Starting phenix.real_space_refine on Mon Jul 6 22:14:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eit_48093/07_2026/9eit_48093_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eit_48093/07_2026/9eit_48093.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9eit_48093/07_2026/9eit_48093.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eit_48093/07_2026/9eit_48093.map" model { file = "/net/cci-nas-00/data/ceres_data/9eit_48093/07_2026/9eit_48093_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eit_48093/07_2026/9eit_48093_trim.cif" } resolution = 3.35 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= 0.091 sd= 6.084 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 4 9.91 5 S 120 5.16 5 C 12208 2.51 5 N 3272 2.21 5 O 3908 1.98 5 H 18768 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 38280 Number of models: 1 Model: "" Number of chains: 28 Chain: "H" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1794 Classifications: {'peptide': 117} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "L" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1709 Classifications: {'peptide': 112} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "A" Number of atoms: 5936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 5936 Classifications: {'peptide': 393} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 375} Chain: "I" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1794 Classifications: {'peptide': 117} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "M" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1709 Classifications: {'peptide': 112} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "D" Number of atoms: 5936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 5936 Classifications: {'peptide': 393} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 375} Chain: "N" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1794 Classifications: {'peptide': 117} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "O" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1709 Classifications: {'peptide': 112} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "G" Number of atoms: 5936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 5936 Classifications: {'peptide': 393} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 375} Chain: "S" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1794 Classifications: {'peptide': 117} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 112} Chain: "T" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 1709 Classifications: {'peptide': 112} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 8, 'TRANS': 103} Chain: "P" Number of atoms: 5936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 393, 5936 Classifications: {'peptide': 393} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 375} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 28 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 18 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "L" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 18 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "A" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 66 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "I" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 21 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "M" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 15 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 66 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "N" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 18 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "O" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 18 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 66 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "S" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 18 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "T" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 18 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "P" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 66 Classifications: {'water': 22} Link IDs: {None: 21} Time building chain proxies: 7.06, per 1000 atoms: 0.18 Number of scatterers: 38280 At special positions: 0 Unit cell: (140.36, 140.36, 84.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 4 19.99 S 120 16.00 O 3908 8.00 N 3272 7.00 C 12208 6.00 H 18768 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS H 12 " - pdb=" SG CYS H 87 " distance=2.04 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 46 " distance=2.04 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 148 " distance=2.03 Simple disulfide: pdb=" SG CYS A 150 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 235 " - pdb=" SG CYS A 254 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 369 " distance=2.03 Simple disulfide: pdb=" SG CYS I 12 " - pdb=" SG CYS I 87 " distance=2.04 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 46 " distance=2.03 Simple disulfide: pdb=" SG CYS D 101 " - pdb=" SG CYS D 148 " distance=2.02 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 155 " distance=2.04 Simple disulfide: pdb=" SG CYS D 196 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 207 " distance=2.03 Simple disulfide: pdb=" SG CYS D 235 " - pdb=" SG CYS D 254 " distance=2.03 Simple disulfide: pdb=" SG CYS D 343 " - pdb=" SG CYS D 369 " distance=2.03 Simple disulfide: pdb=" SG CYS N 12 " - pdb=" SG CYS N 87 " distance=2.04 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 46 " distance=2.04 Simple disulfide: pdb=" SG CYS G 101 " - pdb=" SG CYS G 148 " distance=2.02 Simple disulfide: pdb=" SG CYS G 150 " - pdb=" SG CYS G 155 " distance=2.03 Simple disulfide: pdb=" SG CYS G 196 " - pdb=" SG CYS G 209 " distance=2.03 Simple disulfide: pdb=" SG CYS G 198 " - pdb=" SG CYS G 207 " distance=2.03 Simple disulfide: pdb=" SG CYS G 235 " - pdb=" SG CYS G 254 " distance=2.03 Simple disulfide: pdb=" SG CYS G 343 " - pdb=" SG CYS G 369 " distance=2.03 Simple disulfide: pdb=" SG CYS S 12 " - pdb=" SG CYS S 87 " distance=2.04 Simple disulfide: pdb=" SG CYS P 41 " - pdb=" SG CYS P 46 " distance=2.04 Simple disulfide: pdb=" SG CYS P 101 " - pdb=" SG CYS P 148 " distance=2.03 Simple disulfide: pdb=" SG CYS P 150 " - pdb=" SG CYS P 155 " distance=2.03 Simple disulfide: pdb=" SG CYS P 196 " - pdb=" SG CYS P 209 " distance=2.03 Simple disulfide: pdb=" SG CYS P 198 " - pdb=" SG CYS P 207 " distance=2.03 Simple disulfide: pdb=" SG CYS P 235 " - pdb=" SG CYS P 254 " distance=2.03 Simple disulfide: pdb=" SG CYS P 343 " - pdb=" SG CYS P 369 " 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=0, symmetry=0 Links applied NAG-ASN " NAG A 401 " - " ASN A 63 " " NAG A 402 " - " ASN A 3 " " NAG D 401 " - " ASN D 63 " " NAG D 402 " - " ASN D 3 " " NAG G 401 " - " ASN G 63 " " NAG G 402 " - " ASN G 3 " " NAG P 401 " - " ASN P 63 " " NAG P 402 " - " ASN P 3 " Time building additional restraints: 3.69 Conformation dependent library (CDL) restraints added in 1.2 seconds 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4504 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 52 sheets defined 6.0% alpha, 44.