7336 (tt0) REVERT: D 606 LYS cc_start: 0.6524 (mttt) cc_final: 0.6027 (mmmt) REVERT: E 44 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6760 (m-10) REVERT: E 264 TRP cc_start: 0.7641 (OUTLIER) cc_final: 0.7243 (m-10) REVERT: E 435 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7716 (mtpm) REVERT: E 558 TYR cc_start: 0.7310 (t80) cc_final: 0.6996 (t80) REVERT: E 606 LYS cc_start: 0.6695 (mttt) cc_final: 0.6177 (mmmt) REVERT: F 64 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7775 (mp) REVERT: F 120 TYR cc_start: 0.8042 (t80) cc_final: 0.7692 (t80) REVERT: F 180 ARG cc_start: 0.8045 (OUTLIER) cc_final: 0.6984 (mtt180) REVERT: F 264 TRP cc_start: 0.7751 (OUTLIER) cc_final: 0.7403 (m-10) REVERT: F 558 TYR cc_start: 0.7388 (t80) cc_final: 0.7066 (t80) outliers start: 98 outliers final: 57 residues processed: 381 average time/residue: 2.4870 time to fit residues: 1152.3523 Evaluate side-chains 377 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 304 time to evaluate : 3.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 515 ASN Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 568 THR Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 264 TRP Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 418 GLN Chi-restraints excluded: chain C residue 434 LEU Chi-restraints excluded: chain C residue 452 LEU Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain D residue 44 PHE Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 264 TRP Chi-restraints excluded: chain D residue 418 GLN Chi-restraints excluded: chain D residue 631 MET Chi-restraints excluded: chain D residue 636 GLU Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 180 ARG Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 568 THR Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 153 THR Chi-restraints excluded: chain F residue 180 ARG Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 418 GLN Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain F residue 452 LEU Chi-restraints excluded: chain F residue 568 THR Chi-restraints excluded: chain F residue 631 MET Chi-restraints excluded: chain F residue 663 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 352 optimal weight: 9.9990 chunk 41 optimal weight: 6.9990 chunk 208 optimal weight: 4.9990 chunk 267 optimal weight: 8.9990 chunk 206 optimal weight: 3.9990 chunk 307 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 364 optimal weight: 4.9990 chunk 228 optimal weight: 2.9990 chunk 222 optimal weight: 0.4980 chunk 168 optimal weight: 0.2980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 320 GLN B 86 ASN ** B 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN C 86 ASN C 480 ASN C 539 ASN D 86 ASN D 320 GLN E 86 ASN E 480 ASN ** E 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 ASN F 86 ASN F 206 HIS F 480 ASN ** F 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 539 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 33096 Z= 0.191 Angle : 0.535 6.071 45102 Z= 0.274 Chirality : 0.042 0.164 5274 Planarity : 0.004 0.097 5610 Dihedral : 6.053 51.066 5490 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.64 % Allowed : 10.18 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.21 (0.13), residues: 3768 helix: 1.48 (0.14), residues: 1416 sheet: -0.02 (0.20), residues: 594 loop : -0.91 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 440 HIS 0.005 0.001 HIS C 483 PHE 0.010 0.001 PHE B 43 TYR 0.021 0.001 TYR F 196 ARG 0.009 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 312 time to evaluate : 3.818 Fit side-chains revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7929 (mp) cc_final: 0.7701 (mt) REVERT: A 78 HIS cc_start: 0.7238 (OUTLIER) cc_final: 0.6807 (m-70) REVERT: A 180 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.6793 (mtt180) REVERT: A 540 GLU cc_start: 0.7596 (tt0) cc_final: 0.7349 (tt0) REVERT: A 606 LYS cc_start: 0.6507 (mttt) cc_final: 0.6060 (mmmt) REVERT: B 44 PHE cc_start: 0.7047 (OUTLIER) cc_final: 0.6505 (m-10) REVERT: B 264 TRP cc_start: 0.7639 (OUTLIER) cc_final: 0.7212 (m-10) REVERT: B 435 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7669 (mtpm) REVERT: B 558 TYR cc_start: 0.7328 (t80) cc_final: 0.7108 (t80) REVERT: C 64 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7807 (mp) REVERT: C 120 TYR cc_start: 0.8068 (t80) cc_final: 0.7733 (t80) REVERT: C 180 ARG cc_start: 0.7994 (OUTLIER) cc_final: 0.6966 (mtt180) REVERT: C 264 TRP cc_start: 0.7743 (OUTLIER) cc_final: 0.7376 (m-10) REVERT: C 558 TYR cc_start: 0.7396 (t80) cc_final: 0.7102 (t80) REVERT: D 70 LEU cc_start: 0.7926 (mp) cc_final: 0.7703 (mt) REVERT: D 78 HIS cc_start: 0.7220 (OUTLIER) cc_final: 0.6826 (m-70) REVERT: D 180 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.6667 (mtt180) REVERT: D 540 GLU cc_start: 0.7583 (tt0) cc_final: 0.7344 (tt0) REVERT: D 606 LYS cc_start: 0.6509 (mttt) cc_final: 0.6053 (mmmt) REVERT: E 44 PHE cc_start: 0.7032 (OUTLIER) cc_final: 0.6667 (m-10) REVERT: E 264 TRP cc_start: 0.7617 (OUTLIER) cc_final: 0.7189 (m-10) REVERT: E 435 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.7673 (mtpm) REVERT: E 515 ASN cc_start: 0.6534 (m110) cc_final: 0.6316 (m-40) REVERT: E 558 TYR cc_start: 0.7315 (t80) cc_final: 0.7091 (t80) REVERT: E 606 LYS cc_start: 0.6655 (mttt) cc_final: 0.6172 (mmmt) REVERT: F 120 TYR cc_start: 0.8057 (t80) cc_final: 0.7727 (t80) REVERT: F 180 ARG cc_start: 0.8029 (OUTLIER) cc_final: 0.6974 (mtt180) REVERT: F 264 TRP cc_start: 0.7735 (OUTLIER) cc_final: 0.7359 (m-10) REVERT: F 558 TYR cc_start: 0.7403 (t80) cc_final: 0.7108 (t80) outliers start: 93 outliers final: 43 residues processed: 367 average time/residue: 2.4241 time to fit residues: 1073.5409 Evaluate side-chains 369 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 311 time to evaluate : 3.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 515 ASN Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 264 TRP Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 418 GLN Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 418 GLN Chi-restraints excluded: chain D residue 631 MET Chi-restraints excluded: chain D residue 636 GLU Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 180 ARG Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 180 ARG Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 418 GLN Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain F residue 631 MET Chi-restraints excluded: chain F residue 663 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 225 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 217 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 231 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 286 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 320 GLN A 539 ASN B 86 ASN B 206 HIS B 480 ASN ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN B 548 GLN C 480 ASN ** C 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 ASN C 539 ASN D 86 ASN D 320 GLN D 539 ASN E 86 ASN E 480 ASN ** E 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 ASN F 480 ASN ** F 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 515 ASN F 539 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 33096 Z= 0.243 Angle : 0.558 6.709 45102 Z= 0.286 Chirality : 0.042 0.153 5274 Planarity : 0.004 0.108 5610 Dihedral : 6.348 55.314 5490 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.66 % Allowed : 10.63 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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 (0.13), residues: 3768 helix: 1.23 (0.13), residues: 1488 sheet: 0.05 (0.20), residues: 570 loop : -1.04 (0.14), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 198 HIS 0.004 0.001 HIS E 483 PHE 0.009 0.001 PHE E 43 TYR 0.033 0.002 TYR A 196 ARG 0.009 0.001 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 316 time to evaluate : 3.830 Fit side-chains revert: symmetry clash REVERT: A 78 HIS cc_start: 0.7273 (OUTLIER) cc_final: 0.6840 (m-70) REVERT: A 540 GLU cc_start: 0.7595 (tt0) cc_final: 0.7353 (tt0) REVERT: B 44 PHE cc_start: 0.7055 (OUTLIER) cc_final: 0.6613 (m-10) REVERT: B 264 TRP cc_start: 0.7623 (OUTLIER) cc_final: 0.7195 (m-10) REVERT: B 435 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.7679 (mtpm) REVERT: B 558 TYR cc_start: 0.7342 (t80) cc_final: 0.7117 (t80) REVERT: C 64 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7775 (mp) REVERT: C 78 HIS cc_start: 0.7289 (OUTLIER) cc_final: 0.6890 (m-70) REVERT: C 120 TYR cc_start: 0.8091 (t80) cc_final: 0.7748 (t80) REVERT: C 180 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.6890 (mtt180) REVERT: C 264 TRP cc_start: 0.7754 (OUTLIER) cc_final: 0.7372 (m-10) REVERT: C 558 TYR cc_start: 0.7442 (t80) cc_final: 0.7188 (t80) REVERT: D 78 HIS cc_start: 0.7281 (OUTLIER) cc_final: 0.6857 (m-70) REVERT: D 180 