Starting phenix.real_space_refine on Fri Feb 6 14:15:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rbr_53903/02_2026/9rbr_53903.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rbr_53903/02_2026/9rbr_53903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rbr_53903/02_2026/9rbr_53903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rbr_53903/02_2026/9rbr_53903.map" model { file = "/net/cci-nas-00/data/ceres_data/9rbr_53903/02_2026/9rbr_53903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rbr_53903/02_2026/9rbr_53903.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.003 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: 4 Type Number sf(0) Gaussians S 201 5.16 5 C 15912 2.51 5 N 4341 2.21 5 O 4818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25272 Number of models: 1 Model: "" Number of chains: 21 Chain: "D" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 415 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "E" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 415 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "F" Number of atoms: 415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 415 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 5, 'TRANS': 48} Chain: "G" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3329 Classifications: {'peptide': 438} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "H" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3329 Classifications: {'peptide': 438} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "I" Number of atoms: 3329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3329 Classifications: {'peptide': 438} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 409} Chain: "J" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3282 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 31, 'TRANS': 389} Chain: "K" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3282 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 31, 'TRANS': 389} Chain: "L" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3282 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 31, 'TRANS': 389} Chain: "M" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1250 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "N" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1250 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "O" Number of atoms: 1250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1250 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 154} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "P" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "d" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "Q" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "j" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "p" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 5.33, per 1000 atoms: 0.21 Number of scatterers: 25272 At special positions: 0 Unit cell: (155.52, 153.36, 189, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 201 16.00 O 4818 8.00 N 4341 7.00 C 15912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=46, symmetry=0 Simple disulfide: pdb=" SG CYS D 9 " - pdb=" SG CYS D 18 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 27 " distance=2.03 Simple disulfide: pdb=" SG CYS D 26 " - pdb=" SG CYS D 58 " distance=2.03 Simple disulfide: pdb=" SG CYS E 9 " - pdb=" SG CYS E 18 " distance=2.03 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 27 " distance=2.03 Simple disulfide: pdb=" SG CYS E 26 " - pdb=" SG CYS E 58 " distance=2.03 Simple disulfide: pdb=" SG CYS F 9 " - pdb=" SG CYS F 18 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 27 " distance=2.03 Simple disulfide: pdb=" SG CYS F 26 " - pdb=" SG CYS F 58 " distance=2.03 Simple disulfide: pdb=" SG CYS G 49 " - pdb=" SG CYS G 114 " distance=2.04 Simple disulfide: pdb=" SG CYS G 62 " - pdb=" SG CYS G 94 " distance=2.03 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 78 " distance=2.04 Simple disulfide: pdb=" SG CYS G 259 " - pdb=" SG CYS G 271 " distance=2.03 Simple disulfide: pdb=" SG CYS G 301 " - pdb=" SG CYS G 376 " distance=2.03 Simple disulfide: pdb=" SG CYS G 306 " - pdb=" SG CYS G 380 " distance=2.03 Simple disulfide: pdb=" SG CYS G 328 " - pdb=" SG CYS G 370 " distance=2.03 Simple disulfide: pdb=" SG CYS H 49 " - pdb=" SG CYS H 114 " distance=2.04 Simple disulfide: pdb=" SG CYS H 62 " - pdb=" SG CYS H 94 " distance=2.03 Simple disulfide: pdb=" SG CYS H 63 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 259 " - pdb=" SG CYS H 271 " distance=2.03 Simple disulfide: pdb=" SG CYS H 301 " - pdb=" SG CYS H 376 " distance=2.03 Simple disulfide: pdb=" SG CYS H 306 " - pdb=" SG CYS H 380 " distance=2.03 Simple disulfide: pdb=" SG CYS H 328 " - pdb=" SG CYS H 370 " distance=2.03 Simple disulfide: pdb=" SG CYS I 49 " - pdb=" SG CYS I 114 " distance=2.04 Simple disulfide: pdb=" SG CYS I 62 " - pdb=" SG CYS I 94 " distance=2.03 Simple disulfide: pdb=" SG CYS I 63 " - pdb=" SG CYS I 96 " distance=2.03 Simple disulfide: pdb=" SG CYS I 68 " - pdb=" SG CYS I 78 " distance=2.03 Simple disulfide: pdb=" SG CYS I 259 " - pdb=" SG CYS I 271 " distance=2.03 Simple disulfide: pdb=" SG CYS I 301 " - pdb=" SG CYS I 376 " distance=2.03 Simple disulfide: pdb=" SG CYS I 306 " - pdb=" SG CYS I 380 " distance=2.03 Simple disulfide: pdb=" SG CYS I 328 " - pdb=" SG CYS I 370 " distance=2.03 Simple disulfide: pdb=" SG CYS J 19 " - pdb=" SG CYS J 125 " distance=2.04 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 28 " distance=2.03 Simple disulfide: pdb=" SG CYS J 91 " - pdb=" SG CYS J 105 " distance=2.03 Simple disulfide: pdb=" SG CYS J 201 " - pdb=" SG CYS J 225 " distance=2.03 Simple disulfide: pdb=" SG CYS J 203 " - pdb=" SG CYS J 220 " distance=2.03 Simple disulfide: pdb=" SG CYS K 19 " - pdb=" SG CYS K 125 " distance=2.04 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 28 " distance=2.03 Simple disulfide: pdb=" SG CYS K 91 " - pdb=" SG CYS K 105 " distance=2.03 Simple disulfide: pdb=" SG CYS K 201 " - pdb=" SG CYS K 225 " distance=2.03 Simple disulfide: pdb=" SG CYS L 19 " - pdb=" SG CYS L 125 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 28 " distance=2.03 Simple disulfide: pdb=" SG CYS L 91 " - pdb=" SG CYS L 105 " distance=2.03 Simple disulfide: pdb=" SG CYS L 201 " - pdb=" SG CYS L 225 " distance=2.03 Simple disulfide: pdb=" SG CYS L 203 " - pdb=" SG CYS L 220 " distance=2.03 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=1, symmetry=0 Links applied ALPHA1-6 " NAG A 1 " - " MAN A 4 " " NAG B 1 " - " MAN B 4 " " NAG C 1 " - " MAN C 4 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " NAG P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG Q 2 " - " NAG Q 3 " " NAG R 1 " - " NAG R 2 " " NAG R 2 " - " NAG R 3 " " NAG d 1 " - " NAG d 2 " " NAG d 2 " - " NAG d 3 " " NAG j 1 " - " NAG j 2 " " NAG j 2 " - " NAG j 3 " " NAG p 1 " - " NAG p 2 " " NAG p 2 " - " NAG p 3 " BETA1-6 " NAG d 3 " - " NAG d 4 " " NAG j 3 " - " NAG j 4 " " NAG p 3 " - " NAG p 4 " NAG-ASN " NAG A 1 " - " ASN G 141 " " NAG B 1 " - " ASN H 141 " " NAG C 1 " - " ASN I 141 " " NAG P 1 " - " ASN J 200 " " NAG Q 1 " - " ASN K 200 " " NAG R 1 " - " ASN L 200 " " NAG d 1 " - " ASN J 262 " " NAG j 1 " - " ASN K 262 " " NAG p 1 " - " ASN L 262 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.67 Conformation dependent library (CDL) restraints added in 1.2 seconds 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5988 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 72 sheets defined 17.0% alpha, 39.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'D' and resid 26 through 31 Processing helix chain 'D' and resid 31 through 42 Processing helix chain 'D' and resid 47 through 56 Processing helix chain 'E' and resid 26 through 31 Processing helix chain 'E' and resid 31 through 42 Processing helix chain 'E' and resid 47 through 56 Processing helix chain 'F' and resid 26 through 31 Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 47 through 56 Processing helix chain 'G' and resid 238 through 246 Processing helix chain 'G' and resid 250 through 255 removed outlier: 3.574A pdb=" N LYS G 254 " --> pdb=" O ALA G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 256 through 259 Processing helix chain 'G' and resid 283 through 287 Processing helix chain 'G' and resid 404 through 438 removed outlier: 3.617A pdb=" N VAL G 410 " --> pdb=" O ALA G 406 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 247 removed outlier: 3.517A pdb=" N LYS H 245 " --> pdb=" O LYS H 241 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 254 Processing helix chain 'H' and resid 255 through 259 removed outlier: 4.052A pdb=" N GLY H 258 " --> pdb=" O ALA H 255 " (cutoff:3.500A) Processing helix chain 'H' and resid 283 through 287 Processing helix chain 'H' and resid 404 through 438 Processing helix chain 'I' and resid 238 through 246 Processing helix chain 'I' and resid 250 through 254 Processing helix chain 'I' and resid 255 through 259 removed outlier: 3.976A pdb=" N GLY I 258 " --> pdb=" O ALA I 255 " (cutoff:3.500A) Processing helix chain 'I' and resid 283 through 287 Processing helix chain 'I' and resid 404 through 438 removed outlier: 3.684A pdb=" N VAL I 410 " --> pdb=" O ALA I 406 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 6 Processing helix chain 'J' and resid 7 through 10 Processing helix chain 'J' and resid 81 through 83 No H-bonds generated for 'chain 'J' and resid 81 through 83' Processing helix chain 'J' and resid 221 through 223 No H-bonds generated for 'chain 'J' and resid 221 through 223' Processing helix chain 'J' and resid 350 through 360 Processing helix chain 'J' and resid 362 through 402 Proline residue: J 398 - end of helix Processing helix chain 'J' and resid 408 through 415 removed outlier: 3.720A pdb=" N ILE J 413 " --> pdb=" O TRP J 409 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU J 414 " --> pdb=" O THR J 410 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 7 removed outlier: 3.572A pdb=" N PHE K 6 " --> pdb=" O VAL K 2 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN K 7 " --> pdb=" O SER K 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 2 through 7' Processing helix chain 'K' and resid 8 through 10 No H-bonds generated for 'chain 'K' and resid 8 through 10' Processing helix chain 'K' and resid 81 through 83 No H-bonds generated for 'chain 'K' and resid 81 through 83' Processing helix chain 'K' and resid 221 through 223 No H-bonds generated for 'chain 'K' and resid 221 