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'H' and resid 53 through 56 Processing helix chain 'H' and resid 78 through 82 Processing helix chain 'L' and resid 84 through 88 removed outlier: 4.116A pdb=" N VAL L 88 " --> pdb=" O ALA L 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 27 removed outlier: 3.551A pdb=" N SER A 27 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 63 removed outlier: 3.589A pdb=" N ASN A 63 " --> pdb=" O LYS A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 118 Processing helix chain 'A' and resid 331 through 336 Processing helix chain 'I' and resid 53 through 56 Processing helix chain 'I' and resid 78 through 82 Processing helix chain 'D' and resid 21 through 26 Processing helix chain 'D' and resid 59 through 63 removed outlier: 3.614A pdb=" N ASN D 63 " --> pdb=" O LYS D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 118 Processing helix chain 'D' and resid 331 through 336 Processing helix chain 'D' and resid 388 through 392 Processing helix chain 'N' and resid 53 through 56 Processing helix chain 'N' and resid 65 through 67 No H-bonds generated for 'chain 'N' and resid 65 through 67' Processing helix chain 'N' and resid 78 through 82 Processing helix chain 'O' and resid 84 through 88 removed outlier: 4.113A pdb=" N VAL O 88 " --> pdb=" O ALA O 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 26 Processing helix chain 'G' and resid 59 through 63 Processing helix chain 'G' and resid 115 through 118 Processing helix chain 'G' and resid 331 through 336 Processing helix chain 'S' and resid 53 through 56 Processing helix chain 'S' and resid 78 through 82 Processing helix chain 'T' and resid 84 through 88 removed outlier: 4.272A pdb=" N VAL T 88 " --> pdb=" O ALA T 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 21 through 26 Processing helix chain 'P' and resid 59 through 63 Processing helix chain 'P' and resid 115 through 118 Processing helix chain 'P' and resid 331 through 336 Processing helix chain 'P' and resid 388 through 392 removed outlier: 3.630A pdb=" N LYS P 392 " --> pdb=" O ASP P 389 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 8 through 13 Processing sheet with id=AA2, first strand: chain 'H' and resid 49 through 51 removed outlier: 6.561A pdb=" N TRP H 28 " --> pdb=" O ILE H 40 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN H 42 " --> pdb=" O TRP H 26 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TRP H 26 " --> pdb=" O ASN H 42 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N CYS H 87 " --> pdb=" O VAL H 106 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL H 106 " --> pdb=" O CYS H 87 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ARG H 89 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LEU H 104 " --> pdb=" O ARG H 89 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY H 91 " --> pdb=" O PHE H 102 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR H 100 " --> pdb=" O SER H 93 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 49 through 51 removed outlier: 6.561A pdb=" N TRP H 28 " --> pdb=" O ILE H 40 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN H 42 " --> pdb=" O TRP H 26 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N TRP H 26 " --> pdb=" O ASN H 42 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.751A pdb=" N TYR L 75 " --> pdb=" O SER L 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 5.211A pdb=" N LEU L 38 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N TYR L 54 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ASN L 58 " --> pdb=" O TYR L 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.591A pdb=" N THR L 102 " --> pdb=" O GLN L 95 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 13 through 19 removed outlier: 6.729A pdb=" N VAL A 367 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS A 19 " --> pdb=" O SER A 365 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N SER A 365 " --> pdb=" O LYS A 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 37 through 41 removed outlier: 6.715A pdb=" N LEU A 75 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 97 through 102 removed outlier: 3.876A pdb=" N SER A 97 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP A 131 " --> pdb=" O ILE A 123 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TYR A 125 " --> pdb=" O PRO A 129 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 142 through 143 Processing sheet with id=AB2, first strand: chain 'A' and resid 142 through 143 removed outlier: 5.888A pdb=" N HIS A 176 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N VAL A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 197 through 201 Processing sheet with id=AB4, first strand: chain 'A' and resid 272 through 275 removed outlier: 8.424A pdb=" N SER A 291 " --> pdb=" O LEU A 316 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N LEU A 316 " --> pdb=" O SER A 291 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N PHE A 293 " --> pdb=" O GLU A 314 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N GLU A 314 " --> pdb=" O PHE A 293 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N ILE A 295 " --> pdb=" O LYS A 312 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS A 312 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU A 297 " --> pdb=" O VAL A 310 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 8 through 13 Processing sheet with id=AB6, first strand: chain 'I' and resid 49 through 51 removed outlier: 6.382A pdb=" N TRP I 28 " --> pdb=" O ILE I 40 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASN I 42 " --> pdb=" O TRP I 26 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP I 26 " --> pdb=" O ASN I 42 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N CYS I 87 " --> pdb=" O VAL I 106 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N VAL I 106 " --> pdb=" O CYS I 87 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ARG I 89 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU I 104 " --> pdb=" O ARG I 89 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLY I 91 " --> pdb=" O PHE I 102 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR I 100 " --> pdb=" O SER I 93 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 49 through 51 removed outlier: 6.382A pdb=" N TRP I 28 " --> pdb=" O ILE I 40 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASN I 42 " --> pdb=" O TRP I 26 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP I 26 " --> pdb=" O ASN I 42 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 4 through 6 removed outlier: 3.565A pdb=" N TYR M 75 " --> pdb=" O SER M 72 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'M' and resid 10 through 13 removed outlier: 4.032A pdb=" N GLY M 89 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N LEU M 38 " --> pdb=" O TYR M 54 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR M 54 " --> pdb=" O LEU M 38 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP M 40 " --> pdb=" O LEU M 52 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ASN M 58 " --> pdb=" O TYR M 54 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 10 through 13 removed outlier: 4.032A pdb=" N GLY M 89 " --> pdb=" O VAL M 109 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N THR M 102 " --> pdb=" O GLN M 95 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 13 through 19 removed outlier: 6.775A pdb=" N VAL D 367 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS D 19 " --> pdb=" O SER D 365 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N SER D 365 " --> pdb=" O LYS D 19 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 32 through 41 removed outlier: 4.864A pdb=" N PHE D 32 " --> pdb=" O ALA D 55 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ALA D 55 " --> pdb=" O PHE D 32 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ILE D 34 " --> pdb=" O GLN D 53 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLN D 53 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLU D 36 " --> pdb=" O LEU D 51 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N SER D 77 " --> pdb=" O PHE D 91 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N PHE D 91 " --> pdb=" O SER D 77 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 97 through 102 removed outlier: 4.083A pdb=" N SER D 97 " --> pdb=" O ILE D 112 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASP D 131 " --> pdb=" O ILE D 123 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N TYR D 125 " --> pdb=" O PRO D 129 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 142 through 143 Processing sheet with id=AC6, first strand: chain 'D' and resid 142 through 143 removed outlier: 3.531A pdb=" N TRP D 157 " --> pdb=" O PHE D 173 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N TYR D 170 " --> pdb=" O VAL D 186 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS D 174 " --> pdb=" O ASN D 182 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN D 182 " --> pdb=" O LYS D 174 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N HIS D 176 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 5.727A pdb=" N VAL D 180 " --> pdb=" O