Starting phenix.real_space_refine on Fri Sep 27 05:41:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cad_16524/09_2024/8cad_16524_trim.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cad_16524/09_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cad_16524/09_2024/8cad_16524.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cad_16524/09_2024/8cad_16524.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cad_16524/09_2024/8cad_16524_trim.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cad_16524/09_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 24.21, per 1000 atoms: 0.38 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: 13.90 Conformation dependent library (CDL) restraints added in 3.9 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: 4.16 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: 24.86 Time building geometry restraints manager: 16.85 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: 4.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.930 Extract box with map and model: 1.940 Check model and map are aligned: 0.380 Set scattering table: 0.460 Process input model: 108.370 Find NCS groups from input model: 2.120 Set up NCS constraints: 0.400 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:10.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.640 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 574 time to evaluate : 3.781 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: 2.2217 time to fit residues: 1559.1857 Evaluate side-chains 352 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 352 time to evaluate : 3.834 ------------------------------------------------------------------------------- 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 : 7.948 75.236 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 fitting. rotamer outliers: 43 poor density : 357 time to evaluate : 3.810 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: 2.4913 time to fit residues: 1119.7509 Evaluate side-chains 338 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 315 time to evaluate : 4.006 ------------------------------------------------------------------------------- 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: 9.9990 chunk 106 optimal weight: 5.9990 chunk 285 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 343 optimal weight: 2.9990 chunk 371 optimal weight: 6.9990 chunk 306 optimal weight: 0.9980 chunk 341 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 275 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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: 0.8093 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 33096 Z= 0.186 Angle : 0.515 4.572 45102 Z= 0.263 Chirality : 0.041 0.207 5274 Planarity : 0.004 0.057 5610 Dihedral : 6.895 59.945 5490 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.70 % Allowed : 10.15 % Favored : 88.15 % 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: 0.45 (0.13), residues: 3768 helix: 1.55 (0.14), residues: 1422 sheet: -0.04 (0.19), residues: 588 loop : -0.59 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 198 HIS 0.006 0.001 HIS D 133 PHE 0.010 0.001 PHE E 43 TYR 0.013 0.001 TYR A 192 ARG 0.003 0.000 ARG E 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 399 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 339 time to evaluate : 4.287 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: A 78 HIS cc_start: 0.7108 (OUTLIER) cc_final: 0.6727 (m-70) REVERT: A 121 ASP cc_start: 0.6839 (OUTLIER) cc_final: 0.6623 (t0) REVERT: A 180 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.6821 (mtt180) REVERT: B 44 PHE cc_start: 0.6912 (OUTLIER) cc_final: 0.6426 (m-10) REVERT: B 157 ARG cc_start: 0.7203 (mmt90) cc_final: 0.6930 (mmm160) REVERT: B 180 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.6904 (mtt180) REVERT: C 78 HIS cc_start: 0.6940 (m-70) cc_final: 0.6661 (m170) REVERT: C 180 ARG cc_start: 0.8043 (OUTLIER) cc_final: 0.6928 (mtt180) REVERT: C 606 LYS cc_start: 0.6365 (mttt) cc_final: 0.5931 (mmmt) REVERT: C 636 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6857 (mp0) REVERT: D 78 HIS cc_start: 0.7106 (OUTLIER) cc_final: 0.6730 (m-70) REVERT: D 121 ASP cc_start: 0.6835 (OUTLIER) cc_final: 0.6617 (t0) REVERT: D 180 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.6841 (mtt180) REVERT: E 44 PHE cc_start: 0.6922 (OUTLIER) cc_final: 0.6546 (m-10) REVERT: F 78 HIS cc_start: 0.6922 (m-70) cc_final: 0.6648 (m170) REVERT: F 180 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.6928 (mtt180) REVERT: F 606 LYS cc_start: 0.6373 (mttt) cc_final: 0.5940 (mmmt) REVERT: F 636 GLU cc_start: 0.7104 (OUTLIER) cc_final: 0.6846 (mp0) outliers start: 60 outliers final: 31 residues processed: 367 average time/residue: 2.5459 time to fit residues: 1129.1662 Evaluate side-chains 368 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 324 time to evaluate : 4.007 ------------------------------------------------------------------------------- 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 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 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 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: 3.9990 chunk 258 optimal weight: 5.9990 chunk 178 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 230 optimal weight: 7.9990 chunk 345 optimal weight: 3.9990 chunk 365 optimal weight: 2.9990 chunk 180 optimal weight: 6.9990 chunk 327 optimal weight: 5.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 539 ASN B 36 GLN B 154 GLN B 186 GLN B 515 ASN B 539 ASN C 36 GLN C 186 GLN C 206 HIS C 515 ASN C 539 ASN D 36 GLN D 186 GLN D 523 HIS D 539 ASN E 36 GLN E 154 GLN E 186 GLN E 480 ASN E 515 ASN E 539 ASN F 36 GLN F 186 GLN ** F 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 515 ASN F 539 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 33096 Z= 0.234 Angle : 0.546 4.690 45102 Z= 0.280 Chirality : 0.043 0.184 5274 Planarity : 0.004 0.088 5610 Dihedral : 6.480 58.767 5490 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.86 % Allowed : 9.38 % 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: 0.29 (0.13), residues: 3768 helix: 1.48 (0.13), residues: 1416 sheet: -0.11 (0.19), residues: 594 loop : -0.75 (0.14), residues: 1758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 62 HIS 0.008 0.001 HIS D 45 PHE 0.011 0.001 PHE E 43 TYR 0.015 0.001 TYR C 196 ARG 0.007 0.000 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 438 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 337 time to evaluate : 4.128 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: A 78 HIS cc_start: 0.7171 (OUTLIER) cc_final: 0.6793 (m-70) REVERT: A 180 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.6709 (mtt180) REVERT: A 540 GLU cc_start: 0.7607 (tt0) cc_final: 0.7330 (tt0) REVERT: B 180 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.6914 (mtt180) REVERT: B 264 TRP cc_start: 0.7694 (OUTLIER) cc_final: 0.7235 (m-10) REVERT: B 340 MET cc_start: 0.8889 (ttp) cc_final: 0.8672 (ttp) REVERT: B 435 LYS cc_start: 0.8401 (OUTLIER) cc_final: 0.7662 (mtpm) REVERT: B 606 LYS cc_start: 0.6520 (mttt) cc_final: 0.6151 (mmmt) REVERT: C 64 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7731 (mp) REVERT: C 78 HIS cc_start: 0.7022 (m-70) cc_final: 0.6749 (m170) REVERT: C 120 TYR cc_start: 0.7978 (t80) cc_final: 0.7615 (t80) REVERT: C 180 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.6969 (mtt180) REVERT: C 558 TYR cc_start: 0.7333 (t80) cc_final: 0.6937 (t80) REVERT: C 606 LYS cc_start: 0.6457 (mttt) cc_final: 0.6036 (mmmt) REVERT: D 78 HIS cc_start: 0.7156 (OUTLIER) cc_final: 0.6798 (m-70) REVERT: D 180 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.6687 (mtt180) REVERT: D 540 GLU cc_start: 0.7577 (tt0) cc_final: 0.7310 (tt0) REVERT: E 44 PHE cc_start: 0.7015 (OUTLIER) cc_final: 0.6549 (m-10) REVERT: E 264 TRP cc_start: 0.7658 (OUTLIER) cc_final: 0.7203 (m-10) REVERT: E 435 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7663 (mtpm) REVERT: E 606 LYS cc_start: 0.6514 (mttt) cc_final: 0.6100 (mmmt) REVERT: F 64 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7740 (mp) REVERT: F 78 HIS cc_start: 0.7003 (m-70) cc_final: 0.6738 (m170) REVERT: F 120 TYR cc_start: 0.7985 (t80) cc_final: 0.7626 (t80) REVERT: F 180 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.6911 (mtt180) REVERT: F 558 TYR cc_start: 0.7304 (t80) cc_final: 0.6980 (t80) REVERT: F 606 LYS cc_start: 0.6460 (mttt) cc_final: 0.6039 (mmmt) outliers start: 101 outliers final: 50 residues processed: 395 average time/residue: 2.5580 time to fit residues: 1215.5915 Evaluate side-chains 378 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 314 time to evaluate : 3.766 ------------------------------------------------------------------------------- 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 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 