through 223' Processing helix chain 'K' and resid 350 through 360 Processing helix chain 'K' and resid 365 through 402 Proline residue: K 398 - end of helix Processing helix chain 'K' and resid 408 through 415 removed outlier: 3.634A pdb=" N ILE K 413 " --> pdb=" O TRP K 409 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LEU K 414 " --> pdb=" O THR K 410 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 6 Processing helix chain 'L' and resid 7 through 11 removed outlier: 3.652A pdb=" N ALA L 11 " --> pdb=" O VAL L 8 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing helix chain 'L' and resid 221 through 223 No H-bonds generated for 'chain 'L' and resid 221 through 223' Processing helix chain 'L' and resid 350 through 360 Processing helix chain 'L' and resid 362 through 394 Processing helix chain 'L' and resid 396 through 401 Processing helix chain 'L' and resid 408 through 415 removed outlier: 3.591A pdb=" N ILE L 413 " --> pdb=" O TRP L 409 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU L 414 " --> pdb=" O THR L 410 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS L 415 " --> pdb=" O LEU L 411 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 120 removed outlier: 4.149A pdb=" N LYS M 114 " --> pdb=" O ARG M 110 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE M 115 " --> pdb=" O MET M 111 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP M 118 " --> pdb=" O LYS M 114 " (cutoff:3.500A) Processing helix chain 'M' and resid 152 through 158 Processing helix chain 'M' and resid 174 through 181 removed outlier: 3.517A pdb=" N ARG M 178 " --> pdb=" O VAL M 175 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N SER M 179 " --> pdb=" O HIS M 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 112 through 120 removed outlier: 4.076A pdb=" N GLU N 116 " --> pdb=" O CYS N 112 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASN N 117 " --> pdb=" O MET N 113 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N ASP N 118 " --> pdb=" O LYS N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 152 through 158 removed outlier: 3.503A pdb=" N LYS N 157 " --> pdb=" O ALA N 153 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU N 158 " --> pdb=" O ASP N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 174 through 178 Processing helix chain 'O' and resid 109 through 119 removed outlier: 4.299A pdb=" N MET O 113 " --> pdb=" O GLU O 109 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N LYS O 114 " --> pdb=" O ARG O 110 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE O 115 " --> pdb=" O MET O 111 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ASP O 118 " --> pdb=" O LYS O 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 152 through 157 Processing sheet with id=AA1, first strand: chain 'D' and resid 9 through 10 Processing sheet with id=AA2, first strand: chain 'E' and resid 8 through 11 Processing sheet with id=AA3, first strand: chain 'F' and resid 8 through 11 Processing sheet with id=AA4, first strand: chain 'G' and resid 2 through 8 Processing sheet with id=AA5, first strand: chain 'G' and resid 15 through 19 removed outlier: 6.385A pdb=" N LYS G 132 " --> pdb=" O VAL G 34 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR G 36 " --> pdb=" O LYS G 130 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS G 130 " --> pdb=" O THR G 36 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU G 38 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N SER G 128 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR G 126 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU G 42 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA G 124 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU G 44 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR G 122 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TYR G 46 " --> pdb=" O SER G 120 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N SER G 120 " --> pdb=" O TYR G 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 140 through 147 removed outlier: 4.761A pdb=" N SER G 120 " --> pdb=" O TYR G 46 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TYR G 46 " --> pdb=" O SER G 120 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR G 122 " --> pdb=" O LEU G 44 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU G 44 " --> pdb=" O TYR G 122 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA G 124 " --> pdb=" O LEU G 42 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LEU G 42 " --> pdb=" O ALA G 124 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR G 126 " --> pdb=" O PRO G 40 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N SER G 128 " --> pdb=" O LEU G 38 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU G 38 " --> pdb=" O SER G 128 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS G 130 " --> pdb=" O THR G 36 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR G 36 " --> pdb=" O LYS G 130 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LYS G 132 " --> pdb=" O VAL G 34 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AA8, first strand: chain 'G' and resid 51 through 54 removed outlier: 4.007A pdb=" N ALA G 106 " --> pdb=" O GLN G 77 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=AB1, first strand: chain 'G' and resid 203 through 205 Processing sheet with id=AB2, first strand: chain 'G' and resid 220 through 221 Processing sheet with id=AB3, first strand: chain 'G' and resid 297 through 306 removed outlier: 5.321A pdb=" N ASP G 298 " --> pdb=" O LYS G 321 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LYS G 321 " --> pdb=" O ASP G 298 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL G 315 " --> pdb=" O ALA G 304 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 343 through 346 removed outlier: 3.892A pdb=" N ALA G 344 " --> pdb=" O CYS G 328 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS G 328 " --> pdb=" O ALA G 344 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 387 through 388 Processing sheet with id=AB6, first strand: chain 'H' and resid 2 through 8 Processing sheet with id=AB7, first strand: chain 'H' and resid 14 through 19 removed outlier: 5.390A pdb=" N MET H 31 " --> pdb=" O MET H 136 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N MET H 136 " --> pdb=" O MET H 31 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL H 33 " --> pdb=" O ARG H 134 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG H 134 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR H 41 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N THR H 126 " --> pdb=" O THR H 41 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASN H 43 " --> pdb=" O ALA H 124 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ALA H 124 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLU H 45 " --> pdb=" O TYR H 122 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N TYR H 122 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE H 47 " --> pdb=" O SER H 120 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N SER H 120 " --> pdb=" O ILE H 47 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 140 through 147 removed outlier: 6.671A pdb=" N SER H 120 " --> pdb=" O ILE H 47 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ILE H 47 " --> pdb=" O SER H 120 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N TYR H 122 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N GLU H 45 " --> pdb=" O TYR H 122 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ALA H 124 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASN H 43 " --> pdb=" O ALA H 124 " (cutoff:3.500A) removed outlier: 5.488A pdb=" N THR H 126 " --> pdb=" O THR H 41 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR H 41 " --> pdb=" O THR H 126 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG H 134 " --> pdb=" O VAL H 33 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N VAL H 33 " --> pdb=" O ARG H 134 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N MET H 136 " --> pdb=" O MET H 31 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N MET H 31 " --> pdb=" O MET H 136 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 51 through 54 Processing sheet with id=AC1, first strand: chain 'H' and resid 51 through 54 Processing sheet with id=AC2, first strand: chain 'H' and resid 203 through 205 Processing sheet with id=AC3, first strand: chain 'H' and resid 220 through 221 Processing sheet with id=AC4, first strand: chain 'H' and resid 296 through 306 removed outlier: 5.295A pdb=" N ASP H 298 " --> pdb=" O LYS H 321 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS H 321 " --> pdb=" O ASP H 298 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL H 315 " --> pdb=" O ALA H 304 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 343 through 346 Processing sheet with id=AC6, first strand: chain 'H' and resid 387 through 388 Processing sheet with id=AC7, first strand: chain 'I' and resid 2 through 8 Processing sheet with id=AC8, first strand: chain 'I' and resid 15 through 19 removed outlier: 5.225A pdb=" N MET I 31 " --> pdb=" O MET I 136 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N MET I 136 " --> pdb=" O MET I 31 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL I 33 " --> pdb=" O ARG I 134 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG I 134 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR I 41 " --> pdb=" O THR I 126 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N THR I 126 " --> pdb=" O THR I 41 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ASN I 43 " --> pdb=" O ALA I 124 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ALA I 124 " --> pdb=" O ASN I 43 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLU I 45 " --> pdb=" O TYR I 122 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N TYR I 122 " --> pdb=" O GLU I 45 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE I 47 " --> pdb=" O SER I 120 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER I 120 " --> pdb=" O ILE I 47 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 140 through 147 removed outlier: 6.682A pdb=" N SER I 120 " --> pdb=" O ILE I 47 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE I 47 " --> pdb=" O SER I 120 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N TYR I 122 " --> pdb=" O GLU I 45 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N GLU I 45 " --> pdb=" O TYR I 122 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N ALA I 124 " --> pdb=" O ASN I 43 