HIS D 176 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 197 through 201 Processing sheet with id=AC8, first strand: chain 'D' and resid 272 through 275 removed outlier: 8.324A pdb=" N SER D 291 " --> pdb=" O LEU D 316 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N LEU D 316 " --> pdb=" O SER D 291 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N PHE D 293 " --> pdb=" O GLU D 314 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLU D 314 " --> pdb=" O PHE D 293 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE D 295 " --> pdb=" O LYS D 312 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LYS D 312 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU D 297 " --> pdb=" O VAL D 310 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 8 through 13 Processing sheet with id=AD1, first strand: chain 'N' and resid 49 through 51 removed outlier: 5.708A pdb=" N TRP N 39 " --> pdb=" O ARG N 30 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG N 30 " --> pdb=" O TRP N 39 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N CYS N 87 " --> pdb=" O VAL N 106 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N VAL N 106 " --> pdb=" O CYS N 87 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N ARG N 89 " --> pdb=" O LEU N 104 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU N 104 " --> pdb=" O ARG N 89 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLY N 91 " --> pdb=" O PHE N 102 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 49 through 51 removed outlier: 5.708A pdb=" N TRP N 39 " --> pdb=" O ARG N 30 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG N 30 " --> pdb=" O TRP N 39 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 4 through 6 removed outlier: 3.640A pdb=" N TYR O 75 " --> pdb=" O SER O 72 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 10 through 13 removed outlier: 3.933A pdb=" N GLY O 89 " --> pdb=" O VAL O 109 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N LEU O 38 " --> pdb=" O TYR O 54 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N TYR O 54 " --> pdb=" O LEU O 38 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TRP O 40 " --> pdb=" O LEU O 52 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN O 58 " --> pdb=" O TYR O 54 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'O' and resid 10 through 13 removed outlier: 3.933A pdb=" N GLY O 89 " --> pdb=" O VAL O 109 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR O 102 " --> pdb=" O GLN O 95 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 13 through 19 removed outlier: 6.560A pdb=" N VAL G 367 " --> pdb=" O VAL G 17 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N LYS G 19 " --> pdb=" O SER G 365 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N SER G 365 " --> pdb=" O LYS G 19 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'G' and resid 32 through 41 removed outlier: 4.873A pdb=" N PHE G 32 " --> pdb=" O ALA G 55 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ALA G 55 " --> pdb=" O PHE G 32 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N ILE G 34 " --> pdb=" O GLN G 53 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLN G 53 " --> pdb=" O ILE G 34 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N GLU G 36 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA G 74 " --> pdb=" O THR G 52 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU G 75 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 98 through 102 removed outlier: 3.708A pdb=" N ASP G 131 " --> pdb=" O ILE G 123 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TYR G 125 " --> pdb=" O PRO G 129 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 141 through 143 Processing sheet with id=AE1, first strand: chain 'G' and resid 141 through 143 removed outlier: 7.137A pdb=" N TYR G 170 " --> pdb=" O GLU G 185 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLU G 185 " --> pdb=" O TYR G 170 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE G 172 " --> pdb=" O GLU G 183 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLU G 183 " --> pdb=" O ILE G 172 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N LYS G 174 " --> pdb=" O THR G 181 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET G 179 " --> pdb=" O HIS G 176 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 197 through 201 Processing sheet with id=AE3, first strand: chain 'G' and resid 272 through 275 removed outlier: 8.402A pdb=" N SER G 291 " --> pdb=" O LEU G 316 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N LEU G 316 " --> pdb=" O SER G 291 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N PHE G 293 " --> pdb=" O GLU G 314 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLU G 314 " --> pdb=" O PHE G 293 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ILE G 295 " --> pdb=" O LYS G 312 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS G 312 " --> pdb=" O ILE G 295 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU G 297 " --> pdb=" O VAL G 310 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'S' and resid 8 through 13 Processing sheet with id=AE5, first strand: chain 'S' and resid 49 through 51 removed outlier: 5.388A pdb=" N TRP S 39 " --> pdb=" O ARG S 30 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG S 30 " --> pdb=" O TRP S 39 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY S 41 " --> pdb=" O TRP S 28 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N CYS S 87 " --> pdb=" O VAL S 106 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL S 106 " --> pdb=" O CYS S 87 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ARG S 89 " --> pdb=" O LEU S 104 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU S 104 " --> pdb=" O ARG S 89 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLY S 91 " --> pdb=" O PHE S 102 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TYR S 100 " --> pdb=" O SER S 93 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'S' and resid 49 through 51 removed outlier: 5.388A pdb=" N TRP S 39 " --> pdb=" O ARG S 30 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG S 30 " --> pdb=" O TRP S 39 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY S 41 " --> pdb=" O TRP S 28 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'T' and resid 4 through 6 removed outlier: 3.594A pdb=" N TYR T 75 " --> pdb=" O SER T 72 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'T' and resid 10 through 13 removed outlier: 6.633A pdb=" N TRP T 40 " --> pdb=" O LEU T 52 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'T' and resid 10 through 13 removed outlier: 3.589A pdb=" N THR T 102 " --> pdb=" O GLN T 95 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 13 through 19 removed outlier: 6.714A pdb=" N VAL P 367 " --> pdb=" O VAL P 17 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N LYS P 19 " --> pdb=" O SER P 365 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N SER P 365 " --> pdb=" O LYS P 19 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'P' and resid 37 through 41 removed outlier: 3.684A pdb=" N ALA P 74 " --> pdb=" O THR P 52 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU P 75 " --> pdb=" O GLU P 92 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 98 through 102 removed outlier: 3.700A pdb=" N ASP P 131 " --> pdb=" O ILE P 123 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N TYR P 125 " --> pdb=" O PRO P 129 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'P' and resid 142 through 143 Processing sheet with id=AF5, first strand: chain 'P' and resid 142 through 143 removed outlier: 4.774A pdb=" N TYR P 170 " --> pdb=" O VAL P 186 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N HIS P 176 " --> pdb=" O VAL P 180 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N VAL P 180 " --> pdb=" O HIS P 176 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'P' and resid 198 through 201 Processing sheet with id=AF7, first strand: chain 'P' and resid 272 through 275 removed outlier: 8.379A pdb=" N SER P 291 " --> pdb=" O LEU P 316 " (cutoff:3.500A) removed outlier: 7.968A pdb=" N LEU P 316 " --> pdb=" O SER P 291 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N PHE P 293 " --> pdb=" O GLU P 314 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLU P 314 " --> pdb=" O PHE P 293 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE P 295 " --> pdb=" O LYS P 312 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N LYS P 312 " --> pdb=" O ILE P 295 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N LEU P 297 " --> pdb=" O VAL P 310 " (cutoff:3.500A) 722 hydrogen bonds defined for protein. 