515 ASN 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 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 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 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 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 515 ASN 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 304 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 5 optimal weight: 9.9990 chunk 272 optimal weight: 4.9990 chunk 150 optimal weight: 3.9990 chunk 311 optimal weight: 9.9990 chunk 252 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 327 optimal weight: 4.9990 chunk 92 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 320 GLN A 539 ASN B 86 ASN ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN C 86 ASN C 206 HIS ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 515 ASN C 539 ASN D 320 GLN D 523 HIS D 539 ASN E 86 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: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 33096 Z= 0.454 Angle : 0.677 6.563 45102 Z= 0.353 Chirality : 0.047 0.194 5274 Planarity : 0.005 0.070 5610 Dihedral : 7.358 59.528 5490 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.15 % Allowed : 9.18 % Favored : 87.67 % 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: -0.30 (0.13), residues: 3768 helix: 0.89 (0.13), residues: 1434 sheet: -0.31 (0.20), residues: 594 loop : -1.04 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 62 HIS 0.008 0.001 HIS D 481 PHE 0.014 0.002 PHE B 43 TYR 0.017 0.002 TYR C 196 ARG 0.010 0.001 ARG B 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 431 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 320 time to evaluate : 3.816 Fit side-chains REVERT: A 78 HIS cc_start: 0.7255 (OUTLIER) cc_final: 0.6933 (m-70) REVERT: A 180 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.6777 (mtt180) REVERT: A 264 TRP cc_start: 0.7717 (OUTLIER) cc_final: 0.7405 (m-10) REVERT: A 540 GLU cc_start: 0.7609 (tt0) cc_final: 0.7331 (tt0) REVERT: B 44 PHE cc_start: 0.7152 (OUTLIER) cc_final: 0.6669 (m-10) REVERT: B 180 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.6912 (mtt180) REVERT: B 254 LYS cc_start: 0.6814 (OUTLIER) cc_final: 0.6586 (mmtp) REVERT: B 264 TRP cc_start: 0.7685 (OUTLIER) cc_final: 0.7295 (m-10) REVERT: B 435 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.7795 (mtpm) REVERT: B 606 LYS cc_start: 0.6682 (mttt) cc_final: 0.6140 (mmmt) REVERT: C 64 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7771 (mp) REVERT: C 78 HIS cc_start: 0.7179 (m-70) cc_final: 0.6770 (m-70) REVERT: C 120 TYR cc_start: 0.8054 (t80) cc_final: 0.7708 (t80) REVERT: C 180 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7065 (mtt180) REVERT: C 264 TRP cc_start: 0.7760 (OUTLIER) cc_final: 0.7388 (m-10) REVERT: C 558 TYR cc_start: 0.7393 (t80) cc_final: 0.7067 (t80) REVERT: D 78 HIS cc_start: 0.7275 (OUTLIER) cc_final: 0.6930 (m-70) REVERT: D 180 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.6823 (mtt180) REVERT: D 264 TRP cc_start: 0.7712 (OUTLIER) cc_final: 0.7401 (m-10) REVERT: D 540 GLU cc_start: 0.7593 (tt0) cc_final: 0.7323 (tt0) REVERT: D 606 LYS cc_start: 0.6563 (mttt) cc_final: 0.6072 (mmmt) REVERT: E 44 PHE cc_start: 0.7219 (OUTLIER) cc_final: 0.6698 (m-10) REVERT: E 180 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.6995 (mtt180) REVERT: E 254 LYS cc_start: 0.6811 (OUTLIER) cc_final: 0.6585 (mmtp) REVERT: E 264 TRP cc_start: 0.7674 (OUTLIER) cc_final: 0.7284 (m-10) REVERT: E 435 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.7769 (mtpm) REVERT: E 452 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8675 (mp) REVERT: E 606 LYS cc_start: 0.6677 (mttt) cc_final: 0.6142 (mmmt) REVERT: F 64 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7758 (mp) REVERT: F 78 HIS cc_start: 0.7166 (m-70) cc_final: 0.6761 (m-70) REVERT: F 120 TYR cc_start: 0.8054 (t80) cc_final: 0.7708 (t80) REVERT: F 180 ARG cc_start: 0.8138 (OUTLIER) cc_final: 0.7014 (mtt180) REVERT: F 264 TRP cc_start: 0.7758 (OUTLIER) cc_final: 0.7386 (m-10) REVERT: F 558 TYR cc_start: 0.7410 (t80) cc_final: 0.7068 (t80) outliers start: 111 outliers final: 59 residues processed: 388 average time/residue: 2.5301 time to fit residues: 1187.6546 Evaluate side-chains 391 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 309 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 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 331 GLU 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 