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ASN I 43 " --> pdb=" O ALA I 124 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N THR I 126 " --> pdb=" O THR I 41 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR I 41 " --> pdb=" O THR I 126 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ARG I 134 " --> pdb=" O VAL I 33 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N VAL I 33 " --> pdb=" O ARG I 134 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N MET I 136 " --> pdb=" O MET I 31 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N MET I 31 " --> pdb=" O MET I 136 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 51 through 54 Processing sheet with id=AD2, first strand: chain 'I' and resid 51 through 54 removed outlier: 3.576A pdb=" N ALA I 106 " --> pdb=" O GLN I 77 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 203 through 204 Processing sheet with id=AD4, first strand: chain 'I' and resid 220 through 221 Processing sheet with id=AD5, first strand: chain 'I' and resid 297 through 306 removed outlier: 5.346A pdb=" N ASP I 298 " --> pdb=" O LYS I 321 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS I 321 " --> pdb=" O ASP I 298 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N VAL I 315 " --> pdb=" O ALA I 304 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 343 through 346 removed outlier: 3.673A pdb=" N ALA I 344 " --> pdb=" O CYS I 328 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS I 328 " --> pdb=" O ALA I 344 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 387 through 388 Processing sheet with id=AD8, first strand: chain 'J' and resid 17 through 19 Processing sheet with id=AD9, first strand: chain 'J' and resid 34 through 38 removed outlier: 6.741A pdb=" N GLN J 49 " --> pdb=" O GLU J 35 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL J 37 " --> pdb=" O LYS J 47 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LYS J 47 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 9.689A pdb=" N SER J 51 " --> pdb=" O ALA J 70 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ALA J 70 " --> pdb=" O SER J 51 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N LYS J 66 " --> pdb=" O GLY J 55 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 34 through 38 removed outlier: 6.741A pdb=" N GLN J 49 " --> pdb=" O GLU J 35 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N VAL J 37 " --> pdb=" O LYS J 47 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LYS J 47 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 10.968A pdb=" N ILE J 48 " --> pdb=" O LYS J 104 " (cutoff:3.500A) removed outlier: 10.931A pdb=" N LYS J 104 " --> pdb=" O ILE J 48 " (cutoff:3.500A) removed outlier: 11.677A pdb=" N PHE J 50 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 11.140A pdb=" N LEU J 102 " --> pdb=" O PHE J 50 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N ALA J 52 " --> pdb=" O PHE J 100 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N PHE J 100 " --> pdb=" O ALA J 52 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N ILE J 56 " --> pdb=" O THR J 96 " (cutoff:3.500A) removed outlier: 12.254A pdb=" N THR J 96 " --> pdb=" O ILE J 56 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'J' and resid 84 through 86 removed outlier: 4.069A pdb=" N GLU J 109 " --> pdb=" O TYR J 129 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'J' and resid 149 through 156 Processing sheet with id=AE4, first strand: chain 'J' and resid 236 through 237 Processing sheet with id=AE5, first strand: chain 'J' and resid 175 through 176 Processing sheet with id=AE6, first strand: chain 'J' and resid 181 through 182 Processing sheet with id=AE7, first strand: chain 'J' and resid 274 through 278 removed outlier: 3.740A pdb=" N GLU J 281 " --> pdb=" O GLY J 278 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'K' and resid 17 through 19 Processing sheet with id=AE9, first strand: chain 'K' and resid 34 through 38 removed outlier: 6.817A pdb=" N GLN K 49 " --> pdb=" O GLU K 35 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL K 37 " --> pdb=" O LYS K 47 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS K 47 " --> pdb=" O VAL K 37 " (cutoff:3.500A) removed outlier: 9.654A pdb=" N SER K 51 " --> pdb=" O ALA K 70 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ALA K 70 " --> pdb=" O SER K 51 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N LYS K 66 " --> pdb=" O GLY K 55 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'K' and resid 34 through 38 removed outlier: 6.817A pdb=" N GLN K 49 " --> pdb=" O GLU K 35 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N VAL K 37 " --> pdb=" O LYS K 47 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N LYS K 47 " --> pdb=" O VAL K 37 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N HIS K 99 " --> pdb=" O PHE K 50 " (cutoff:3.500A) removed outlier: 9.409A pdb=" N ALA K 52 " --> pdb=" O MET K 97 " (cutoff:3.500A) removed outlier: 8.211A pdb=" N MET K 97 " --> pdb=" O ALA K 52 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N ILE K 54 " --> pdb=" O GLY K 95 " (cutoff:3.500A) removed outlier: 10.864A pdb=" N GLY K 95 " --> pdb=" O ILE K 54 " (cutoff:3.500A) removed outlier: 15.472A pdb=" N ILE K 56 " --> pdb=" O VAL K 93 " (cutoff:3.500A) removed outlier: 18.207A pdb=" N VAL K 93 " --> pdb=" O ILE K 56 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'K' and resid 84 through 86 removed outlier: 4.033A pdb=" N GLU K 109 " --> pdb=" O TYR K 129 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'K' and resid 149 through 156 Processing sheet with id=AF4, first strand: chain 'K' and resid 166 through 167 Processing sheet with id=AF5, first strand: chain 'K' and resid 169 through 170 Processing sheet with id=AF6, first strand: chain 'K' and resid 175 through 176 Processing sheet with id=AF7, first strand: chain 'K' and resid 181 through 183 removed outlier: 3.644A pdb=" N MET K 215 " --> pdb=" O ILE K 190 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 274 through 278 Processing sheet with id=AF9, first strand: chain 'L' and resid 17 through 19 Processing sheet with id=AG1, first strand: chain 'L' and resid 34 through 38 removed outlier: 8.513A pdb=" N ILE L 34 " --> pdb=" O SER L 51 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER L 51 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA L 36 " --> pdb=" O GLN L 49 " (cutoff:3.500A) removed outlier: 9.653A pdb=" N SER L 51 " --> pdb=" O ALA L 70 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N ALA L 70 " --> pdb=" O SER L 51 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS L 66 " --> pdb=" O GLY L 55 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'L' and resid 34 through 38 removed outlier: 8.513A pdb=" N ILE L 34 " --> pdb=" O SER L 51 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER L 51 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALA L 36 " --> pdb=" O GLN L 49 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N HIS L 99 " --> pdb=" O PHE L 50 " (cutoff:3.500A) removed outlier: 9.196A pdb=" N ALA L 52 " --> pdb=" O MET L 97 " (cutoff:3.500A) removed outlier: 8.215A pdb=" N MET L 97 " --> pdb=" O ALA L 52 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N ILE L 54 " --> pdb=" O GLY L 95 " (cutoff:3.500A) removed outlier: 10.699A pdb=" N GLY L 95 " --> pdb=" O ILE L 54 " (cutoff:3.500A) removed outlier: 15.747A pdb=" N ILE L 56 " --> pdb=" O VAL L 93 " (cutoff:3.500A) removed outlier: 18.572A pdb=" N VAL L 93 " --> pdb=" O ILE L 56 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 84 through 86 removed outlier: 4.129A pdb=" N GLU L 109 " --> pdb=" O TYR L 129 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'L' and resid 149 through 156 Processing sheet with id=AG5, first strand: chain 'L' and resid 166 through 167 Processing sheet with id=AG6, first strand: chain 'L' and resid 169 through 170 Processing sheet with id=AG7, first strand: chain 'L' and resid 175 through 176 Processing sheet with id=AG8, first strand: chain 'L' and resid 181 through 184 Processing sheet with id=AG9, first strand: chain 'L' and resid 274 through 278 removed outlier: 3.653A pdb=" N GLU L 281 " --> pdb=" O GLY L 278 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'M' and resid 149 through 150 removed outlier: 3.853A pdb=" N VAL M 123 " --> pdb=" O GLY M 131 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N GLY M 131 " --> pdb=" O VAL M 123 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N TYR M 132 " --> pdb=" O PRO M 143 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS M 170 " --> pdb=" O LYS M 161 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'M' and resid 256 through 257 removed outlier: 4.766A pdb=" N PHE M 207 " --> pdb=" O LEU M 246 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N ALA M 199 " --> pdb=" O PRO M 210 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ILE M 223 " --> pdb=" O VAL M 231 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'M' and resid 256 through 257 removed outlier: 6.250A pdb=" N VAL M 249 " --> pdb=" O VAL M 234 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N VAL M 234 " --> pdb=" O VAL M 249 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N TRP M 251 " --> pdb=" O ALA M 232 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ALA M 232 " --> pdb=" O TRP M 251 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'N' and resid 149 through 150 removed outlier: 3.734A pdb=" N VAL N 123 " --> pdb=" O GLY N 131 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N GLY N 131 " --> pdb=" O VAL N 123 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N HIS N 125 " --> pdb=" O VAL N 129 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N VAL N 129 " --> pdb=" O HIS N 125 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N TYR N 132 " --> pdb=" O PRO N 143 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'N' and resid 256 through 259 removed outlier: 5.057A pdb=" N PHE N 207 " --> pdb=" O LEU N 246 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN N 201 " --> pdb=" O THR N 208 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N ALA N 199 " --> pdb=" O PRO N 210 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY N 191 " --> pdb=" O TYR N 202 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N ILE N 223 " --> pdb=" O VAL N 231 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'N' and resid 256 through 259 removed outlier: 5.362A pdb=" N VAL N 249 " --> pdb=" O