1824 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.05 Time building geometry restraints manager: 5.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.81 - 1.02: 18750 1.02 - 1.22: 44 1.22 - 1.43: 8662 1.43 - 1.63: 11012 1.63 - 1.84: 160 Bond restraints: 38628 Sorted by residual: bond pdb=" CD1 TYR L 92 " pdb=" HD1 TYR L 92 " ideal model delta sigma weight residual 0.930 1.005 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CD1 PHE D 188 " pdb=" HD1 PHE D 188 " ideal model delta sigma weight residual 0.930 1.004 -0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" CZ PHE A 38 " pdb=" HZ PHE A 38 " ideal model delta sigma weight residual 0.930 0.998 -0.068 2.00e-02 2.50e+03 1.14e+01 bond pdb=" CD1 PHE A 38 " pdb=" CE1 PHE A 38 " ideal model delta sigma weight residual 1.382 1.482 -0.100 3.00e-02 1.11e+03 1.12e+01 bond pdb=" CZ PHE D 188 " pdb=" HZ PHE D 188 " ideal model delta sigma weight residual 0.930 0.864 0.066 2.00e-02 2.50e+03 1.09e+01 ... (remaining 38623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 67468 3.51 - 7.02: 1278 7.02 - 10.53: 214 10.53 - 14.04: 62 14.04 - 17.56: 18 Bond angle restraints: 69040 Sorted by residual: angle pdb=" N CYS D 196 " pdb=" CA CYS D 196 " pdb=" C CYS D 196 " ideal model delta sigma weight residual 110.24 118.35 -8.11 1.30e+00 5.92e-01 3.89e+01 angle pdb=" N ILE G 193 " pdb=" CA ILE G 193 " pdb=" CB ILE G 193 " ideal model delta sigma weight residual 112.40 105.40 7.00 1.17e+00 7.31e-01 3.58e+01 angle pdb=" CA GLN O 105 " pdb=" CB GLN O 105 " pdb=" HB2 GLN O 105 " ideal model delta sigma weight residual 109.00 91.44 17.56 3.00e+00 1.11e-01 3.42e+01 angle pdb=" CG LYS N 67 " pdb=" CB LYS N 67 " pdb=" HB3 LYS N 67 " ideal model delta sigma weight residual 108.00 125.35 -17.35 3.00e+00 1.11e-01 3.34e+01 angle pdb=" CD2 TRP D 378 " pdb=" CE3 TRP D 378 " pdb=" HE3 TRP D 378 " ideal model delta sigma weight residual 120.70 103.43 17.27 3.00e+00 1.11e-01 3.31e+01 ... (remaining 69035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 16498 17.87 - 35.73: 1238 35.73 - 53.60: 429 53.60 - 71.46: 287 71.46 - 89.33: 24 Dihedral angle restraints: 18476 sinusoidal: 9936 harmonic: 8540 Sorted by residual: dihedral pdb=" CA GLN O 6 " pdb=" C GLN O 6 " pdb=" N SER O 7 " pdb=" CA SER O 7 " ideal model delta harmonic sigma weight residual -180.00 -145.20 -34.80 0 5.00e+00 4.00e-02 4.84e+01 dihedral pdb=" CA ILE P 303 " pdb=" C ILE P 303 " pdb=" N ARG P 304 " pdb=" CA ARG P 304 " ideal model delta harmonic sigma weight residual 180.00 -147.92 -32.08 0 5.00e+00 4.00e-02 4.12e+01 dihedral pdb=" CA ILE A 34 " pdb=" C ILE A 34 " pdb=" N ARG A 35 " pdb=" CA ARG A 35 " ideal model delta harmonic sigma weight residual 180.00 149.18 30.82 0 5.00e+00 4.00e-02 3.80e+01 ... (remaining 18473 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2554 0.098 - 0.196: 357 0.196 - 0.294: 34 0.294 - 0.393: 3 0.393 - 0.491: 4 Chirality restraints: 2952 Sorted by residual: chirality pdb=" CG LEU D 141 " pdb=" CB LEU D 141 " pdb=" CD1 LEU D 141 " pdb=" CD2 LEU D 141 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 6.02e+00 chirality pdb=" CG LEU A 57 " pdb=" CB LEU A 57 " pdb=" CD1 LEU A 57 " pdb=" CD2 LEU A 57 " both_signs ideal model delta sigma weight residual False -2.59 -2.10 -0.49 2.00e-01 2.50e+01 5.90e+00 chirality pdb=" CG LEU T 29 " pdb=" CB LEU T 29 " pdb=" CD1 LEU T 29 " pdb=" CD2 LEU T 29 " both_signs ideal model delta sigma weight residual False -2.59 -2.12 -0.47 2.00e-01 2.50e+01 5.54e+00 ... (remaining 2949 not shown) Planarity restraints: 5828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP N 39 " 0.033 2.00e-02 2.50e+03 4.30e-02 7.40e+01 pdb=" CG TRP N 39 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TRP N 39 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TRP N 39 " -0.116 2.00e-02 2.50e+03 pdb=" NE1 TRP N 39 " -0.026 2.00e-02 2.50e+03 pdb=" CE2 TRP N 39 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP N 39 " -0.014 2.00e-02 2.50e+03 pdb=" CZ2 TRP N 39 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP N 39 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP N 39 " 0.003 2.00e-02 2.50e+03 pdb=" HD1 TRP N 39 " -0.006 2.00e-02 2.50e+03 pdb=" HE1 TRP N 39 " 0.020 2.00e-02 2.50e+03 pdb=" HE3 TRP N 39 " 0.094 2.00e-02 2.50e+03 pdb=" HZ2 TRP N 39 " 0.049 2.00e-02 2.50e+03 pdb=" HZ3 TRP N 39 " -0.039 2.00e-02 2.50e+03 pdb=" HH2 TRP N 39 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 210 " -0.326 9.50e-02 1.11e+02 1.18e-01 5.89e+01 pdb=" NE ARG G 210 " 0.005 2.00e-02 2.50e+03 pdb=" CZ ARG G 210 " -0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG G 210 " 0.117 2.00e-02 2.50e+03 pdb=" NH2 ARG G 210 " 0.001 2.00e-02 2.50e+03 pdb="HH11 ARG G 210 " -0.025 2.00e-02 2.50e+03 pdb="HH12 ARG G 210 " -0.064 2.00e-02 2.50e+03 pdb="HH21 ARG G 210 " -0.002 2.00e-02 2.50e+03 pdb="HH22 ARG G 210 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR O 92 " -0.057 2.00e-02 2.50e+03 4.30e-02 5.55e+01 pdb=" CG TYR O 92 " 0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR O 92 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR O 92 " 0.102 2.00e-02 2.50e+03 pdb=" CE1 TYR O 92 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR O 92 " -0.089 2.00e-02 2.50e+03 pdb=" CZ TYR O 92 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR O 92 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 TYR O 92 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 TYR O 92 " 0.009 2.00e-02 2.50e+03 pdb=" HE1 TYR O 92 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR O 92 " -0.005 2.00e-02 2.50e+03 ... (remaining 5825 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.30: 8151 2.30 - 2.88: 83015 2.88 - 3.45: 94914 3.45 - 4.03: 139727 4.03 - 4.60: 211248 Nonbonded interactions: 537055 Sorted by model distance: nonbonded pdb=" H THR P 130 " pdb=" HG1 THR P 130 " model vdw 1.729 2.100 nonbonded pdb=" H ILE D 385 " pdb=" HE1 HIS G 61 " model vdw 1.781 2.100 nonbonded pdb=" HH TYR G 199 " pdb=" H ARG G 274 " model vdw 1.796 2.100 nonbonded pdb=" HB2 LYS N 67 " pdb=" HG3 LYS N 67 " model vdw 1.816 1.952 nonbonded pdb=" H THR I 78 " pdb=" HG1 THR I 78 " model vdw 1.828 2.100 ... (remaining 537050 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'G' selection = chain 'P' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'N' selection = chain 'S' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'O' selection = chain 'T' } 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: 2.220 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: 0.260 Extract box with map and model: 0.580 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 38.890 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.090 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6496 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 : 0.008 0.102 19900 Z= 0.359 Angle : 1.262 15.672 27092 Z= 0.696 Chirality : 0.071 0.491 2952 Planarity : 0.014 0.211 3460 Dihedral : 13.074 89.330 7192 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 1.55 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.18 % Favored : 92.49 % Rotamer: Outliers : 2.86 % Allowed : 3.00 % Favored : 94.