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.6752 (mtt180) REVERT: E 44 PHE cc_start: 0.7133 (OUTLIER) cc_final: 0.6691 (m-10) REVERT: E 435 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7715 (mtpm) REVERT: E 515 ASN cc_start: 0.6670 (m110) cc_final: 0.6430 (m-40) REVERT: E 558 TYR cc_start: 0.7337 (t80) cc_final: 0.7101 (t80) REVERT: F 64 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7726 (mp) REVERT: F 120 TYR cc_start: 0.8094 (t80) cc_final: 0.7747 (t80) REVERT: F 180 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.6881 (mtt180) REVERT: F 264 TRP cc_start: 0.7763 (OUTLIER) cc_final: 0.7378 (m-10) REVERT: F 558 TYR cc_start: 0.7450 (t80) cc_final: 0.7195 (t80) outliers start: 94 outliers final: 45 residues processed: 378 average time/residue: 2.4111 time to fit residues: 1102.3748 Evaluate side-chains 367 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 307 time to evaluate : 3.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 264 TRP Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 515 ASN Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 64 LEU Chi-restraints excluded: chain C residue 78 HIS Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 264 TRP Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 418 GLN Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 223 SER Chi-restraints excluded: chain D residue 418 GLN Chi-restraints excluded: chain D residue 631 MET Chi-restraints excluded: chain D residue 636 GLU Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 180 ARG Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 223 SER Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 180 ARG Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 223 SER Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 418 GLN Chi-restraints excluded: chain F residue 434 LEU Chi-restraints excluded: chain F residue 631 MET Chi-restraints excluded: chain F residue 663 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 331 optimal weight: 2.9990 chunk 349 optimal weight: 4.9990 chunk 318 optimal weight: 9.9990 chunk 339 optimal weight: 3.9990 chunk 348 optimal weight: 0.5980 chunk 204 optimal weight: 1.9990 chunk 147 optimal weight: 0.7980 chunk 266 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 306 optimal weight: 8.9990 chunk 321 optimal weight: 0.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN B 86 ASN B 206 HIS B 480 ASN ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN B 548 GLN C 86 ASN C 480 ASN ** C 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 ASN C 539 ASN C 548 GLN D 86 ASN E 86 ASN E 480 ASN ** E 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 ASN F 480 ASN ** F 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 515 ASN F 539 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 33096 Z= 0.162 Angle : 0.524 7.567 45102 Z= 0.267 Chirality : 0.041 0.158 5274 Planarity : 0.004 0.088 5610 Dihedral : 5.809 57.521 5490 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.10 % Allowed : 11.39 % Favored : 86.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.44 (0.13), residues: 3768 helix: 1.65 (0.14), residues: 1416 sheet: 0.25 (0.20), residues: 564 loop : -0.80 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 440 HIS 0.004 0.001 HIS D 133 PHE 0.010 0.001 PHE A 139 TYR 0.029 0.001 TYR D 196 ARG 0.012 0.000 ARG B 205 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 308 time to evaluate : 3.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7943 (mp) cc_final: 0.7706 (mt) REVERT: A 78 HIS cc_start: 0.7233 (OUTLIER) cc_final: 0.6798 (m-70) REVERT: A 606 LYS cc_start: 0.6520 (mttt) cc_final: 0.6103 (mmmt) REVERT: B 44 PHE cc_start: 0.7027 (OUTLIER) cc_final: 0.6576 (m-10) REVERT: B 435 LYS cc_start: 0.8413 (OUTLIER) cc_final: 0.7654 (mtpm) REVERT: C 120 TYR cc_start: 0.8073 (t80) cc_final: 0.7738 (t80) REVERT: C 180 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.6892 (mtt180) REVERT: C 264 TRP cc_start: 0.7738 (OUTLIER) cc_final: 0.7363 (m-10) REVERT: C 558 TYR cc_start: 0.7379 (t80) cc_final: 0.7153 (t80) REVERT: D 70 LEU cc_start: 0.7942 (mp) cc_final: 0.7711 (mt) REVERT: D 78 HIS cc_start: 0.7231 (OUTLIER) cc_final: 0.6807 (m-70) REVERT: D 180 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.6761 (mtt180) REVERT: D 606 LYS cc_start: 0.6514 (mttt) cc_final: 0.6096 (mmmt) REVERT: E 44 PHE cc_start: 0.7018 (OUTLIER) cc_final: 0.6641 (m-10) REVERT: E 435 