254 LYS 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 446 HIS Chi-restraints excluded: chain B residue 480 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 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 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 331 GLU 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 223 SER Chi-restraints excluded: chain E residue 254 LYS 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 446 HIS 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 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: 6.9990 chunk 72 optimal weight: 7.9990 chunk 214 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 365 optimal weight: 4.9990 chunk 303 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 192 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 133 HIS A 320 GLN B 86 ASN ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 ASN ** C 480 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 539 ASN D 86 ASN D 133 HIS 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 206 HIS ** 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 33096 Z= 0.252 Angle : 0.578 5.451 45102 Z= 0.299 Chirality : 0.043 0.162 5274 Planarity : 0.004 0.078 5610 Dihedral : 6.746 56.738 5490 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 2.89 % Allowed : 9.55 % Favored : 87.56 % 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: -0.15 (0.13), residues: 3768 helix: 1.08 (0.13), residues: 1452 sheet: -0.20 (0.20), residues: 594 loop : -1.07 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 198 HIS 0.004 0.001 HIS A 133 PHE 0.011 0.001 PHE B 43 TYR 0.021 0.002 TYR D 196 ARG 0.009 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 412 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 310 time to evaluate : 3.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 180 ARG cc_start: 0.7921 (OUTLIER) cc_final: 0.6764 (mtt180) REVERT: A 264 TRP cc_start: 0.7703 (OUTLIER) cc_final: 0.7386 (m-10) REVERT: A 540 GLU cc_start: 0.7608 (tt0) cc_final: 0.7349 (tt0) REVERT: A 606 LYS cc_start: 0.6537 (mttt) cc_final: 0.6033 (mmmt) REVERT: B 180 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.6847 (mtt180) REVERT: B 254 LYS cc_start: 0.6673 (OUTLIER) cc_final: 0.6456 (mmtp) REVERT: B 264 TRP cc_start: 0.7654 (OUTLIER) cc_final: 0.7268 (m-10) REVERT: B 435 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.7742 (mtpm) REVERT: B 558 TYR cc_start: 0.7252 (t80) cc_final: 0.6892 (t80) REVERT: B 606 LYS cc_start: 0.6672 (mttt) cc_final: 0.6159 (mmmt) REVERT: C 64 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7776 (mp) REVERT: C 120 TYR cc_start: 0.8042 (t80) cc_final: 0.7686 (t80) REVERT: C 180 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.6994 (mtt180) REVERT: C 264 TRP cc_start: 0.7757 (OUTLIER) cc_final: 0.7399 (m-10) REVERT: C 558 TYR cc_start: 0.7391 (t80) cc_final: 0.7073 (t80) REVERT: D 78 HIS cc_start: 0.7237 (OUTLIER) cc_final: 0.6901 (m-70) REVERT: D 180 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.6795 (mtt180) REVERT: D 264 TRP cc_start: 0.7703 (OUTLIER) cc_final: 0.7385 (m-10) REVERT: D 540 GLU cc_start: 0.7590 (tt0) cc_final: 0.7343 (tt0) REVERT: D 606 LYS cc_start: 0.6534 (mttt) cc_final: 0.6028 (mmmt) REVERT: E 44 PHE cc_start: 0.7179 (OUTLIER) cc_final: 0.6760 (m-10) REVERT: E 254 LYS cc_start: 0.6669 (OUTLIER) cc_final: 0.6455 (mmtp) REVERT: E 264 TRP cc_start: 0.7639 (OUTLIER) cc_final: 0.7253 (m-10) REVERT: E 435 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7742 (mtpm) REVERT: E 558 TYR cc_start: 0.7264 (t80) cc_final: 0.6911 (t80) REVERT: E 606 LYS cc_start: 0.6689 (mttt) cc_final: 0.6170 (mmmt) REVERT: F 64 LEU cc_start: 0.8009 (OUTLIER) cc_final: 0.7753 (mp) REVERT: F 120 TYR cc_start: 0.8042 (t80) cc_final: 0.7688 (t80) REVERT: F 180 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7004 (mtt180) REVERT: F 264 TRP cc_start: 0.7754 (OUTLIER) cc_final: 0.7397 (m-10) REVERT: F 558 TYR cc_start: 0.7403 (t80) cc_final: 0.7067 (t80) outliers start: 102 outliers final: 57 residues processed: 373 average time/residue: 2.5505 time to fit residues: 1156.3735 Evaluate side-chains 381 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 305 time to evaluate : 3.