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % 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: -2.49 (0.15), residues: 2464 helix: -4.20 (0.33), residues: 48 sheet: -1.01 (0.16), residues: 948 loop : -2.06 (0.14), residues: 1468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.083 0.004 ARG P 218 TYR 0.105 0.007 TYR O 92 PHE 0.100 0.008 PHE G 14 TRP 0.104 0.007 TRP N 39 HIS 0.072 0.005 HIS D 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00849 / 0.36 (19860) covalent geometry : angle 1.25221 / 0.69 (27004) SS BOND : bond 0.00574 / 0.41 ( 32) SS BOND : angle 2.07679 / 1.33 ( 64) hydrogen bonds : bond 0.18028 / 11.92 ( 639) hydrogen bonds : angle 8.63782 / 5.93 ( 1824) link_NAG-ASN : bond 0.00587 / 0.28 ( 8) link_NAG-ASN : angle 4.58857 / 2.81 ( 24) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 410 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 43 ILE cc_start: 0.7314 (OUTLIER) cc_final: 0.6933 (tp) REVERT: L 35 TYR cc_start: 0.7860 (m-80) cc_final: 0.7255 (m-80) REVERT: L 36 THR cc_start: 0.8187 (m) cc_final: 0.7839 (p) REVERT: L 79 LYS cc_start: 0.7047 (mmtt) cc_final: 0.6751 (mmtp) REVERT: A 68 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.5867 (m-30) REVERT: A 92 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7195 (mm-30) REVERT: A 105 LYS cc_start: 0.7670 (mtpt) cc_final: 0.7339 (mttp) REVERT: A 128 MET cc_start: 0.7023 (ptp) cc_final: 0.6714 (ptp) REVERT: A 151 MET cc_start: 0.7291 (mtm) cc_final: 0.7005 (mtm) REVERT: A 179 MET cc_start: 0.5909 (OUTLIER) cc_final: 0.5496 (mtt) REVERT: A 204 LYS cc_start: 0.6292 (OUTLIER) cc_final: 0.6043 (mmtp) REVERT: A 230 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6700 (mt-10) REVERT: A 289 SER cc_start: 0.8300 (m) cc_final: 0.7790 (p) REVERT: A 334 MET cc_start: 0.7523 (mtp) cc_final: 0.7274 (mtp) REVERT: I 25 TYR cc_start: 0.8548 (m-80) cc_final: 0.7712 (m-80) REVERT: I 43 ILE cc_start: 0.7235 (OUTLIER) cc_final: 0.6892 (tp) REVERT: I 51 TYR cc_start: 0.8609 (m-80) cc_final: 0.8361 (m-80) REVERT: M 35 TYR cc_start: 0.7633 (m-80) cc_final: 0.7083 (m-80) REVERT: M 36 THR cc_start: 0.8251 (m) cc_final: 0.8043 (p) REVERT: M 79 LYS cc_start: 0.7037 (mmtt) cc_final: 0.6824 (mmtp) REVERT: D 36 GLU cc_start: 0.6481 (pm20) cc_final: 0.5956 (pm20) REVERT: D 68 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.6245 (m-30) REVERT: D 92 GLU cc_start: 0.7602 (mm-30) cc_final: 0.7346 (mm-30) REVERT: D 118 ASP cc_start: 0.6935 (t0) cc_final: 0.6575 (p0) REVERT: D 151 MET cc_start: 0.7059 (mtm) cc_final: 0.6808 (mtm) REVERT: D 165 ASN cc_start: 0.8448 (m-40) cc_final: 0.8133 (m-40) REVERT: D 204 LYS cc_start: 0.6298 (OUTLIER) cc_final: 0.5918 (mmtp) REVERT: D 230 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6706 (mt-10) REVERT: D 266 TYR cc_start: 0.8895 (t80) cc_final: 0.8670 (t80) REVERT: D 289 SER cc_start: 0.8521 (m) cc_final: 0.8075 (p) REVERT: D 319 LYS cc_start: 0.8270 (pttt) cc_final: 0.8031 (pttp) REVERT: D 334 MET cc_start: 0.7549 (mtp) cc_final: 0.7266 (mtp) REVERT: D 348 MET cc_start: 0.8611 (mtm) cc_final: 0.8303 (mpp) REVERT: N 64 ASP cc_start: 0.7443 (t0) cc_final: 0.7168 (t70) REVERT: O 35 TYR cc_start: 0.7856 (m-80) cc_final: 0.7091 (m-80) REVERT: O 36 THR cc_start: 0.8318 (m) cc_final: 0.8056 (p) REVERT: O 68 SER cc_start: 0.6178 (t) cc_final: 0.5899 (m) REVERT: O 79 LYS cc_start: 0.7379 (mmtt) cc_final: 0.7075 (mmtp) REVERT: G 68 ASP cc_start: 0.7400 (OUTLIER) cc_final: 0.6375 (m-30) REVERT: G 105 LYS cc_start: 0.7707 (mtpt) cc_final: 0.7212 (mmtt) REVERT: G 128 MET cc_start: 0.7098 (ptp) cc_final: 0.6718 (ptt) REVERT: G 179 MET cc_start: 0.6060 (OUTLIER) cc_final: 0.5320 (pp-130) REVERT: G 204 LYS cc_start: 0.6483 (OUTLIER) cc_final: 0.6202 (mmtp) REVERT: G 230 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6574 (mt-10) REVERT: G 289 SER cc_start: 0.8436 (m) cc_final: 0.8025 (p) REVERT: S 43 ILE cc_start: 0.7139 (OUTLIER) cc_final: 0.6831 (tt) REVERT: S 51 TYR cc_start: 0.8506 (m-80) cc_final: 0.8279 (m-80) REVERT: S 64 ASP cc_start: 0.7471 (t0) cc_final: 0.7267 (t70) REVERT: T 35 TYR cc_start: 0.7768 (m-80) cc_final: 0.7310 (m-80) REVERT: T 79 LYS cc_start: 0.7234 (mmtt) cc_final: 0.7024 (mmtp) REVERT: T 112 LYS cc_start: 0.6875 (tttt) cc_final: 0.6589 (tppt) REVERT: P 68 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.6103 (m-30) REVERT: P 92 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7495 (mm-30) REVERT: P 105 LYS cc_start: 0.7786 (mtpt) cc_final: 0.7436 (mtpp) REVERT: P 128 MET cc_start: 0.7225 (ptp) cc_final: 0.6945 (ptt) REVERT: P 131 ASP cc_start: 0.8476 (t0) cc_final: 0.8186 (t70) REVERT: P 204 LYS cc_start: 0.6235 (OUTLIER) cc_final: 0.6009 (mmtp) REVERT: P 230 GLU cc_start: 0.7175 (mm-30) cc_final: 0.6432 (mt-10) REVERT: P 289 SER cc_start: 0.8310 (m) cc_final: 0.7750 (p) REVERT: P 319 LYS cc_start: 0.8168 (pttt) cc_final: 0.7902 (pttm) REVERT: P 334 MET cc_start: 0.7874 (mtp) cc_final: 0.7582 (mtp) REVERT: P 390 ILE cc_start: 0.7803 (tp) cc_final: 0.7485 (tt) outliers start: 61 outliers final: 23 residues processed: 460 average time/residue: 0.3705 time to fit residues: 251.5700 Evaluate side-chains 314 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 278 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 43 ILE Chi-restraints excluded: chain L residue 39 ASP Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 116 ASP Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 204 LYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain I residue 43 ILE Chi-restraints excluded: chain M residue 1 ASP Chi-restraints excluded: chain M residue 39 ASP Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 135 SER Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 170 TYR Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 204 LYS Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain S residue 43 ILE Chi-restraints excluded: chain T residue 65 ASP Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 135 SER Chi-restraints excluded: chain P residue 146 SER Chi-restraints excluded: chain P residue 170 TYR Chi-restraints excluded: chain P residue 204 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 1.9990 chunk 227 optimal weight: 0.4980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 235 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN D 256 ASN G 256 ASN P 256 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.158174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.142735 restraints weight = 57698.026| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.02 r_work: 0.3192 rms_B_bonded: 1.06 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19900 Z= 0.146 Angle : 0.637 6.224 27092 Z= 0.346 Chirality : 0.049 0.167 2952 Planarity : 0.006 0.057 3460 Dihedral : 8.025 59.751 2957 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.19 % Allowed : 7.13 % Favored : 89.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.20 (0.15), residues: 2464 helix: -3.56 (0.44), residues: 48 sheet: -0.82 (0.16), residues: 984 loop : -1.89 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG S 98 TYR 0.013 0.001 TYR O 54 PHE 0.022 0.002 PHE G 250 TRP 0.018 0.002 TRP A 96 HIS 0.004 0.001 HIS D 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (19860) covalent geometry : angle 0.62960 / 0.34 (27004) SS BOND : bond 0.00201 / 0.15 ( 32) SS BOND : angle 0.89500 / 0.59 ( 64) hydrogen bonds : bond 0.04519 / 2.99 ( 639) hydrogen bonds : angle 6.48058 / 4.44 ( 1824) link_NAG-ASN : bond 0.00388 / 0.20 ( 8) link_NAG-ASN : angle 3.09066 / 1.81 ( 24) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 262 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.6569 (mp0) cc_final: 0.6234 (mp0) REVERT: H 56 LYS cc_start: 0.7998 (tptp) cc_final: 0.7786 (tptp) REVERT: L 35 TYR cc_start: 0.8692 (m-80) cc_final: 0.8105 (m-80) REVERT: L 79 LYS cc_start: 0.7919 (mmtt) cc_final: 0.7630 (mmtp) REVERT: A 35 ARG cc_start: 0.6124 (OUTLIER) cc_final: 0.5918 (tpt170) REVERT: A 68 ASP cc_start: 0.7534 (OUTLIER) cc_final: 0.6350 (m-30) REVERT: A 105 LYS cc_start: 0.8194 (mtpt) cc_final: 0.7933 (mttt) REVERT: M 61 SER cc_start: 0.8147 (t) cc_final: 0.7892 (t) REVERT: M 79 LYS cc_start: 0.7918 (mmtt) cc_final: 0.7700 (mmtp) REVERT: D 35 ARG cc_start: 0.6428 (OUTLIER) cc_final: 0.6208 (tpt90) REVERT: D 68 ASP cc_start: 0.7861 (OUTLIER) cc_final: 0.6945 (m-30) REVERT: D 92 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7341 (mm-30) REVERT: D 179 MET cc_start: 0.7816 (OUTLIER) cc_final: 0.7397 (pp-130) REVERT: N 6 GLU cc_start: 0.6751 (mp0) cc_final: 0.6456 (mp0) REVERT: N 81 ASP cc_start: 0.7875 (t70) cc_final: 0.7490 (t0) REVERT: O 35 TYR cc_start: 