VAL N 234 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N VAL N 234 " --> pdb=" O VAL N 249 " (cutoff:3.500A) removed outlier: 8.084A pdb=" N TRP N 251 " --> pdb=" O ALA N 232 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ALA N 232 " --> pdb=" O TRP N 251 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'O' and resid 149 through 150 removed outlier: 3.658A pdb=" N PHE O 121 " --> pdb=" O ALA O 133 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N TYR O 132 " --> pdb=" O PRO O 143 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET O 141 " --> pdb=" O CYS O 134 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'O' and resid 256 through 259 removed outlier: 4.779A pdb=" N PHE O 207 " --> pdb=" O LEU O 246 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR O 208 " --> pdb=" O GLN O 201 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ALA O 199 " --> pdb=" O PRO O 210 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TYR O 202 " --> pdb=" O GLY O 191 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLY O 191 " --> pdb=" O TYR O 202 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA O 232 " --> pdb=" O ILE O 223 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'O' and resid 256 through 259 removed outlier: 5.760A pdb=" N VAL O 249 " --> pdb=" O VAL O 234 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N VAL O 234 " --> pdb=" O VAL O 249 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N TRP O 251 " --> pdb=" O ALA O 232 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ALA O 232 " --> pdb=" O TRP O 251 " (cutoff:3.500A) 998 hydrogen bonds defined for protein. 2598 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: 5.79 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8174 1.34 - 1.47: 6245 1.47 - 1.59: 11230 1.59 - 1.71: 1 1.71 - 1.83: 273 Bond restraints: 25923 Sorted by residual: bond pdb=" N PRO J 248 " pdb=" CD PRO J 248 " ideal model delta sigma weight residual 1.473 1.643 -0.170 1.40e-02 5.10e+03 1.48e+02 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.46e+01 bond pdb=" C1 NAG Q 3 " pdb=" O5 NAG Q 3 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.89e+00 bond pdb=" C1 NAG p 4 " pdb=" O5 NAG p 4 " ideal model delta sigma weight residual 1.406 1.439 -0.033 2.00e-02 2.50e+03 2.69e+00 bond pdb=" C1 NAG P 3 " pdb=" O5 NAG P 3 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.54e+00 ... (remaining 25918 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.69: 35031 2.69 - 5.37: 250 5.37 - 8.06: 19 8.06 - 10.74: 0 10.74 - 13.43: 1 Bond angle restraints: 35301 Sorted by residual: angle pdb=" N SER K 88 " pdb=" CA SER K 88 " pdb=" C SER K 88 " ideal model delta sigma weight residual 114.56 107.46 7.10 1.27e+00 6.20e-01 3.12e+01 angle pdb=" CA SER K 88 " pdb=" C SER K 88 " pdb=" N GLY K 89 " ideal model delta sigma weight residual 119.26 115.31 3.95 1.14e+00 7.69e-01 1.20e+01 angle pdb=" N PRO J 248 " pdb=" CD PRO J 248 " pdb=" CG PRO J 248 " ideal model delta sigma weight residual 103.20 98.09 5.11 1.50e+00 4.44e-01 1.16e+01 angle pdb=" CA CYS I 78 " pdb=" CB CYS I 78 " pdb=" SG CYS I 78 " ideal model delta sigma weight residual 114.40 122.21 -7.81 2.30e+00 1.89e-01 1.15e+01 angle pdb=" C GLU J 247 " pdb=" N PRO J 248 " pdb=" CD PRO J 248 " ideal model delta sigma weight residual 125.00 111.57 13.43 4.10e+00 5.95e-02 1.07e+01 ... (remaining 35296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.47: 15135 23.47 - 46.94: 695 46.94 - 70.41: 97 70.41 - 93.88: 50 93.88 - 117.35: 43 Dihedral angle restraints: 16020 sinusoidal: 6678 harmonic: 9342 Sorted by residual: dihedral pdb=" CB CYS H 328 " pdb=" SG CYS H 328 " pdb=" SG CYS H 370 " pdb=" CB CYS H 370 " ideal model delta sinusoidal sigma weight residual -86.00 -34.76 -51.24 1 1.00e+01 1.00e-02 3.59e+01 dihedral pdb=" CA CYS G 328 " pdb=" C CYS G 328 " pdb=" N SER G 329 " pdb=" CA SER G 329 " ideal model delta harmonic sigma weight residual -180.00 -152.08 -27.92 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA CYS I 328 " pdb=" C CYS I 328 " pdb=" N SER I 329 " pdb=" CA SER I 329 " ideal model delta harmonic sigma weight residual 180.00 -153.48 -26.52 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 16017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 3331 0.055 - 0.109: 580 0.109 - 0.164: 103 0.164 - 0.219: 5 0.219 - 0.273: 4 Chirality restraints: 4023 Sorted by residual: chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 4020 not shown) Planarity restraints: 4527 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU J 247 " -0.100 5.00e-02 4.00e+02 1.52e-01 3.67e+01 pdb=" N PRO J 248 " 0.262 5.00e-02 4.00e+02 pdb=" CA PRO J 248 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO J 248 " -0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS O 215 " 0.035 5.00e-02 4.00e+02 5.39e-02 4.65e+00 pdb=" N PRO O 216 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO O 216 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO O 216 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 50 " 0.011 2.00e-02 2.50e+03 1.62e-02 4.61e+00 pdb=" CG PHE L 50 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE L 50 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE L 50 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE L 50 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE L 50 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE L 50 " -0.000 2.00e-02 2.50e+03 ... (remaining 4524 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.32: 29 2.32 - 2.97: 11853 2.97 - 3.61: 36622 3.61 - 4.26: 61382 4.26 - 4.90: 100609 Nonbonded interactions: 210495 Sorted by model distance: nonbonded pdb=" NE2 HIS L 421 " pdb=" NE2 GLN O 172 " model vdw 1.680 3.200 nonbonded pdb=" CE1 HIS L 421 " pdb=" NE2 GLN O 172 " model vdw 2.050 3.340 nonbonded pdb=" OE1 GLU L 40 " pdb=" OH TYR L 156 " model vdw 2.164 3.040 nonbonded pdb=" OG SER G 57 " pdb=" O VAL J 242 " model vdw 2.184 3.040 nonbonded pdb=" OG1 THR H 300 " pdb=" OG1 THR H 319 " model vdw 2.184 3.040 ... (remaining 210490 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' and resid 1 through 2) selection = (chain 'B' and resid 1 through 2) selection = (chain 'C' and resid 1 through 2) selection = (chain 'd' and resid 1 through 2) selection = (chain 'j' and resid 1 through 2) selection = (chain 'p' and resid 1 through 2) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' } ncs_group { reference = chain 'P' selection = chain 'Q' 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.610 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 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 : 0.004 0.170 26003 Z= 0.174 Angle : 0.564 13.428 35492 Z= 0.278 Chirality : 0.044 0.273 4023 Planarity : 0.004 0.152 4518 Dihedral : 15.320 117.353 9894 Min Nonbonded Distance : 1.680 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.15), residues: 3201 helix: 0.46 (0.26), residues: 414 sheet: 0.11 (0.16), residues: 987 loop : -0.31 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 373 TYR 0.015 0.001 TYR G 122 PHE 0.034 0.001 PHE L 50 TRP 0.027 0.001 TRP O 195 HIS 0.017 0.001 HIS H 230 Details of bonding type rmsd covalent geometry : bond 0.00354 (25923) covalent geometry : angle 0.55529 (35301) SS BOND : bond 0.00233 ( 46) SS BOND : angle 1.34261 ( 92) hydrogen bonds : bond 0.21804 ( 948) hydrogen bonds : angle 8.38195 ( 2598) Misc. bond : bond 0.03249 ( 1) link_ALPHA1-6 : bond 0.00351 ( 3) link_ALPHA1-6 : angle 1.63090 ( 9) link_BETA1-4 : bond 0.00575 ( 18) link_BETA1-4 : angle 1.44223 ( 54) link_BETA1-6 : bond 0.00836 ( 3) link_BETA1-6 : angle 1.99088 ( 9) link_NAG-ASN : bond 0.00267 ( 9) link_NAG-ASN : angle 1.71068 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 405 time to evaluate : 0.995 Fit side-chains revert: symmetry clash REVERT: M 122 GLU cc_start: 0.6403 (tp30) cc_final: 0.6125 (tm-30) REVERT: M 169 GLU cc_start: 0.7759 (pt0) cc_final: 0.7471 (pt0) REVERT: N 121 PHE cc_start: 0.8263 (m-80) cc_final: 0.7817 (m-80) REVERT: N 194 ASN cc_start: 0.7979 (m110) cc_final: 0.7407 (m110) REVERT: N 240 GLU cc_start: 0.2933 (tm-30) cc_final: 0.2634 (tm-30) REVERT: O 116 GLU cc_start: 0.6592 (tt0) cc_final: 0.5975 (tm-30) REVERT: O 162 LYS cc_start: 0.7939 (tmtt) cc_final: 0.7685 (tmtt) outliers start: 0 outliers final: 0 residues processed: 405 average time/residue: 0.6261 time to fit residues: 291.5138 Evaluate side-chains 343 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 0.0270 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 0.0170 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 9.9990 overall best weight: 2.2082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 281 ASN I 3 HIS I 235 GLN I 281 ASN J 158 GLN J 170 HIS J 212 ASN J 224 GLN K 255 HIS L 218 ASN L 356 GLN N 145 HIS O 252 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.155354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.094539 restraints weight = 28255.533| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 2.08 r_work: 0.2709 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 26003 Z= 0.153 Angle : 0.591 9.418 35492 Z= 0.302 Chirality : 0.046 0.275 4023 Planarity : 0.004 0.071 4518 Dihedral : 11.047 104.090 4167 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.61 % Allowed : 8.39 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3201 helix: 0.92 (0.24), residues: 441 sheet: 0.03 (0.16), residues: 981 loop : -0.38 (0.14), residues: 1779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 206 TYR 0.013 0.002 TYR G 122 PHE 0.029 0.002 PHE J 50 TRP 0.014 0.001 TRP O 195 HIS 0.012 0.001 HIS H 230 Details of bonding type rmsd covalent geometry : bond 0.00340 (25923) covalent geometry : angle 0.58277 (35301) SS BOND : bond 0.00293 ( 46) SS BOND : angle 1.10784 ( 92) hydrogen bonds : bond 0.04497 ( 948) hydrogen bonds : angle 6.23371 ( 2598) Misc. bond : bond 0.00043 ( 1) link_ALPHA1-6 : bond 0.00346 ( 3) link_ALPHA1-6 : angle 1.79143 ( 9) link_BETA1-4 : bond 0.00552 ( 18) link_BETA1-4 : angle 1.86545 ( 54) link_BETA1-6 : bond 0.00908 ( 3) link_BETA1-6 : angle 1.86710 ( 9) link_NAG-ASN : bond 0.00242 ( 9) link_NAG-ASN : angle 1.57574 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 407 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 363 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 38 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6988 (ttp) REVERT: G 2 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7461 (mm-30) REVERT: G 281 ASN cc_start: 0.9058 (OUTLIER) cc_final: 