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE 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 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 223 SER Chi-restraints excluded: chain B residue 254 LYS 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 446 HIS 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 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 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 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 254 LYS 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 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 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: 5.9990 chunk 41 optimal weight: 6.9990 chunk 208 optimal weight: 3.9990 chunk 267 optimal weight: 7.9990 chunk 206 optimal weight: 0.9990 chunk 307 optimal weight: 9.9990 chunk 204 optimal weight: 9.9990 chunk 364 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 222 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.8160 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 33096 Z= 0.180 Angle : 0.533 5.799 45102 Z= 0.273 Chirality : 0.042 0.153 5274 Planarity : 0.004 0.094 5610 Dihedral : 6.076 49.604 5490 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % 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: 0.15 (0.13), residues: 3768 helix: 1.34 (0.13), residues: 1452 sheet: -0.03 (0.20), residues: 594 loop : -0.90 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 440 HIS 0.003 0.001 HIS F 483 PHE 0.010 0.001 PHE B 43 TYR 0.025 0.001 TYR A 196 ARG 0.011 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 411 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 318 time to evaluate : 3.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 HIS cc_start: 0.7224 (OUTLIER) cc_final: 0.6785 (m-70) REVERT: A 180 ARG cc_start: 0.7868 (OUTLIER) cc_final: 0.6771 (mtt180) REVERT: A 540 GLU cc_start: 0.7589 (tt0) cc_final: 0.7339 (tt0) REVERT: A 606 LYS cc_start: 0.6514 (mttt) cc_final: 0.6029 (mmmt) REVERT: B 44 PHE cc_start: 0.7052 (OUTLIER) cc_final: 0.6502 (m-10) REVERT: B 254 LYS cc_start: 0.6667 (OUTLIER) cc_final: 0.6459 (mmtp) REVERT: B 264 TRP cc_start: 0.7648 (OUTLIER) cc_final: 0.7212 (m-10) REVERT: B 435 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7685 (mtpm) REVERT: B 558 TYR cc_start: 0.7251 (t80) cc_final: 0.6965 (t80) REVERT: B 606 LYS cc_start: 0.6658 (mttt) cc_final: 0.6163 (mmmt) REVERT: C 120 TYR cc_start: 0.8039 (t80) cc_final: 0.7698 (t80) REVERT: C 180 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.6959 (mtt180) REVERT: C 264 TRP cc_start: 0.7756 (OUTLIER) cc_final: 0.7353 (m-10) REVERT: C 558 TYR cc_start: 0.7403 (t80) cc_final: 0.7107 (t80) REVERT: D 78 HIS cc_start: 0.7214 (OUTLIER) cc_final: 0.6818 (m-70) REVERT: D 180 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.6717 (mtt180) REVERT: D 540 GLU cc_start: 0.7577 (tt0) cc_final: 0.7336 (tt0) REVERT: D 606 LYS cc_start: 0.6516 (mttt) cc_final: 0.6023 (mmmt) REVERT: E 44 PHE cc_start: 0.7035 (OUTLIER) cc_final: 0.6678 (m-10) REVERT: E 254 LYS cc_start: 0.6663 (OUTLIER) cc_final: 0.6455 (mmtp) REVERT: E 264 TRP cc_start: 0.7632 (OUTLIER) cc_final: 0.7198 (m-10) REVERT: E 435 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7673 (mtpm) REVERT: E 558 TYR cc_start: 0.7276 (t80) cc_final: 0.7015 (t80) REVERT: F 120 TYR cc_start: 0.8036 (t80) cc_final: 0.7699 (t80) REVERT: F 180 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.6968 (mtt180) REVERT: F 264 TRP cc_start: 0.7755 (OUTLIER) cc_final: 0.7351 (m-10) REVERT: F 558 TYR cc_start: 0.7398 (t80) cc_final: 0.7100 (t80) outliers start: 93 outliers final: 48 residues processed: 378 average time/residue: 2.5389 time to fit residues: 1157.9198 Evaluate side-chains 374 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 310 time to evaluate : 3.807 ------------------------------------------------------------------------------- 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 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 215 CYS Chi-restraints excluded: chain B residue 254 LYS 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 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 452 LEU 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 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 254 LYS 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: 2.9990 chunk 217 optimal weight: 3.9990 chunk 109 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 231 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 180 optimal weight: 9.9990 chunk 33 optimal weight: 0.8980 chunk 286 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** A 