0.8744 (m-80) cc_final: 0.8095 (m-80) REVERT: O 79 LYS cc_start: 0.8081 (mmtt) cc_final: 0.7752 (mmtp) REVERT: G 68 ASP cc_start: 0.7484 (OUTLIER) cc_final: 0.6319 (m-30) REVERT: G 105 LYS cc_start: 0.8217 (mtpt) cc_final: 0.7977 (mttt) REVERT: G 179 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.7072 (pp-130) REVERT: G 195 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7757 (mt-10) REVERT: S 58 ARG cc_start: 0.6306 (mtm-85) cc_final: 0.5997 (mtm-85) REVERT: T 79 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7758 (mmtp) REVERT: P 68 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.6906 (m-30) REVERT: P 92 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7518 (mm-30) REVERT: P 105 LYS cc_start: 0.8229 (mtpt) cc_final: 0.7979 (mttt) REVERT: P 195 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8035 (mt-10) outliers start: 68 outliers final: 35 residues processed: 316 average time/residue: 0.3394 time to fit residues: 162.8084 Evaluate side-chains 275 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 230 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain A residue 35 ARG Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 35 ARG Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain N residue 43 ILE Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 68 ASP Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 170 TYR Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain T residue 5 THR Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 68 ASP Chi-restraints excluded: chain P residue 148 CYS Chi-restraints excluded: chain P residue 170 TYR Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 268 VAL Chi-restraints excluded: chain P residue 336 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 243 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 211 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 168 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.155673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.139491 restraints weight = 58038.104| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 1.05 r_work: 0.3153 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19900 Z= 0.169 Angle : 0.594 5.613 27092 Z= 0.322 Chirality : 0.048 0.163 2952 Planarity : 0.005 0.061 3460 Dihedral : 6.977 53.338 2919 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.81 % Allowed : 9.24 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.17 (0.16), residues: 2464 helix: -4.01 (0.32), residues: 72 sheet: -0.81 (0.16), residues: 936 loop : -1.76 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 73 TYR 0.016 0.001 TYR O 54 PHE 0.019 0.002 PHE S 70 TRP 0.018 0.002 TRP I 39 HIS 0.004 0.001 HIS G 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.17 (19860) covalent geometry : angle 0.58918 / 0.32 (27004) SS BOND : bond 0.00266 / 0.19 ( 32) SS BOND : angle 0.89993 / 0.58 ( 64) hydrogen bonds : bond 0.03839 / 2.57 ( 639) hydrogen bonds : angle 5.97345 / 4.10 ( 1824) link_NAG-ASN : bond 0.00398 / 0.20 ( 8) link_NAG-ASN : angle 2.44775 / 1.46 ( 24) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 240 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.6679 (mp0) cc_final: 0.6201 (mp0) REVERT: H 58 ARG cc_start: 0.6224 (mtm-85) cc_final: 0.5975 (mtm-85) REVERT: H 81 ASP cc_start: 0.8166 (t0) cc_final: 0.7952 (t0) REVERT: L 35 TYR cc_start: 0.8759 (m-80) cc_final: 0.8170 (m-80) REVERT: A 68 ASP cc_start: 0.7703 (OUTLIER) cc_final: 0.6393 (m-30) REVERT: A 105 LYS cc_start: 0.8291 (mtpt) cc_final: 0.7968 (mttt) REVERT: I 6 GLU cc_start: 0.7238 (mp0) cc_final: 0.6681 (mp0) REVERT: M 35 TYR cc_start: 0.8626 (m-80) cc_final: 0.7977 (m-80) REVERT: M 79 LYS cc_start: 0.7983 (mmtt) cc_final: 0.7782 (mmtp) REVERT: D 68 ASP cc_start: 0.7902 (p0) cc_final: 0.6914 (m-30) REVERT: D 92 GLU cc_start: 0.7890 (mm-30) cc_final: 0.7636 (mm-30) REVERT: D 179 MET cc_start: 0.7900 (OUTLIER) cc_final: 0.7575 (pp-130) REVERT: N 6 GLU cc_start: 0.6901 (mp0) cc_final: 0.6456 (mp0) REVERT: N 81 ASP cc_start: 0.7881 (t70) cc_final: 0.7680 (t0) REVERT: O 35 TYR cc_start: 0.8820 (m-80) cc_final: 0.8206 (m-80) REVERT: O 79 LYS cc_start: 0.8055 (mmtt) cc_final: 0.7695 (mmtp) REVERT: G 35 ARG cc_start: 0.6496 (OUTLIER) cc_final: 0.4036 (tmm160) REVERT: G 68 ASP cc_start: 0.7827 (p0) cc_final: 0.6604 (m-30) REVERT: G 105 LYS cc_start: 0.8287 (mtpt) cc_final: 0.8013 (mttt) REVERT: G 179 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7303 (pp-130) REVERT: G 336 SER cc_start: 0.8255 (m) cc_final: 0.7697 (p) REVERT: S 6 GLU cc_start: 0.6933 (mp0) cc_final: 0.6588 (mp0) REVERT: S 58 ARG cc_start: 0.6319 (mtm-85) cc_final: 0.5986 (mtm-85) REVERT: T 35 TYR cc_start: 0.8852 (m-80) cc_final: 0.8290 (m-80) REVERT: T 79 LYS cc_start: 0.8012 (mmtt) cc_final: 0.7771 (mmtp) REVERT: P 35 ARG cc_start: 0.6628 (OUTLIER) cc_final: 0.4176 (tmm160) REVERT: P 68 ASP cc_start: 0.7950 (p0) cc_final: 0.6976 (m-30) REVERT: P 105 LYS cc_start: 0.8294 (mtpt) cc_final: 0.7968 (mttt) REVERT: P 151 MET cc_start: 0.7944 (mtm) cc_final: 0.7714 (mtp) REVERT: P 334 MET cc_start: 0.7917 (ttm) cc_final: 0.7599 (mtp) outliers start: 60 outliers final: 47 residues processed: 280 average time/residue: 0.3179 time to fit residues: 134.7438 Evaluate side-chains 271 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 219 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 253 SER Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 179 MET Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 5 THR Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 170 TYR Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 348 MET Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain T residue 14 THR Chi-restraints excluded: chain T residue 23 CYS Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 148 CYS Chi-restraints excluded: chain P residue 170 TYR Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 220 ILE Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 268 VAL Chi-restraints excluded: chain P residue 306 SER Chi-restraints excluded: chain P residue 336 SER Chi-restraints excluded: chain P residue 348 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 163 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 192 optimal weight: 0.8980 chunk 168 optimal weight: 0.9980 chunk 128 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 228 optimal weight: 2.9990 chunk 210 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 223 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN ** G 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.155074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.139194 restraints weight = 57929.171| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.04 r_work: 0.3484 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 2.09 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19900 Z= 0.150 Angle : 0.555 5.548 27092 Z= 0.298 Chirality : 0.047 0.158 2952 Planarity : 0.005 0.059 3460 Dihedral : 6.324 48.911 2902 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.86 % Allowed : 10.08 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -2.08 (0.16), residues: 2464 helix: -3.90 (0.34), residues: 72 sheet: -0.80 (0.16), residues: 916 loop : -1.66 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 73 TYR 0.015 0.001 TYR O 54 PHE 0.018 0.002 PHE S 70 TRP 0.018 0.001 TRP H 39 HIS 0.004 0.001 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (19860) covalent geometry : angle 0.55027 / 0.30 (27004) SS BOND : bond 0.00228 / 0.16 ( 32) SS BOND : angle 0.82110 / 0.54 ( 64) hydrogen bonds : bond 0.03349 / 2.24 ( 639) hydrogen bonds : angle 5.69463 / 3.93 ( 1824) link_NAG-ASN : bond 0.00393 / 0.20 ( 8) link_NAG-ASN : angle 2.37870 / 1.39 ( 24) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 233 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.6904 (mp0) cc_final: 0.6375 (mp0) REVERT: L 35 TYR cc_start: 0.8840 (m-80) cc_final: 0.8221 (m-80) REVERT: L 79 LYS cc_start: 0.8025 (mmtp) cc_final: 0.7699 (mmtt) REVERT: A 68 ASP cc_start: 0.7695 (p0) cc_final: 0.6361 (m-30) REVERT: A 105 LYS cc_start: 0.8256 (mtpt) cc_final: 0.7983 (mttt) REVERT: A 202 LEU cc_start: 