0.8519 (t0) REVERT: G 302 THR cc_start: 0.9130 (m) cc_final: 0.8815 (p) REVERT: G 321 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8426 (mtpp) REVERT: I 260 GLN cc_start: 0.9252 (OUTLIER) cc_final: 0.8852 (mt0) REVERT: I 280 MET cc_start: 0.9472 (ptp) cc_final: 0.9113 (ptp) REVERT: K 158 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.7559 (mp10) REVERT: L 119 ARG cc_start: 0.8606 (mtm-85) cc_final: 0.8255 (mtm180) REVERT: L 134 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.7969 (mp10) REVERT: L 171 MET cc_start: 0.8705 (tpp) cc_final: 0.8487 (tpp) REVERT: M 122 GLU cc_start: 0.6526 (tp30) cc_final: 0.6234 (tm-30) REVERT: M 166 TYR cc_start: 0.8089 (m-80) cc_final: 0.7776 (m-80) REVERT: M 169 GLU cc_start: 0.7696 (pt0) cc_final: 0.7399 (pt0) REVERT: N 121 PHE cc_start: 0.8382 (m-80) cc_final: 0.7750 (m-80) REVERT: N 194 ASN cc_start: 0.7991 (m110) cc_final: 0.7368 (m110) REVERT: N 224 PHE cc_start: 0.8263 (m-80) cc_final: 0.8005 (m-80) REVERT: O 121 PHE cc_start: 0.8507 (m-10) cc_final: 0.8280 (m-10) REVERT: O 162 LYS cc_start: 0.7972 (tmtt) cc_final: 0.7750 (tmtt) REVERT: O 169 GLU cc_start: 0.6055 (tm-30) cc_final: 0.5804 (tm-30) REVERT: O 190 GLU cc_start: 0.7122 (tp30) cc_final: 0.6863 (tp30) REVERT: O 192 HIS cc_start: 0.7248 (t70) cc_final: 0.6976 (t-90) outliers start: 44 outliers final: 15 residues processed: 373 average time/residue: 0.5534 time to fit residues: 241.0869 Evaluate side-chains 360 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 338 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 MET Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 281 ASN Chi-restraints excluded: chain G residue 300 THR Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 194 SER Chi-restraints excluded: chain I residue 260 GLN Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain J residue 323 ASP Chi-restraints excluded: chain J residue 381 ILE Chi-restraints excluded: chain K residue 158 GLN Chi-restraints excluded: chain K residue 323 ASP Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 134 GLN Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 367 VAL Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain O residue 208 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 131 optimal weight: 7.9990 chunk 317 optimal weight: 9.9990 chunk 129 optimal weight: 0.0670 chunk 74 optimal weight: 1.9990 chunk 5 optimal weight: 50.0000 chunk 81 optimal weight: 3.9990 chunk 262 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 160 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 overall best weight: 1.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 264 ASN H 32 GLN H 142 GLN ** J 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 212 ASN J 232 HIS L 356 GLN O 252 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.155669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.094955 restraints weight = 28328.200| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.07 r_work: 0.2717 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26003 Z= 0.131 Angle : 0.562 9.510 35492 Z= 0.282 Chirality : 0.045 0.265 4023 Planarity : 0.004 0.055 4518 Dihedral : 8.897 99.614 4167 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 1.76 % Allowed : 10.55 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.14), residues: 3201 helix: 1.24 (0.24), residues: 441 sheet: 0.07 (0.16), residues: 960 loop : -0.41 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 206 TYR 0.012 0.001 TYR G 122 PHE 0.025 0.001 PHE J 50 TRP 0.011 0.001 TRP O 195 HIS 0.009 0.001 HIS H 230 Details of bonding type rmsd covalent geometry : bond 0.00292 (25923) covalent geometry : angle 0.55311 (35301) SS BOND : bond 0.00253 ( 46) SS BOND : angle 0.99230 ( 92) hydrogen bonds : bond 0.03754 ( 948) hydrogen bonds : angle 5.75002 ( 2598) Misc. bond : bond 0.00052 ( 1) link_ALPHA1-6 : bond 0.00320 ( 3) link_ALPHA1-6 : angle 1.63603 ( 9) link_BETA1-4 : bond 0.00570 ( 18) link_BETA1-4 : angle 1.87584 ( 54) link_BETA1-6 : bond 0.00853 ( 3) link_BETA1-6 : angle 1.98279 ( 9) link_NAG-ASN : bond 0.00124 ( 9) link_NAG-ASN : angle 1.48154 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 350 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 145 ASP cc_start: 0.8932 (m-30) cc_final: 0.8591 (m-30) REVERT: G 302 THR cc_start: 0.9165 (m) cc_final: 0.8849 (p) REVERT: G 321 LYS cc_start: 0.8871 (OUTLIER) cc_final: 0.8440 (mtpp) REVERT: I 182 ASP cc_start: 0.8963 (m-30) cc_final: 0.8759 (m-30) REVERT: I 245 LYS cc_start: 0.8701 (OUTLIER) cc_final: 0.8464 (mtmt) REVERT: J 212 ASN cc_start: 0.8570 (t0) cc_final: 0.8174 (t0) REVERT: J 409 TRP cc_start: 0.6739 (t60) cc_final: 0.6308 (t-100) REVERT: J 411 LEU cc_start: 0.8049 (mm) cc_final: 0.7657 (tt) REVERT: K 157 GLN cc_start: 0.8466 (mm110) cc_final: 0.8195 (tp40) REVERT: K 158 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7477 (mp10) REVERT: L 90 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8606 (m-30) REVERT: L 119 ARG cc_start: 0.8544 (mtm-85) cc_final: 0.8196 (mtm180) REVERT: L 134 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.8022 (mp10) REVERT: L 171 MET cc_start: 0.8633 (tpp) cc_final: 0.8426 (tpp) REVERT: L 359 TYR cc_start: 0.9196 (t80) cc_final: 0.8970 (t80) REVERT: M 116 GLU cc_start: 0.7049 (pt0) cc_final: 0.6007 (tm-30) REVERT: M 122 GLU cc_start: 0.6571 (tp30) cc_final: 0.6321 (tm-30) REVERT: M 166 TYR cc_start: 0.8182 (m-80) cc_final: 0.7613 (m-80) REVERT: M 187 GLU cc_start: 0.7931 (pm20) cc_final: 0.7605 (pm20) REVERT: N 111 MET cc_start: 0.6470 (tmm) cc_final: 0.6143 (pp-130) REVERT: N 121 PHE cc_start: 0.8405 (m-80) cc_final: 0.7721 (m-80) REVERT: N 194 ASN cc_start: 0.7986 (m110) cc_final: 0.7331 (m110) REVERT: O 121 PHE cc_start: 0.8570 (m-10) cc_final: 0.8303 (m-80) REVERT: O 162 LYS cc_start: 0.8032 (tmtt) cc_final: 0.7819 (tmtt) REVERT: O 192 HIS cc_start: 0.7181 (t70) cc_final: 0.6908 (t-90) outliers start: 48 outliers final: 19 residues processed: 368 average time/residue: 0.5677 time to fit residues: 244.3242 Evaluate side-chains 358 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 334 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain H residue 297 ILE Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 194 SER Chi-restraints excluded: chain I residue 245 LYS Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain J residue 323 ASP Chi-restraints excluded: chain K residue 158 GLN Chi-restraints excluded: chain K residue 323 ASP Chi-restraints excluded: chain K residue 393 SER Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 134 GLN Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 367 VAL Chi-restraints excluded: chain L residue 389 VAL Chi-restraints excluded: chain N residue 229 ARG Chi-restraints excluded: chain O residue 208 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 94 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 219 optimal weight: 3.9990 chunk 135 optimal weight: 9.9990 chunk 59 optimal weight: 1.9990 chunk 221 optimal weight: 2.9990 chunk 293 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 311 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 chunk 232 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 142 GLN ** J 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 232 HIS O 252 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.154788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.093493 restraints weight = 28301.559| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.07 r_work: 0.2698 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 26003 Z= 0.160 Angle : 0.567 9.676 35492 Z= 0.285 Chirality : 0.045 0.285 4023 Planarity : 0.004 0.055 4518 Dihedral : 7.536 94.543 4167 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.34 % Allowed : 11.76 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.14), residues: 3201 helix: 1.46 (0.24), residues: 441 sheet: 0.09 (0.16), residues: 963 loop : -0.42 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 206 TYR 0.013 0.002 TYR J 327 PHE 0.026 0.002 PHE K 50 TRP 0.009 0.001 TRP O 195 HIS 0.008 0.001 HIS I 308 Details of bonding type rmsd covalent geometry : bond 0.00365 (25923) covalent geometry : angle 0.55772 (35301) SS BOND : bond 0.00308 ( 46) SS BOND : angle 1.07933 ( 92) hydrogen bonds : bond 0.03519 ( 948) hydrogen bonds : angle 5.55123 ( 2598) Misc. bond : bond 0.00003 ( 1) link_ALPHA1-6 : bond 0.00257 ( 3) link_ALPHA1-6 : angle 1.67353 ( 9) link_BETA1-4 : bond 0.00606 ( 18) link_BETA1-4 : angle 1.91813 ( 54) link_BETA1-6 : bond 0.00789 ( 3) link_BETA1-6 : angle 2.10218 ( 9) link_NAG-ASN : bond 0.00145 ( 9) link_NAG-ASN : angle 1.52563 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 357 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 2 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7525 (mm-30) REVERT: G 145 ASP cc_start: 0.8969 (m-30) cc_final: 0.8610 (m-30) REVERT: G 289 ARG cc_start: 0.7943 (OUTLIER) cc_final: 0.6867 (mmm160) REVERT: G 302 THR cc_start: 0.9179 (m) cc_final: 0.8857 (p) REVERT: G 321 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8440 (mtpp) REVERT: I 182 ASP cc_start: 0.8966 (m-30) cc_final: 0.8737 (m-30) REVERT: I 245 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8481 (mtmt) REVERT: J 212 ASN cc_start: 0.8642 (t0) cc_final: 0.8371 (t0) REVERT: J 409 TRP cc_start: 0.6742 (t60) cc_final: 0.6306 (t-100) REVERT: J 411 LEU cc_start: 0.8035 (mm) cc_final: 0.7643 (tt) REVERT: K 157 GLN cc_start: 0.8488 (mm110) cc_final: 0.8271 (tp40) REVERT: K 158 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.7423 (mp10) REVERT: L 134 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.7894 (mp10) REVERT: M 111 MET cc_start: 0.6031 (OUTLIER) cc_final: 0.5748 (ppp) REVERT: M 116 GLU cc_start: 0.7040 (pt0) cc_final: 0.5979 (tm-30) REVERT: M 122 GLU cc_start: 0.6568 (tp30) cc_final: 0.6347 (tm-30) REVERT: M 166 TYR cc_start: 0.8271 (m-80) cc_final: 0.7744 (m-80) REVERT: N 111 MET cc_start: 0.6283 (tmm) cc_final: 0.5960 (pp-130) REVERT: N 121 PHE cc_start: 0.8458 (m-80) cc_final: 0.7719 (m-80) REVERT: N 194 ASN cc_start: 0.8000 (m110) cc_final: 0.7370 (m110) REVERT: O 121 PHE cc_start: 0.8644 (m-10) cc_final: 0.8430 (m-80) REVERT: O 162 LYS cc_start: 0.8063 (tmtt) cc_final: 0.7847 (tmtt) REVERT: O 192 HIS cc_start: 0.7303 (t70) cc_final: 0.7011 (t-90) outliers start: 64 outliers final: 30 residues processed: 380 average time/residue: 0.5898 time to fit residues: 261.5945 Evaluate side-chains 375 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 338 