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 86 ASN C 480 ASN ** C 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 539 ASN D 86 ASN ** D 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 539 ASN E 86 ASN E 480 ASN ** E 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 539 ASN E 548 GLN F 86 ASN F 480 ASN ** F 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 539 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 33096 Z= 0.235 Angle : 0.553 6.686 45102 Z= 0.284 Chirality : 0.042 0.155 5274 Planarity : 0.004 0.109 5610 Dihedral : 6.269 57.438 5490 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.64 % Allowed : 10.52 % Favored : 86.85 % 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: 1.47 (0.14), residues: 1416 sheet: 0.07 (0.20), residues: 570 loop : -0.92 (0.14), residues: 1782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 440 HIS 0.004 0.001 HIS E 483 PHE 0.009 0.001 PHE E 43 TYR 0.020 0.001 TYR C 196 ARG 0.010 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 409 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 316 time to evaluate : 3.915 Fit side-chains revert: symmetry clash REVERT: A 78 HIS cc_start: 0.7257 (OUTLIER) cc_final: 0.6821 (m-70) REVERT: A 180 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.6798 (mtt180) REVERT: A 264 TRP cc_start: 0.7713 (OUTLIER) cc_final: 0.7348 (m-10) REVERT: A 540 GLU cc_start: 0.7595 (tt0) cc_final: 0.7350 (tt0) REVERT: A 606 LYS cc_start: 0.6515 (mttt) cc_final: 0.6090 (mmmt) REVERT: B 44 PHE cc_start: 0.7042 (OUTLIER) cc_final: 0.6594 (m-10) REVERT: B 254 LYS cc_start: 0.6635 (OUTLIER) cc_final: 0.6430 (mmtp) REVERT: B 435 LYS cc_start: 0.8461 (OUTLIER) cc_final: 0.7691 (mtpm) REVERT: B 515 ASN cc_start: 0.6615 (m110) cc_final: 0.6388 (m-40) REVERT: B 558 TYR cc_start: 0.7272 (t80) cc_final: 0.7014 (t80) REVERT: C 64 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7754 (mp) REVERT: C 78 HIS cc_start: 0.7276 (OUTLIER) cc_final: 0.6917 (m-70) REVERT: C 120 TYR cc_start: 0.8086 (t80) cc_final: 0.7740 (t80) REVERT: C 180 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.6898 (mtt180) REVERT: C 264 TRP cc_start: 0.7757 (OUTLIER) cc_final: 0.7368 (m-10) REVERT: C 558 TYR cc_start: 0.7453 (t80) cc_final: 0.7191 (t80) REVERT: D 78 HIS cc_start: 0.7269 (OUTLIER) cc_final: 0.6843 (m-70) REVERT: D 180 ARG cc_start: 0.7923 (OUTLIER) cc_final: 0.6703 (mtt180) REVERT: D 264 TRP cc_start: 0.7713 (OUTLIER) cc_final: 0.7349 (m-10) REVERT: D 540 GLU cc_start: 0.7582 (tt0) cc_final: 0.7345 (tt0) REVERT: D 606 LYS cc_start: 0.6510 (mttt) cc_final: 0.6083 (mmmt) REVERT: E 44 PHE cc_start: 0.7043 (OUTLIER) cc_final: 0.6586 (m-10) REVERT: E 254 LYS cc_start: 0.6634 (OUTLIER) cc_final: 0.6429 (mmtp) REVERT: E 435 LYS cc_start: 0.8462 (OUTLIER) cc_final: 0.7702 (mtpm) REVERT: E 515 ASN cc_start: 0.6583 (m110) cc_final: 0.6353 (m-40) REVERT: E 558 TYR cc_start: 0.7307 (t80) cc_final: 0.7040 (t80) REVERT: F 64 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7742 (mp) REVERT: F 120 TYR cc_start: 0.8068 (t80) cc_final: 0.7727 (t80) REVERT: F 180 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.6881 (mtt180) REVERT: F 264 TRP cc_start: 0.7756 (OUTLIER) cc_final: 0.7367 (m-10) REVERT: F 558 TYR cc_start: 0.7468 (t80) cc_final: 0.7193 (t80) outliers start: 93 outliers final: 47 residues processed: 377 average time/residue: 2.5674 time to fit residues: 1175.4011 Evaluate side-chains 379 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 313 time to evaluate : 3.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 HIS 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 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 215 CYS Chi-restraints excluded: chain B residue 223 SER Chi-restraints excluded: chain B residue 254 LYS Chi-restraints excluded: chain B residue 331 GLU Chi-restraints excluded: chain B residue 435 LYS 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 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 631 MET Chi-restraints excluded: chain C residue 663 THR Chi-restraints excluded: chain D residue 78 HIS 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 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 223 SER Chi-restraints excluded: chain E residue 254 LYS 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: 0.9990 chunk 349 optimal weight: 0.0770 chunk 318 optimal weight: 9.9990 chunk 339 optimal weight: 3.9990 chunk 348 optimal weight: 0.5980 chunk 204 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 266 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 306 optimal weight: 7.9990 chunk 321 optimal weight: 0.