0.8500 (tp) cc_final: 0.8300 (pp) REVERT: I 6 GLU cc_start: 0.7307 (mp0) cc_final: 0.6738 (mp0) REVERT: I 58 ARG cc_start: 0.5964 (mtm-85) cc_final: 0.5697 (mtp85) REVERT: M 35 TYR cc_start: 0.8684 (m-80) cc_final: 0.8017 (m-80) REVERT: M 66 ARG cc_start: 0.7887 (ptp90) cc_final: 0.7586 (mtm110) REVERT: M 79 LYS cc_start: 0.8043 (mmtt) cc_final: 0.7791 (mmtp) REVERT: D 68 ASP cc_start: 0.7840 (p0) cc_final: 0.6797 (m-30) REVERT: D 336 SER cc_start: 0.8068 (OUTLIER) cc_final: 0.7693 (p) REVERT: N 6 GLU cc_start: 0.7043 (mp0) cc_final: 0.6541 (mp0) REVERT: N 56 LYS cc_start: 0.7165 (tttm) cc_final: 0.6807 (tptp) REVERT: N 58 ARG cc_start: 0.6468 (mtm-85) cc_final: 0.6235 (mtm-85) REVERT: O 35 TYR cc_start: 0.8830 (m-80) cc_final: 0.8256 (m-80) REVERT: O 79 LYS cc_start: 0.8092 (mmtt) cc_final: 0.7751 (mmtp) REVERT: G 35 ARG cc_start: 0.6547 (OUTLIER) cc_final: 0.3907 (tmm160) REVERT: G 68 ASP cc_start: 0.7823 (p0) cc_final: 0.6554 (m-30) REVERT: G 105 LYS cc_start: 0.8280 (mtpt) cc_final: 0.8042 (mttt) REVERT: G 179 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.7283 (pp-130) REVERT: G 336 SER cc_start: 0.8201 (m) cc_final: 0.7768 (p) REVERT: T 35 TYR cc_start: 0.8848 (m-80) cc_final: 0.8250 (m-80) REVERT: T 79 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7801 (mmtp) REVERT: P 35 ARG cc_start: 0.6524 (OUTLIER) cc_final: 0.3965 (tmm160) REVERT: P 68 ASP cc_start: 0.7772 (p0) cc_final: 0.6655 (m-30) REVERT: P 105 LYS cc_start: 0.8336 (mtpt) cc_final: 0.8007 (mttt) REVERT: P 195 GLU cc_start: 0.8548 (OUTLIER) cc_final: 0.8290 (mt-10) REVERT: P 334 MET cc_start: 0.7910 (ttm) cc_final: 0.7523 (mtp) outliers start: 61 outliers final: 40 residues processed: 279 average time/residue: 0.3605 time to fit residues: 152.9538 Evaluate side-chains 269 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 224 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain M residue 5 THR Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 170 TYR Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 348 MET Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 148 CYS Chi-restraints excluded: chain P residue 170 TYR Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 268 VAL Chi-restraints excluded: chain P residue 295 ILE Chi-restraints excluded: chain P residue 348 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 193 optimal weight: 0.0070 chunk 236 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 127 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 34 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 159 optimal weight: 0.7980 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.154888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.138633 restraints weight = 57875.733| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.07 r_work: 0.3494 rms_B_bonded: 1.25 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19900 Z= 0.153 Angle : 0.555 7.932 27092 Z= 0.296 Chirality : 0.047 0.198 2952 Planarity : 0.005 0.075 3460 Dihedral : 6.187 48.806 2900 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 2.67 % Allowed : 10.32 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.99 (0.16), residues: 2464 helix: -3.84 (0.36), residues: 72 sheet: -0.73 (0.17), residues: 896 loop : -1.60 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 210 TYR 0.015 0.001 TYR O 54 PHE 0.018 0.002 PHE H 70 TRP 0.018 0.001 TRP H 39 HIS 0.004 0.001 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (19860) covalent geometry : angle 0.55060 / 0.29 (27004) SS BOND : bond 0.00221 / 0.16 ( 32) SS BOND : angle 0.81383 / 0.54 ( 64) hydrogen bonds : bond 0.03251 / 2.18 ( 639) hydrogen bonds : angle 5.61369 / 3.88 ( 1824) link_NAG-ASN : bond 0.00379 / 0.19 ( 8) link_NAG-ASN : angle 2.22740 / 1.30 ( 24) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 238 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.7010 (mp0) cc_final: 0.6453 (mp0) REVERT: L 35 TYR cc_start: 0.8825 (m-80) cc_final: 0.8142 (m-80) REVERT: L 79 LYS cc_start: 0.8030 (mmtp) cc_final: 0.7674 (mmtt) REVERT: A 105 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7986 (mttt) REVERT: A 202 LEU cc_start: 0.8488 (tp) cc_final: 0.8269 (pp) REVERT: I 6 GLU cc_start: 0.7361 (mp0) cc_final: 0.6784 (mp0) REVERT: I 58 ARG cc_start: 0.6284 (mtm-85) cc_final: 0.6061 (mtp85) REVERT: M 35 TYR cc_start: 0.8816 (m-80) cc_final: 0.7990 (m-80) REVERT: M 66 ARG cc_start: 0.7882 (ptp90) cc_final: 0.7561 (mtm110) REVERT: M 79 LYS cc_start: 0.8014 (mmtt) cc_final: 0.7758 (mmtp) REVERT: D 68 ASP cc_start: 0.7874 (p0) cc_final: 0.6847 (m-30) REVERT: D 336 SER cc_start: 0.8085 (OUTLIER) cc_final: 0.7748 (p) REVERT: N 6 GLU cc_start: 0.7087 (mp0) cc_final: 0.6549 (mp0) REVERT: N 56 LYS cc_start: 0.7117 (tttm) cc_final: 0.6751 (tptp) REVERT: N 81 ASP cc_start: 0.7793 (t0) cc_final: 0.7577 (t0) REVERT: O 35 TYR cc_start: 0.8776 (m-80) cc_final: 0.8139 (m-80) REVERT: O 79 LYS cc_start: 0.8103 (mmtt) cc_final: 0.7799 (mmtp) REVERT: O 82 ARG cc_start: 0.7808 (ptm160) cc_final: 0.7598 (ptp-170) REVERT: G 35 ARG cc_start: 0.6615 (OUTLIER) cc_final: 0.3949 (tmm160) REVERT: G 68 ASP cc_start: 0.7850 (p0) cc_final: 0.6518 (m-30) REVERT: G 105 LYS cc_start: 0.8278 (mtpt) cc_final: 0.8018 (mttt) REVERT: G 179 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7255 (pp-130) REVERT: G 336 SER cc_start: 0.8170 (m) cc_final: 0.7771 (p) REVERT: S 6 GLU cc_start: 0.7132 (mp0) cc_final: 0.6810 (mp0) REVERT: T 35 TYR cc_start: 0.8873 (m-80) cc_final: 0.8197 (m-80) REVERT: T 79 LYS cc_start: 0.8061 (mmtt) cc_final: 0.7799 (mmtp) REVERT: P 35 ARG cc_start: 0.6348 (OUTLIER) cc_final: 0.3752 (tmm160) REVERT: P 68 ASP cc_start: 0.7906 (p0) cc_final: 0.6840 (m-30) REVERT: P 105 LYS cc_start: 0.8269 (mtpt) cc_final: 0.7977 (mttt) outliers start: 57 outliers final: 48 residues processed: 280 average time/residue: 0.3503 time to fit residues: 150.3689 Evaluate side-chains 282 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 230 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 195 GLU Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 170 TYR Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 348 MET Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain T residue 23 CYS Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 148 CYS Chi-restraints excluded: chain P residue 170 TYR Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 268 VAL Chi-restraints excluded: chain P residue 295 ILE Chi-restraints excluded: chain P residue 306 SER Chi-restraints excluded: chain P residue 348 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 179 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 101 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 210 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 152 ASN ** G 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 30 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.138503 restraints weight = 58089.254| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 1.02 r_work: 0.3405 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 1.96 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 19900 Z= 0.153 Angle : 0.546 5.429 27092 Z= 0.290 Chirality : 0.047 0.161 2952 Planarity : 0.005 0.078 3460 Dihedral : 6.017 47.988 2900 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.63 % Allowed : 11.21 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.91 (0.16), residues: 2464 helix: -3.80 (0.36), residues: 72 sheet: -0.65 (0.17), residues: 916 loop : -1.57 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 58 TYR 0.016 0.001 TYR O 54 PHE 0.018 0.002 PHE S 70 TRP 0.017 0.001 TRP H 39 HIS 0.003 0.001 HIS G 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (19860) covalent geometry : angle 0.54145 / 0.29 (27004) SS BOND : bond 0.00209 / 0.15 ( 32) SS BOND : angle 0.78323 / 0.51 ( 64) hydrogen bonds : bond 0.03148 / 2.11 ( 639) hydrogen bonds : angle 5.51381 / 3.82 ( 1824) link_NAG-ASN : bond 0.00378 / 0.19 ( 8) link_NAG-ASN : angle 2.17023 / 1.26 ( 24) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 240 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.7103 (mp0) cc_final: 0.6482 (mp0) REVERT: L 35 TYR