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7657 (mtpm) REVERT: E 515 ASN cc_start: 0.6610 (m110) cc_final: 0.6402 (m-40) REVERT: E 558 TYR cc_start: 0.7368 (t80) cc_final: 0.7166 (t80) REVERT: F 64 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7774 (mp) REVERT: F 120 TYR cc_start: 0.8075 (t80) cc_final: 0.7740 (t80) REVERT: F 180 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.6890 (mtt180) REVERT: F 264 TRP cc_start: 0.7751 (OUTLIER) cc_final: 0.7366 (m-10) REVERT: F 558 TYR cc_start: 0.7380 (t80) cc_final: 0.7156 (t80) outliers start: 74 outliers final: 45 residues processed: 355 average time/residue: 2.5165 time to fit residues: 1081.7856 Evaluate side-chains 366 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 309 time to evaluate : 3.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 515 ASN Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 264 TRP Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 418 GLN Chi-restraints excluded: chain C residue 515 ASN Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 418 GLN Chi-restraints excluded: chain D residue 515 ASN Chi-restraints excluded: chain D residue 631 MET Chi-restraints excluded: chain D residue 636 GLU Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 180 ARG Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 180 ARG Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 418 GLN Chi-restraints excluded: chain F residue 515 ASN Chi-restraints excluded: chain F residue 631 MET Chi-restraints excluded: chain F residue 663 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 338 optimal weight: 3.9990 chunk 222 optimal weight: 0.7980 chunk 359 optimal weight: 4.9990 chunk 219 optimal weight: 1.9990 chunk 170 optimal weight: 4.9990 chunk 249 optimal weight: 6.9990 chunk 376 optimal weight: 2.9990 chunk 346 optimal weight: 2.9990 chunk 299 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 231 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 539 ASN B 86 ASN B 480 ASN ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN B 548 GLN C 86 ASN C 480 ASN ** C 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 539 ASN C 548 GLN D 86 ASN E 480 ASN ** E 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 ASN F 480 ASN ** F 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 539 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 33096 Z= 0.191 Angle : 0.530 6.933 45102 Z= 0.270 Chirality : 0.041 0.163 5274 Planarity : 0.004 0.093 5610 Dihedral : 5.746 53.622 5490 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.04 % Allowed : 11.54 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.13), residues: 3768 helix: 1.66 (0.14), residues: 1416 sheet: 0.29 (0.20), residues: 564 loop : -0.80 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 440 HIS 0.006 0.001 HIS B 483 PHE 0.009 0.001 PHE A 139 TYR 0.023 0.001 TYR A 196 ARG 0.014 0.000 ARG B 205 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7536 Ramachandran restraints generated. 3768 Oldfield, 0 Emsley, 3768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 305 time to evaluate : 3.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 78 HIS cc_start: 0.7243 (OUTLIER) cc_final: 0.6803 (m-70) REVERT: A 606 LYS cc_start: 0.6514 (mttt) cc_final: 0.6104 (mmmt) REVERT: B 44 PHE cc_start: 0.7022 (OUTLIER) cc_final: 0.6564 (m-10) REVERT: B 435 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.7658 (mtpm) REVERT: C 120 TYR cc_start: 0.8079 (t80) cc_final: 0.7745 (t80) REVERT: C 180 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.6918 (mtt180) REVERT: C 264 TRP cc_start: 0.7743 (OUTLIER) cc_final: 0.7370 (m-10) REVERT: C 558 TYR cc_start: 0.7439 (t80) cc_final: 0.7214 (t80) REVERT: D 70 LEU cc_start: 0.7962 (mp) cc_final: 0.7730 (mt) REVERT: D 78 HIS cc_start: 0.7246 (OUTLIER) cc_final: 0.6824 (m-70) REVERT: D 180 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.6730 (mtt180) REVERT: D 606 LYS cc_start: 0.6511 (mttt) cc_final: 0.6103 (mmmt) REVERT: E 44 PHE cc_start: 0.7008 (OUTLIER) cc_final: 0.6632 (m-10) REVERT: E 435 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7661 (mtpm) REVERT: E 515 ASN cc_start: 0.6635 (m110) cc_final: 0.6421 (m-40) REVERT: F 64 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7769 (mp) REVERT: F 120 TYR cc_start: 0.8081 (t80) cc_final: 0.7752 (t80) REVERT: F 154 GLN cc_start: 0.6490 (tp40) cc_final: 0.6198 (mm110) REVERT: F 180 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.6909 (mtt180) REVERT: F 264 TRP cc_start: 0.7768 (OUTLIER) cc_final: 0.7381 (m-10) REVERT: F 558 TYR cc_start: 0.7443 (t80) cc_final: 0.7220 (t80) outliers start: 72 outliers final: 44 residues processed: 350 average time/residue: 2.5252 time to fit residues: 1058.7178 Evaluate side-chains 359 residues out of total 3528 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 303 time to evaluate : 3.