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 133 HIS 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 539 ASN D 86 ASN D 133 HIS D 615 HIS E 86 ASN E 480 ASN E 481 HIS E 539 ASN E 548 GLN F 86 ASN F 480 ASN ** F 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 539 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 33096 Z= 0.139 Angle : 0.504 6.156 45102 Z= 0.257 Chirality : 0.041 0.169 5274 Planarity : 0.004 0.087 5610 Dihedral : 5.491 58.247 5490 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.84 % Allowed : 11.39 % Favored : 86.76 % 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: 0.53 (0.13), residues: 3768 helix: 1.62 (0.14), residues: 1452 sheet: 0.32 (0.20), residues: 564 loop : -0.71 (0.14), residues: 1752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 440 HIS 0.004 0.001 HIS A 133 PHE 0.010 0.001 PHE A 139 TYR 0.018 0.001 TYR B 196 ARG 0.011 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 387 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 322 time to evaluate : 3.863 Fit side-chains REVERT: A 70 LEU cc_start: 0.7881 (mp) cc_final: 0.7648 (mt) REVERT: A 606 LYS cc_start: 0.6512 (mttt) cc_final: 0.6079 (mmmt) REVERT: B 44 PHE cc_start: 0.6991 (OUTLIER) cc_final: 0.6629 (m-10) REVERT: B 435 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7568 (mtpm) REVERT: B 558 TYR cc_start: 0.7259 (t80) cc_final: 0.7007 (t80) REVERT: B 606 LYS cc_start: 0.6470 (mttt) cc_final: 0.6032 (mmmt) REVERT: C 120 TYR cc_start: 0.8037 (t80) cc_final: 0.7696 (t80) REVERT: C 180 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.6937 (mtt180) REVERT: C 264 TRP cc_start: 0.7734 (OUTLIER) cc_final: 0.7339 (m-10) REVERT: C 558 TYR cc_start: 0.7390 (t80) cc_final: 0.7160 (t80) REVERT: D 70 LEU cc_start: 0.7917 (mp) cc_final: 0.7683 (mt) REVERT: D 78 HIS cc_start: 0.7192 (OUTLIER) cc_final: 0.6772 (m-70) REVERT: D 180 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.6715 (mtt180) REVERT: D 606 LYS cc_start: 0.6508 (mttt) cc_final: 0.6073 (mmmt) REVERT: E 44 PHE cc_start: 0.6982 (OUTLIER) cc_final: 0.6590 (m-10) REVERT: E 435 LYS cc_start: 0.8309 (OUTLIER) cc_final: 0.7560 (mtpm) REVERT: E 558 TYR cc_start: 0.7272 (t80) cc_final: 0.7030 (t80) REVERT: E 606 LYS cc_start: 0.6476 (mttt) cc_final: 0.6047 (mmmt) REVERT: F 120 TYR cc_start: 0.8042 (t80) cc_final: 0.7712 (t80) REVERT: F 154 GLN cc_start: 0.6441 (tp40) cc_final: 0.6192 (mm110) REVERT: F 180 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.6927 (mtt180) REVERT: F 264 TRP cc_start: 0.7732 (OUTLIER) cc_final: 0.7339 (m-10) REVERT: F 558 TYR cc_start: 0.7398 (t80) cc_final: 0.7141 (t80) outliers start: 65 outliers final: 29 residues processed: 364 average time/residue: 2.6910 time to fit residues: 1195.1148 Evaluate side-chains 352 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 313 time to evaluate : 3.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 631 MET 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 331 GLU Chi-restraints excluded: chain B residue 435 LYS 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 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 180 ARG Chi-restraints excluded: chain D residue 631 MET 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 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 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 434 LEU 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: 0.5980 chunk 359 optimal weight: 0.9980 chunk 219 optimal weight: 0.8980 chunk 170 optimal weight: 0.9980 chunk 249 optimal weight: 6.9990 chunk 376 optimal weight: 1.9990 chunk 346 optimal weight: 3.9990 chunk 299 optimal weight: 7.9990 chunk 31 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 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 D 539 ASN E 86 ASN E 480 ASN E 539 ASN E 548 GLN F 86 ASN F 480 ASN ** F 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 539 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3104 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= 0.152 Angle : 0.503 6.378 45102 Z= 0.255 Chirality : 0.041 0.163 5274 Planarity : 0.004 0.097 5610 Dihedral : 5.179 55.399 5490 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.70 % Allowed : 11.93 % 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: 0.74 (0.13), residues: 3768 helix: 1.88 (0.14), residues: 1416 sheet: 0.43 (0.20), residues: 564 loop : -0.62 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 440 HIS 0.006 0.001 HIS A 133 PHE 0.009 0.001 PHE A 139 TYR 0.022 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 367 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 307 time to evaluate : 3.