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 377 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 155 THR Chi-restraints excluded: chain I residue 194 SER Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 245 LYS Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain K residue 158 GLN Chi-restraints excluded: chain K residue 346 LYS Chi-restraints excluded: chain K residue 367 VAL Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 97 MET Chi-restraints excluded: chain L residue 134 GLN Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 367 VAL Chi-restraints excluded: chain L residue 389 VAL Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 229 ARG Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 208 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 184 optimal weight: 10.0000 chunk 243 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 257 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 132 optimal weight: 10.0000 chunk 196 optimal weight: 0.7980 chunk 277 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 264 ASN H 142 GLN J 170 HIS L 212 ASN O 252 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.156117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.095268 restraints weight = 28233.530| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.09 r_work: 0.2723 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 26003 Z= 0.117 Angle : 0.546 10.065 35492 Z= 0.274 Chirality : 0.044 0.271 4023 Planarity : 0.004 0.055 4518 Dihedral : 7.031 91.174 4167 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.76 % Allowed : 13.63 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.15), residues: 3201 helix: 1.62 (0.25), residues: 438 sheet: 0.13 (0.16), residues: 960 loop : -0.38 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 206 TYR 0.011 0.001 TYR J 64 PHE 0.016 0.001 PHE J 50 TRP 0.008 0.001 TRP O 195 HIS 0.007 0.001 HIS I 308 Details of bonding type rmsd covalent geometry : bond 0.00261 (25923) covalent geometry : angle 0.53671 (35301) SS BOND : bond 0.00252 ( 46) SS BOND : angle 1.18951 ( 92) hydrogen bonds : bond 0.03201 ( 948) hydrogen bonds : angle 5.37615 ( 2598) Misc. bond : bond 0.00001 ( 1) link_ALPHA1-6 : bond 0.00342 ( 3) link_ALPHA1-6 : angle 1.57965 ( 9) link_BETA1-4 : bond 0.00590 ( 18) link_BETA1-4 : angle 1.78407 ( 54) link_BETA1-6 : bond 0.00693 ( 3) link_BETA1-6 : angle 2.13060 ( 9) link_NAG-ASN : bond 0.00107 ( 9) link_NAG-ASN : angle 1.45400 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 347 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 2 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7535 (mm-30) REVERT: G 145 ASP cc_start: 0.8916 (m-30) cc_final: 0.8571 (m-30) REVERT: G 302 THR cc_start: 0.9158 (m) cc_final: 0.8880 (p) REVERT: G 321 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8430 (mtpp) REVERT: H 136 MET cc_start: 0.9303 (mtm) cc_final: 0.9083 (mtp) REVERT: H 269 MET cc_start: 0.9047 (mmm) cc_final: 0.8845 (mmm) REVERT: H 289 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7318 (mtp180) REVERT: I 182 ASP cc_start: 0.8968 (m-30) cc_final: 0.8765 (m-30) REVERT: I 245 LYS cc_start: 0.8680 (OUTLIER) cc_final: 0.8449 (mtmt) REVERT: J 212 ASN cc_start: 0.8601 (t0) cc_final: 0.8336 (t0) REVERT: J 222 ILE cc_start: 0.7977 (pt) cc_final: 0.7714 (pp) REVERT: J 409 TRP cc_start: 0.6728 (t60) cc_final: 0.6297 (t-100) REVERT: J 411 LEU cc_start: 0.8016 (mm) cc_final: 0.7623 (tt) REVERT: L 90 ASP cc_start: 0.8851 (OUTLIER) cc_final: 0.8593 (m-30) REVERT: L 359 TYR cc_start: 0.9036 (t80) cc_final: 0.8810 (t80) REVERT: M 111 MET cc_start: 0.6037 (OUTLIER) cc_final: 0.5753 (ppp) REVERT: M 116 GLU cc_start: 0.7015 (pt0) cc_final: 0.5991 (tm-30) REVERT: M 166 TYR cc_start: 0.8328 (m-80) cc_final: 0.7861 (m-80) REVERT: N 111 MET cc_start: 0.6176 (tmm) cc_final: 0.5935 (pp-130) REVERT: N 121 PHE cc_start: 0.8479 (m-80) cc_final: 0.7786 (m-80) REVERT: N 194 ASN cc_start: 0.8033 (m110) cc_final: 0.7409 (m110) REVERT: O 162 LYS cc_start: 0.8089 (tmtt) cc_final: 0.7832 (tmtt) REVERT: O 169 GLU cc_start: 0.5939 (tm-30) cc_final: 0.5657 (tm-30) REVERT: O 190 GLU cc_start: 0.7133 (tp30) cc_final: 0.6911 (tp30) REVERT: O 192 HIS cc_start: 0.7359 (t70) cc_final: 0.7074 (t-90) REVERT: O 265 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7064 (tm-30) REVERT: O 266 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6781 (tm-30) outliers start: 48 outliers final: 22 residues processed: 368 average time/residue: 0.6164 time to fit residues: 264.1615 Evaluate side-chains 361 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 333 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 370 CYS Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 194 SER Chi-restraints excluded: chain I residue 245 LYS Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain K residue 323 ASP Chi-restraints excluded: chain K residue 346 LYS Chi-restraints excluded: chain K residue 393 SER Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 90 ASP Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 367 VAL Chi-restraints excluded: chain L residue 389 VAL Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 229 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 284 optimal weight: 9.9990 chunk 29 optimal weight: 9.9990 chunk 64 optimal weight: 30.0000 chunk 316 optimal weight: 9.9990 chunk 260 optimal weight: 10.0000 chunk 182 optimal weight: 5.9990 chunk 139 optimal weight: 8.9990 chunk 47 optimal weight: 0.0010 chunk 28 optimal weight: 5.9990 chunk 250 optimal weight: 20.0000 chunk 186 optimal weight: 10.0000 overall best weight: 6.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 264 ASN H 3 HIS ** J 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 224 GLN L 94 HIS L 134 GLN O 252 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.152529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.090855 restraints weight = 28250.617| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.03 r_work: 0.2644 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2511 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 26003 Z= 0.308 Angle : 0.663 10.553 35492 Z= 0.336 Chirality : 0.049 0.322 4023 Planarity : 0.005 0.053 4518 Dihedral : 7.359 85.577 4167 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.67 % Allowed : 13.41 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.14), residues: 3201 helix: 1.49 (0.25), residues: 438 sheet: 0.06 (0.16), residues: 963 loop : -0.48 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 199 TYR 0.018 0.002 TYR J 327 PHE 0.032 0.003 PHE J 50 TRP 0.010 0.002 TRP J 309 HIS 0.013 0.002 HIS I 308 Details of bonding type rmsd covalent geometry : bond 0.00723 (25923) covalent geometry : angle 0.65077 (35301) SS BOND : bond 0.00522 ( 46) SS BOND : angle 1.67596 ( 92) hydrogen bonds : bond 0.03961 ( 948) hydrogen bonds : angle 5.67086 ( 2598) Misc. bond : bond 0.00037 ( 1) link_ALPHA1-6 : bond 0.00184 ( 3) link_ALPHA1-6 : angle 1.83928 ( 9) link_BETA1-4 : bond 0.00636 ( 18) link_BETA1-4 : angle 2.12605 ( 54) link_BETA1-6 : bond 0.00712 ( 3) link_BETA1-6 : angle 2.24819 ( 9) link_NAG-ASN : bond 0.00315 ( 9) link_NAG-ASN : angle 1.81165 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 320 time to evaluate : 1.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 2 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7543 (mm-30) REVERT: G 145 ASP cc_start: 0.8972 (m-30) cc_final: 0.8610 (m-30) REVERT: G 289 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.6784 (mmm160) REVERT: G 302 THR cc_start: 0.9147 (m) cc_final: 0.8742 (p) REVERT: G 321 LYS cc_start: 0.8796 (OUTLIER) cc_final: 0.8359 (mtpp) REVERT: H 289 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7312 (mtp180) REVERT: H 321 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8356 (mtpp) REVERT: I 155 THR cc_start: 0.9231 (m) cc_final: 0.8877 (p) REVERT: I 182 ASP cc_start: 0.8988 (m-30) cc_final: 0.8786 (m-30) REVERT: I 245 LYS cc_start: 0.8725 (mtmp) cc_final: 0.8514 (mtmt) REVERT: J 189 LYS cc_start: 0.7996 (OUTLIER) cc_final: 0.7732 (tttm) REVERT: J 411 LEU cc_start: 0.8064 (mm) cc_final: 0.7651 (tt) REVERT: K 158 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.7435 (mp10) REVERT: K 192 VAL cc_start: 0.8340 (t) cc_final: 0.8102 (t) REVERT: K 302 ASP cc_start: 0.8663 (t0) cc_final: 0.8371 (t70) REVERT: M 111 MET cc_start: 0.5763 (OUTLIER) cc_final: 0.5439 (ppp) REVERT: N 121 PHE cc_start: 0.8450 (m-80) cc_final: 0.7700 (m-80) REVERT: N 194 ASN cc_start: 0.8124 (m110) cc_final: 0.7506 (m110) REVERT: O 162 LYS cc_start: 0.7964 (tmtt) cc_final: 0.7755 (tmtt) REVERT: O 192 HIS cc_start: 0.7283 (t70) cc_final: 0.7006 (t-170) outliers start: 73 outliers final: 44 residues processed: 358 average time/residue: 0.5821 time to fit residues: 245.4358 Evaluate side-chains 364 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 312 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 MET Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 70 THR Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 377 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain H residue 297 ILE Chi-restraints excluded: chain H residue 321 LYS Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain H residue 377 SER Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 75 ASP Chi-restraints excluded: chain I residue 101 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 194 SER Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 346 VAL Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 370 CYS Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 158 GLN Chi-restraints excluded: chain K residue 171 MET Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 323 ASP Chi-restraints excluded: chain K residue 346 LYS Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 208 VAL Chi-restraints excluded: chain L residue 367 VAL Chi-restraints excluded: chain L residue 389 VAL Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 169 GLU Chi-restraints excluded: chain N residue 229 ARG Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 175 VAL Chi-restraints excluded: chain O residue 208 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 228 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 188 optimal weight: 6.9990 chunk 284 optimal weight: 0.0870 chunk 37 optimal weight: 5.9990 chunk 226 optimal weight: 0.0870 chunk 230 optimal weight: 0.7980 chunk 261 optimal weight: 0.8980 chunk 307 optimal weight: 7.9990 chunk 165 optimal weight: 10.0000 chunk 315 optimal weight: 30.0000 overall best weight: 1.