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 HIS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 223 SER Chi-restraints excluded: chain A residue 418 GLN Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 636 GLU Chi-restraints excluded: chain A residue 663 THR Chi-restraints excluded: chain B residue 44 PHE Chi-restraints excluded: chain B residue 94 VAL Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 180 ARG Chi-restraints excluded: chain B residue 215 CYS Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 435 LYS Chi-restraints excluded: chain B residue 515 ASN Chi-restraints excluded: chain B residue 537 VAL Chi-restraints excluded: chain B residue 636 GLU Chi-restraints excluded: chain B residue 663 THR Chi-restraints excluded: chain C residue 44 PHE Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 215 CYS Chi-restraints excluded: chain C residue 264 TRP Chi-restraints excluded: chain C residue 331 GLU Chi-restraints excluded: chain C residue 418 GLN Chi-restraints excluded: chain C residue 631 MET Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 418 GLN Chi-restraints excluded: chain D residue 515 ASN Chi-restraints excluded: chain D residue 631 MET Chi-restraints excluded: chain D residue 636 GLU Chi-restraints excluded: chain D residue 663 THR Chi-restraints excluded: chain E residue 44 PHE Chi-restraints excluded: chain E residue 94 VAL Chi-restraints excluded: chain E residue 98 VAL Chi-restraints excluded: chain E residue 180 ARG Chi-restraints excluded: chain E residue 215 CYS Chi-restraints excluded: chain E residue 331 GLU Chi-restraints excluded: chain E residue 435 LYS Chi-restraints excluded: chain E residue 537 VAL Chi-restraints excluded: chain E residue 636 GLU Chi-restraints excluded: chain E residue 663 THR Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 64 LEU Chi-restraints excluded: chain F residue 98 VAL Chi-restraints excluded: chain F residue 180 ARG Chi-restraints excluded: chain F residue 215 CYS Chi-restraints excluded: chain F residue 264 TRP Chi-restraints excluded: chain F residue 331 GLU Chi-restraints excluded: chain F residue 418 GLN Chi-restraints excluded: chain F residue 631 MET Chi-restraints excluded: chain F residue 663 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 183 optimal weight: 0.0670 chunk 238 optimal weight: 1.9990 chunk 319 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 276 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 300 optimal weight: 6.9990 chunk 125 optimal weight: 0.8980 chunk 308 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 overall best weight: 1.5922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN B 86 ASN B 480 ASN ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN B 548 GLN C 480 ASN ** C 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 539 ASN C 548 GLN D 86 ASN E 480 ASN ** E 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 ASN E 548 GLN F 480 ASN ** F 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 539 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.147823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.109094 restraints weight = 101006.340| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.14 r_work: 0.2963 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 33096 Z= 0.169 Angle : 0.516 6.341 45102 Z= 0.263 Chirality : 0.041 0.160 5274 Planarity : 0.004 0.097 5610 Dihedral : 5.419 59.424 5490 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.96 % Allowed : 11.68 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.58 (0.13), residues: 3768 helix: 1.76 (0.14), residues: 1416 sheet: 0.36 (0.20), residues: 564 loop : -0.72 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 440 HIS 0.004 0.001 HIS D 133 PHE 0.009 0.001 PHE A 139 TYR 0.024 0.001 TYR A 196 ARG 0.015 0.000 ARG B 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17060.83 seconds wall clock time: 293 minutes 47.36 seconds (17627.36 seconds total)