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.7881 (mp) cc_final: 0.7647 (mt) REVERT: A 180 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.6736 (mtt180) REVERT: A 606 LYS cc_start: 0.6489 (mttt) cc_final: 0.6088 (mmmt) REVERT: B 44 PHE cc_start: 0.6939 (OUTLIER) cc_final: 0.6557 (m-10) REVERT: B 435 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.7557 (mtpm) REVERT: B 558 TYR cc_start: 0.7242 (t80) cc_final: 0.7011 (t80) REVERT: C 64 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7737 (mp) REVERT: C 120 TYR cc_start: 0.8036 (t80) cc_final: 0.7697 (t80) REVERT: C 154 GLN cc_start: 0.6408 (tp40) cc_final: 0.6182 (mm110) REVERT: C 558 TYR cc_start: 0.7388 (t80) cc_final: 0.7166 (t80) REVERT: D 70 LEU cc_start: 0.7907 (mp) cc_final: 0.7671 (mt) REVERT: D 78 HIS cc_start: 0.7215 (OUTLIER) cc_final: 0.6783 (m-70) REVERT: D 180 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.6688 (mtt180) REVERT: D 606 LYS cc_start: 0.6484 (mttt) cc_final: 0.6081 (mmmt) REVERT: E 44 PHE cc_start: 0.6934 (OUTLIER) cc_final: 0.6529 (m-10) REVERT: E 435 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7550 (mtpm) REVERT: E 558 TYR cc_start: 0.7257 (t80) cc_final: 0.7019 (t80) REVERT: F 120 TYR cc_start: 0.8039 (t80) cc_final: 0.7697 (t80) REVERT: F 154 GLN cc_start: 0.6390 (tp40) cc_final: 0.6139 (mm110) REVERT: F 558 TYR cc_start: 0.7387 (t80) cc_final: 0.7150 (t80) outliers start: 60 outliers final: 28 residues processed: 341 average time/residue: 2.5610 time to fit residues: 1047.6495 Evaluate side-chains 344 residues out of total 3528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 308 time to evaluate : 3.813 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 PHE Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 631 MET 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 331 GLU Chi-restraints excluded: chain B residue 435 LYS 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 64 LEU Chi-restraints excluded: chain C residue 180 ARG Chi-restraints excluded: chain C residue 215 CYS 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 44 PHE Chi-restraints excluded: chain D residue 78 HIS Chi-restraints excluded: chain D residue 180 ARG Chi-restraints excluded: chain D residue 631 MET 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 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 180 ARG Chi-restraints excluded: chain F residue 215 CYS 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: 5.9990 chunk 238 optimal weight: 1.9990 chunk 319 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 276 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 chunk 300 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 308 optimal weight: 9.9990 chunk 38 optimal weight: 0.8980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN B 480 ASN ** B 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 ASN 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 ** D 320 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 480 ASN E 515 ASN E 539 ASN E 548 GLN F 86 ASN F 480 ASN ** F 481 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 539 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.148326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.108426 restraints weight = 101413.713| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 1.94 r_work: 0.2997 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.337 33096 Z= 0.293 Angle : 0.749 59.296 45102 Z= 0.424 Chirality : 0.042 0.435 5274 Planarity : 0.004 0.097 5610 Dihedral : 5.180 55.299 5490 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.33 % Allowed : 12.19 % Favored : 86.48 % 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: 0.74 (0.13), residues: 3768 helix: 1.88 (0.14), residues: 1416 sheet: 0.43 (0.20), residues: 564 loop : -0.61 (0.14), residues: 1788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 440 HIS 0.004 0.001 HIS A 133 PHE 0.175 0.002 PHE A 44 TYR 0.020 0.001 TYR C 196 ARG 0.009 0.000 ARG B 205 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18465.38 seconds wall clock time: 314 minutes 20.77 seconds (18860.77 seconds total)