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 264 ASN H 142 GLN J 170 HIS J 207 ASN J 218 ASN ** J 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 212 ASN L 94 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.154919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.093108 restraints weight = 28131.261| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 1.94 r_work: 0.2711 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2579 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 26003 Z= 0.130 Angle : 0.562 10.673 35492 Z= 0.283 Chirality : 0.044 0.278 4023 Planarity : 0.004 0.055 4518 Dihedral : 6.877 83.927 4167 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.94 % Allowed : 14.43 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.15), residues: 3201 helix: 1.62 (0.25), residues: 438 sheet: 0.02 (0.16), residues: 966 loop : -0.42 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 206 TYR 0.012 0.001 TYR J 327 PHE 0.017 0.001 PHE J 50 TRP 0.009 0.001 TRP O 195 HIS 0.008 0.001 HIS I 308 Details of bonding type rmsd covalent geometry : bond 0.00292 (25923) covalent geometry : angle 0.55291 (35301) SS BOND : bond 0.00360 ( 46) SS BOND : angle 1.14676 ( 92) hydrogen bonds : bond 0.03254 ( 948) hydrogen bonds : angle 5.40925 ( 2598) Misc. bond : bond 0.00009 ( 1) link_ALPHA1-6 : bond 0.00340 ( 3) link_ALPHA1-6 : angle 1.58512 ( 9) link_BETA1-4 : bond 0.00574 ( 18) link_BETA1-4 : angle 1.77299 ( 54) link_BETA1-6 : bond 0.00689 ( 3) link_BETA1-6 : angle 2.15254 ( 9) link_NAG-ASN : bond 0.00086 ( 9) link_NAG-ASN : angle 1.53967 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 339 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 2 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7529 (mm-30) REVERT: G 145 ASP cc_start: 0.8905 (m-30) cc_final: 0.8549 (m-30) REVERT: G 289 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.6792 (mmm160) REVERT: G 302 THR cc_start: 0.9120 (m) cc_final: 0.8800 (p) REVERT: G 321 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8414 (mtpp) REVERT: H 136 MET cc_start: 0.9291 (mtm) cc_final: 0.9080 (mtp) REVERT: H 289 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7323 (mtp180) REVERT: H 321 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8357 (mtpp) REVERT: I 182 ASP cc_start: 0.9039 (m-30) cc_final: 0.8769 (m-30) REVERT: I 245 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8467 (mtmt) REVERT: I 302 THR cc_start: 0.9106 (m) cc_final: 0.8669 (p) REVERT: J 189 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7836 (tptm) REVERT: J 409 TRP cc_start: 0.6740 (t60) cc_final: 0.6297 (t-100) REVERT: J 411 LEU cc_start: 0.8081 (mm) cc_final: 0.7657 (tt) REVERT: K 158 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.7374 (mp10) REVERT: L 119 ARG cc_start: 0.8387 (mtm-85) cc_final: 0.8110 (mtm180) REVERT: L 212 ASN cc_start: 0.8104 (t0) cc_final: 0.7904 (t0) REVERT: L 359 TYR cc_start: 0.9014 (t80) cc_final: 0.8804 (t80) REVERT: M 111 MET cc_start: 0.6063 (OUTLIER) cc_final: 0.5765 (ppp) REVERT: M 166 TYR cc_start: 0.8307 (m-80) cc_final: 0.7968 (m-80) REVERT: N 121 PHE cc_start: 0.8443 (m-80) cc_final: 0.7707 (m-80) REVERT: N 194 ASN cc_start: 0.7929 (m110) cc_final: 0.7374 (m110) REVERT: O 111 MET cc_start: 0.5967 (pp-130) cc_final: 0.5592 (pp-130) REVERT: O 162 LYS cc_start: 0.8146 (tmtt) cc_final: 0.7915 (tmtt) REVERT: O 192 HIS cc_start: 0.7321 (t70) cc_final: 0.7054 (t-170) outliers start: 53 outliers final: 28 residues processed: 366 average time/residue: 0.5301 time to fit residues: 228.9362 Evaluate side-chains 363 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 326 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain H residue 321 LYS Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 194 SER Chi-restraints excluded: chain I residue 245 LYS Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain J residue 189 LYS Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 158 GLN Chi-restraints excluded: chain K residue 171 MET Chi-restraints excluded: chain K residue 323 ASP Chi-restraints excluded: chain K residue 339 SER Chi-restraints excluded: chain K residue 346 LYS Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 367 VAL Chi-restraints excluded: chain L residue 389 VAL Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 234 VAL Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 229 ARG Chi-restraints excluded: chain O residue 113 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 99 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 225 optimal weight: 6.9990 chunk 246 optimal weight: 4.9990 chunk 186 optimal weight: 0.0970 chunk 163 optimal weight: 0.1980 chunk 208 optimal weight: 20.0000 chunk 213 optimal weight: 7.9990 chunk 80 optimal weight: 0.0070 chunk 253 optimal weight: 9.9990 overall best weight: 1.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 264 ASN H 142 GLN H 264 ASN J 170 HIS K 212 ASN L 187 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.155646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.094530 restraints weight = 28182.605| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.09 r_work: 0.2720 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26003 Z= 0.119 Angle : 0.546 11.049 35492 Z= 0.273 Chirality : 0.043 0.272 4023 Planarity : 0.004 0.055 4518 Dihedral : 6.487 78.305 4167 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.72 % Allowed : 15.13 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.15), residues: 3201 helix: 1.72 (0.25), residues: 438 sheet: 0.07 (0.16), residues: 966 loop : -0.39 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 206 TYR 0.014 0.001 TYR L 64 PHE 0.017 0.001 PHE J 50 TRP 0.011 0.001 TRP O 195 HIS 0.007 0.001 HIS I 308 Details of bonding type rmsd covalent geometry : bond 0.00268 (25923) covalent geometry : angle 0.53718 (35301) SS BOND : bond 0.00299 ( 46) SS BOND : angle 1.04715 ( 92) hydrogen bonds : bond 0.03076 ( 948) hydrogen bonds : angle 5.28099 ( 2598) Misc. bond : bond 0.00001 ( 1) link_ALPHA1-6 : bond 0.00404 ( 3) link_ALPHA1-6 : angle 1.56674 ( 9) link_BETA1-4 : bond 0.00556 ( 18) link_BETA1-4 : angle 1.72109 ( 54) link_BETA1-6 : bond 0.00657 ( 3) link_BETA1-6 : angle 2.10478 ( 9) link_NAG-ASN : bond 0.00078 ( 9) link_NAG-ASN : angle 1.57021 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 332 time to evaluate : 0.832 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 2 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7517 (mm-30) REVERT: G 145 ASP cc_start: 0.8916 (m-30) cc_final: 0.8571 (m-30) REVERT: G 289 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.6817 (mmm160) REVERT: G 302 THR cc_start: 0.9162 (m) cc_final: 0.8869 (p) REVERT: G 321 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8427 (mtpp) REVERT: H 289 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7306 (mtp180) REVERT: H 321 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8355 (mtpp) REVERT: I 182 ASP cc_start: 0.9045 (m-30) cc_final: 0.8794 (m-30) REVERT: I 245 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8462 (mtmt) REVERT: I 302 THR cc_start: 0.9051 (m) cc_final: 0.8645 (p) REVERT: J 409 TRP cc_start: 0.6725 (t60) cc_final: 0.6295 (t-100) REVERT: J 411 LEU cc_start: 0.8072 (mm) cc_final: 0.7640 (tt) REVERT: L 212 ASN cc_start: 0.8105 (t0) cc_final: 0.7904 (t0) REVERT: M 111 MET cc_start: 0.6063 (OUTLIER) cc_final: 0.5765 (ppp) REVERT: M 166 TYR cc_start: 0.8331 (m-80) cc_final: 0.7944 (m-80) REVERT: N 121 PHE cc_start: 0.8441 (m-80) cc_final: 0.8013 (m-80) REVERT: N 194 ASN cc_start: 0.7951 (m110) cc_final: 0.7399 (m110) REVERT: O 111 MET cc_start: 0.6183 (pp-130) cc_final: 0.5805 (pp-130) REVERT: O 162 LYS cc_start: 0.8166 (tmtt) cc_final: 0.7929 (tmtt) REVERT: O 192 HIS cc_start: 0.7307 (t70) cc_final: 0.7020 (t-90) outliers start: 47 outliers final: 27 residues processed: 358 average time/residue: 0.5285 time to fit residues: 223.5693 Evaluate side-chains 358 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 324 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain H residue 321 LYS Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 194 SER Chi-restraints excluded: chain I residue 245 LYS Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 323 ASP Chi-restraints excluded: chain K residue 339 SER Chi-restraints excluded: chain K residue 346 LYS Chi-restraints excluded: chain K residue 393 SER Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 367 VAL Chi-restraints excluded: chain L residue 389 VAL Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 169 GLU Chi-restraints excluded: chain N residue 229 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 146 optimal weight: 0.0970 chunk 302 optimal weight: 30.0000 chunk 178 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 240 optimal weight: 4.9990 chunk 230 optimal weight: 0.9990 chunk 301 optimal weight: 0.6980 chunk 78 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 279 optimal weight: 20.0000 overall best weight: 2.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 264 ASN H 142 GLN H 264 ASN ** J 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 212 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.154688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.093192 restraints weight = 28143.773| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 2.05 r_work: 0.2688 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 26003 Z= 0.166 Angle : 0.578 11.394 35492 Z= 0.290 Chirality : 0.044 0.288 4023 Planarity : 0.004 0.054 4518 Dihedral : 6.472 71.145 4167 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.94 % Allowed : 15.24 % Favored : 82.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 3201 helix: 1.70 (0.25), residues: 438 sheet: 0.08 (0.16), residues: 966 loop : -0.41 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 206 TYR 0.013 0.002 TYR J 327 PHE 0.022 0.002 PHE J 50 TRP 0.009 0.001 TRP O 195 HIS 0.009 0.001 HIS I 308 Details of bonding type rmsd covalent geometry : bond 0.00383 (25923) covalent geometry : angle 0.56718 (35301) SS BOND : bond 0.00330 ( 46) SS BOND : angle 1.44428 ( 92) hydrogen bonds : bond 0.03298 ( 948) hydrogen bonds : angle 5.33480 ( 2598) Misc. bond : bond 0.00008 ( 1) link_ALPHA1-6 : bond 0.00329 ( 3) link_ALPHA1-6 : angle 1.65507 ( 9) link_BETA1-4 : bond 0.00563 ( 18) link_BETA1-4 : angle 1.78701 ( 54) link_BETA1-6 : bond 0.00655 ( 3) link_BETA1-6 : angle 2.11718 ( 9) link_NAG-ASN : bond 0.00132 ( 9) link_NAG-ASN : angle 1.70020 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 324 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 2 GLU cc_start: 0.7816 (OUTLIER) cc_final: 0.7525 (mm-30) REVERT: G 145 ASP cc_start: 0.8912 (m-30) cc_final: 0.8568 (m-30) REVERT: G 289 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.6783 (mmm160) REVERT: G 302 THR cc_start: 0.9175 (m) cc_final: 0.8863 (p) REVERT: G 321 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8425 (mtpp) REVERT: H 289 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7324 (mtp180) REVERT: H 321 LYS cc_start: 0.8873 (OUTLIER) cc_final: 0.8345 (mtpp) REVERT: I 182 ASP cc_start: 0.9044 (m-30) cc_final: 0.8794 (m-30) REVERT: I 245 LYS cc_start: 0.8699 (OUTLIER) cc_final: 0.8468 (mtmt) REVERT: I 302 THR cc_start: 0.9041 (m) cc_final: 0.8618 (p) REVERT: J 409 TRP cc_start: 0.6695 (t60) cc_final: 0.6227 (t-100) REVERT: J 411 LEU cc_start: 0.8075 (mm) cc_final: 0.7646 (tt) REVERT: K 158 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.7288 (mp10) REVERT: K 169 MET cc_start: 0.8854 (mmm) cc_final: 0.8529 (mtt) REVERT: L 212 ASN cc_start: 0.8076 (t0) cc_final: 0.7871 (t0) REVERT: M 111 MET cc_start: 0.6082 (OUTLIER) cc_final: 0.5775 (ppp) REVERT: M 166 TYR cc_start: 0.8347 (m-80) cc_final: 0.7944 (m-80) REVERT: N 121 PHE cc_start: 0.8451 (m-80) cc_final: 0.8052 (m-80) REVERT: N 194 ASN cc_start: 0.8056 (m110) cc_final: 0.7470 (m110) REVERT: O 111 MET cc_start: 0.6169 (pp-130) cc_final: 0.5811 (pp-130) REVERT: O 162 LYS cc_start: 0.8146 (tmtt) cc_final: 0.7909 (tmtt) REVERT: O 192 HIS cc_start: 0.7305 (t70) cc_final: 0.7060 (t-170) outliers start: 53 outliers final: 37 residues processed: 353 average time/residue: 0.5597 time to fit residues: 235.1882 Evaluate side-chains 369 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 324 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 209 GLU Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain H residue 321 LYS Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 194 SER Chi-restraints excluded: chain I residue 245 LYS Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 158 GLN Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 323 ASP Chi-restraints excluded: chain K residue 339 SER Chi-restraints excluded: chain K residue 346 LYS Chi-restraints excluded: chain K residue 393 SER Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 367 VAL Chi-restraints excluded: chain L residue 381 ILE Chi-restraints excluded: chain L residue 389 VAL Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 140 VAL Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 169 GLU Chi-restraints excluded: chain N residue 229 ARG Chi-restraints excluded: chain O residue 113 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 12 optimal weight: 10.0000 chunk 291 optimal weight: 20.0000 chunk 298 optimal weight: 9.9990 chunk 85 optimal weight: 5.9990 chunk 221 optimal weight: 4.9990 chunk 251 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 chunk 259 optimal weight: 7.9990 chunk 290 optimal weight: 30.0000 chunk 84 optimal weight: 1.9990 chunk 269 optimal weight: 30.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 264 ASN H 142 GLN ** J 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 212 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.153118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.090432 restraints weight = 28240.952| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 1.97 r_work: 0.2658 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 3.40 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 26003 Z= 0.274 Angle : 0.650 11.652 35492 Z= 0.328 Chirality : 0.048 0.311 4023 Planarity : 0.004 0.053 4518 Dihedral : 6.674 59.863 4167 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.87 % Allowed : 15.38 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.15), residues: 3201 helix: 1.58 (0.25), residues: 438 sheet: 0.07 (0.16), residues: 963 loop : -0.49 (0.14), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 199 TYR 0.018 0.002 TYR J 327 PHE 0.030 0.002 PHE J 50 TRP 0.009 0.002 TRP J 309 HIS 0.013 0.001 HIS I 308 Details of bonding type rmsd covalent geometry : bond 0.00643 (25923) covalent geometry : angle 0.63562 (35301) SS BOND : bond 0.00483 ( 46) SS BOND : angle 1.93189 ( 92) hydrogen bonds : bond 0.03755 ( 948) hydrogen bonds : angle 5.55978 ( 2598) Misc. bond : bond 0.00031 ( 1) link_ALPHA1-6 : bond 0.00248 ( 3) link_ALPHA1-6 : angle 1.74271 ( 9) link_BETA1-4 : bond 0.00607 ( 18) link_BETA1-4 : angle 1.98988 ( 54) link_BETA1-6 : bond 0.00666 ( 3) link_BETA1-6 : angle 2.19063 ( 9) link_NAG-ASN : bond 0.00296 ( 9) link_NAG-ASN : angle 2.11530 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6402 Ramachandran restraints generated. 3201 Oldfield, 0 Emsley, 3201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 313 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 2 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7582 (mm-30) REVERT: G 145 ASP cc_start: 0.8927 (m-30) cc_final: 0.8560 (m-30) REVERT: G 289 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.6715 (mmm160) REVERT: G 302 THR cc_start: 0.9140 (m) cc_final: 0.8749 (p) REVERT: G 321 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8373 (mtpp) REVERT: H 289 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7359 (mtp180) REVERT: H 321 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8363 (mtpp) REVERT: I 155 THR cc_start: 0.9200 (m) cc_final: 0.8845 (p) REVERT: I 182 ASP cc_start: 0.9002 (m-30) cc_final: 0.8801 (m-30) REVERT: I 245 LYS cc_start: 0.8740 (OUTLIER) cc_final: 0.8381 (mtmt) REVERT: I 302 THR cc_start: 0.9110 (m) cc_final: 0.8608 (p) REVERT: J 221 LEU cc_start: 0.8371 (mp) cc_final: 0.8169 (mt) REVERT: J 411 LEU cc_start: 0.8086 (mm) cc_final: 0.7659 (tt) REVERT: K 158 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.7396 (mp10) REVERT: K 302 ASP cc_start: 0.8660 (t0) cc_final: 0.8362 (t70) REVERT: L 212 ASN cc_start: 0.8091 (t0) cc_final: 0.7881 (t0) REVERT: M 111 MET cc_start: 0.5945 (OUTLIER) cc_final: 0.5640 (ppp) REVERT: M 166 TYR cc_start: 0.8332 (m-80) cc_final: 0.7928 (m-80) REVERT: N 194 ASN cc_start: 0.8094 (m110) cc_final: 0.7495 (m110) REVERT: O 111 MET cc_start: 0.6149 (pp-130) cc_final: 0.5779 (pp-130) REVERT: O 162 LYS cc_start: 0.8114 (tmtt) cc_final: 0.7870 (tmtt) REVERT: O 192 HIS cc_start: 0.7308 (t70) cc_final: 0.7043 (t-170) outliers start: 51 outliers final: 36 residues processed: 343 average time/residue: 0.5505 time to fit residues: 223.5598 Evaluate side-chains 353 residues out of total 2730 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 309 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 2 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain G residue 289 ARG Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 321 LYS Chi-restraints excluded: chain G residue 414 SER Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 140 VAL Chi-restraints excluded: chain H residue 289 ARG Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain H residue 321 LYS Chi-restraints excluded: chain H residue 348 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 34 VAL Chi-restraints excluded: chain I residue 108 VAL Chi-restraints excluded: chain I residue 194 SER Chi-restraints excluded: chain I residue 245 LYS Chi-restraints excluded: chain I residue 297 ILE Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain J residue 50 PHE Chi-restraints excluded: chain J residue 191 THR Chi-restraints excluded: chain K residue 50 PHE Chi-restraints excluded: chain K residue 158 GLN Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 323 ASP Chi-restraints excluded: chain K residue 339 SER Chi-restraints excluded: chain K residue 346 LYS Chi-restraints excluded: chain K residue 397 THR Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 192 VAL Chi-restraints excluded: chain L residue 367 VAL Chi-restraints excluded: chain L residue 381 ILE Chi-restraints excluded: chain L residue 389 VAL Chi-restraints excluded: chain M residue 111 MET Chi-restraints excluded: chain M residue 123 VAL Chi-restraints excluded: chain M residue 140 VAL Chi-restraints excluded: chain M residue 149 VAL Chi-restraints excluded: chain M residue 208 THR Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 169 GLU Chi-restraints excluded: chain N residue 229 ARG Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 208 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 318 random chunks: chunk 247 optimal weight: 8.9990 chunk 9 optimal weight: 8.9990 chunk 199 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 226 optimal weight: 0.0980 chunk 202 optimal weight: 10.0000 chunk 188 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 249 optimal weight: 20.0000 chunk 252 optimal weight: 0.5980 chunk 283 optimal weight: 30.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 264 ASN H 142 GLN H 264 ASN J 170 HIS J 224 GLN K 212 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.155752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.094698 restraints weight = 28233.074| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 2.08 r_work: 0.2720 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26003 Z= 0.115 Angle : 0.559 10.603 35492 Z= 0.279 Chirality : 0.043 0.269 4023 Planarity : 0.004 0.055 4518 Dihedral : 6.056 59.446 4167 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.39 % Allowed : 15.97 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.41 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.15), residues: 3201 helix: 1.70 (0.25), residues: 438 sheet: 0.05 (0.16), residues: 966 loop : -0.41 (0.14), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 206 TYR 0.011 0.001 TYR G 122 PHE 0.016 0.001 PHE N 224 TRP 0.013 0.001 TRP J 235 HIS 0.007 0.001 HIS I 308 Details of bonding type rmsd covalent geometry : bond 0.00257 (25923) covalent geometry : angle 0.54867 (35301) SS BOND : bond 0.00220 ( 46) SS BOND : angle 1.17021 ( 92) hydrogen bonds : bond 0.03063 ( 948) hydrogen bonds : angle 5.28211 ( 2598) Misc. bond : bond 0.00001 ( 1) link_ALPHA1-6 : bond 0.00736 ( 3) link_ALPHA1-6 : angle 1.43596 ( 9) link_BETA1-4 : bond 0.00547 ( 18) link_BETA1-4 : angle 1.62963 ( 54) link_BETA1-6 : bond 0.00704 ( 3) link_BETA1-6 : angle 2.12204 ( 9) link_NAG-ASN : bond 0.00162 ( 9) link_NAG-ASN : angle 2.15108 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11856.89 seconds wall clock time: 202 minutes 18.37 seconds (12138.37 seconds total)