cc_start: 0.8809 (m-80) cc_final: 0.8091 (m-80) REVERT: A 105 LYS cc_start: 0.8221 (mtpt) cc_final: 0.7951 (mttt) REVERT: I 6 GLU cc_start: 0.7365 (mp0) cc_final: 0.6787 (mp0) REVERT: M 35 TYR cc_start: 0.8843 (m-80) cc_final: 0.7988 (m-80) REVERT: M 79 LYS cc_start: 0.8061 (mmtt) cc_final: 0.7787 (mmtp) REVERT: D 68 ASP cc_start: 0.7891 (p0) cc_final: 0.6769 (m-30) REVERT: D 336 SER cc_start: 0.8118 (OUTLIER) cc_final: 0.7814 (p) REVERT: N 6 GLU cc_start: 0.7189 (mp0) cc_final: 0.6645 (mp0) REVERT: N 56 LYS cc_start: 0.7103 (tttm) cc_final: 0.6782 (tptp) REVERT: O 35 TYR cc_start: 0.8744 (m-80) cc_final: 0.7990 (m-80) REVERT: O 79 LYS cc_start: 0.8085 (mmtt) cc_final: 0.7787 (mmtp) REVERT: G 35 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.3879 (tmm160) REVERT: G 68 ASP cc_start: 0.7787 (p0) cc_final: 0.7567 (p0) REVERT: G 105 LYS cc_start: 0.8252 (mtpt) cc_final: 0.8005 (mttt) REVERT: G 179 MET cc_start: 0.7477 (OUTLIER) cc_final: 0.7253 (pp-130) REVERT: G 336 SER cc_start: 0.8221 (OUTLIER) cc_final: 0.7853 (p) REVERT: S 6 GLU cc_start: 0.7087 (mp0) cc_final: 0.6724 (mp0) REVERT: T 35 TYR cc_start: 0.8856 (m-80) cc_final: 0.8191 (m-80) REVERT: T 79 LYS cc_start: 0.7974 (mmtt) cc_final: 0.7677 (mmtp) REVERT: P 68 ASP cc_start: 0.7935 (p0) cc_final: 0.6785 (m-30) REVERT: P 105 LYS cc_start: 0.8258 (mtpt) cc_final: 0.7953 (mttt) outliers start: 56 outliers final: 48 residues processed: 279 average time/residue: 0.3241 time to fit residues: 138.5197 Evaluate side-chains 280 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 228 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 253 SER Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 170 TYR Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 336 SER Chi-restraints excluded: chain G residue 348 MET Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain T residue 23 CYS Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 148 CYS Chi-restraints excluded: chain P residue 170 TYR Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 220 ILE Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 268 VAL Chi-restraints excluded: chain P residue 295 ILE Chi-restraints excluded: chain P residue 306 SER Chi-restraints excluded: chain P residue 348 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 219 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 185 optimal weight: 0.0170 chunk 166 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.155473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.140211 restraints weight = 57762.807| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 0.99 r_work: 0.3206 rms_B_bonded: 0.99 restraints_weight: 0.5000 r_work: 0.3108 rms_B_bonded: 1.75 restraints_weight: 0.2500 r_work (final): 0.3108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.3714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19900 Z= 0.112 Angle : 0.515 7.170 27092 Z= 0.270 Chirality : 0.046 0.151 2952 Planarity : 0.005 0.078 3460 Dihedral : 5.757 49.070 2900 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.77 % Allowed : 11.59 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.75 (0.16), residues: 2464 helix: -3.71 (0.38), residues: 72 sheet: -0.55 (0.16), residues: 956 loop : -1.47 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 58 TYR 0.011 0.001 TYR O 54 PHE 0.016 0.001 PHE S 70 TRP 0.014 0.001 TRP I 39 HIS 0.003 0.001 HIS P 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.11 (19860) covalent geometry : angle 0.51108 / 0.27 (27004) SS BOND : bond 0.00165 / 0.12 ( 32) SS BOND : angle 0.67670 / 0.43 ( 64) hydrogen bonds : bond 0.02917 / 1.96 ( 639) hydrogen bonds : angle 5.32628 / 3.70 ( 1824) link_NAG-ASN : bond 0.00251 / 0.13 ( 8) link_NAG-ASN : angle 2.05824 / 1.18 ( 24) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 248 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.7083 (mp0) cc_final: 0.6415 (mp0) REVERT: L 35 TYR cc_start: 0.8789 (m-80) cc_final: 0.7987 (m-80) REVERT: A 105 LYS cc_start: 0.8228 (mtpt) cc_final: 0.7901 (mttt) REVERT: A 266 TYR cc_start: 0.8379 (t80) cc_final: 0.8176 (t80) REVERT: I 6 GLU cc_start: 0.7348 (mp0) cc_final: 0.6712 (mp0) REVERT: I 58 ARG cc_start: 0.6469 (mtm-85) cc_final: 0.6257 (mtp85) REVERT: M 35 TYR cc_start: 0.8818 (m-80) cc_final: 0.7920 (m-80) REVERT: M 79 LYS cc_start: 0.7957 (mmtt) cc_final: 0.7691 (mmtp) REVERT: D 68 ASP cc_start: 0.7839 (p0) cc_final: 0.6730 (m-30) REVERT: D 224 ASP cc_start: 0.8213 (p0) cc_final: 0.7950 (p0) REVERT: D 336 SER cc_start: 0.8006 (OUTLIER) cc_final: 0.7699 (p) REVERT: N 6 GLU cc_start: 0.7191 (mp0) cc_final: 0.6587 (mp0) REVERT: N 56 LYS cc_start: 0.7064 (tttm) cc_final: 0.6715 (tptp) REVERT: O 35 TYR cc_start: 0.8697 (m-80) cc_final: 0.7879 (m-80) REVERT: O 79 LYS cc_start: 0.8005 (mmtt) cc_final: 0.7681 (mmtp) REVERT: G 35 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.3657 (tmm160) REVERT: G 105 LYS cc_start: 0.8258 (mtpt) cc_final: 0.7963 (mttt) REVERT: G 336 SER cc_start: 0.8107 (OUTLIER) cc_final: 0.7725 (p) REVERT: S 6 GLU cc_start: 0.7006 (mp0) cc_final: 0.6563 (mp0) REVERT: S 58 ARG cc_start: 0.6597 (mtm-85) cc_final: 0.6366 (mtm-85) REVERT: T 35 TYR cc_start: 0.8818 (m-80) cc_final: 0.8073 (m-80) REVERT: T 79 LYS cc_start: 0.7926 (mmtt) cc_final: 0.7647 (mmtp) REVERT: P 68 ASP cc_start: 0.7952 (p0) cc_final: 0.6985 (m-30) REVERT: P 105 LYS cc_start: 0.8248 (mtpt) cc_final: 0.7885 (mttt) outliers start: 59 outliers final: 53 residues processed: 290 average time/residue: 0.3073 time to fit residues: 137.6980 Evaluate side-chains 287 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 231 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain I residue 72 LEU Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 170 TYR Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 253 SER Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 336 SER Chi-restraints excluded: chain G residue 348 MET Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain T residue 23 CYS Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 148 CYS Chi-restraints excluded: chain P residue 170 TYR Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 220 ILE Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 268 VAL Chi-restraints excluded: chain P residue 295 ILE Chi-restraints excluded: chain P residue 306 SER Chi-restraints excluded: chain P residue 348 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 105 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 241 optimal weight: 0.7980 chunk 206 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.153578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.138114 restraints weight = 58202.539| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 1.01 r_work: 0.3179 rms_B_bonded: 0.99 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 1.77 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19900 Z= 0.155 Angle : 0.538 5.979 27092 Z= 0.284 Chirality : 0.047 0.152 2952 Planarity : 0.005 0.074 3460 Dihedral : 5.781 47.998 2900 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 2.77 % Allowed : 12.15 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.82 (0.16), residues: 2464 helix: -3.68 (0.38), residues: 72 sheet: -0.60 (0.16), residues: 956 loop : -1.52 (0.16), residues: 1436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 69 TYR 0.015 0.001 TYR O 54 PHE 0.018 0.002 PHE S 70 TRP 0.018 0.001 TRP H 39 HIS 0.003 0.001 HIS G 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (19860) covalent geometry : angle 0.53394 / 0.28 (27004) SS BOND : bond 0.00205 / 0.15 ( 32) SS BOND : angle 0.77088 / 0.50 ( 64) hydrogen bonds : bond 0.03079 / 2.07 ( 639) hydrogen bonds : angle 5.39547 / 3.74 ( 1824) link_NAG-ASN : bond 0.00380 / 0.19 ( 8) link_NAG-ASN : angle 2.11070 / 1.22 ( 24) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 242 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.7082 (mp0) cc_final: 0.6364 (mp0) REVERT: L 35 TYR cc_start: 0.8786 (m-80) cc_final: 0.8009 (m-80) REVERT: A 105 LYS cc_start: 0.8262 (mtpt) cc_final: 0.7911 (mttt) REVERT: A 266 TYR cc_start: 0.8500 (t80) cc_final: 0.8276 (t80) REVERT: I 6 GLU cc_start: 0.7285 (mp0) cc_final: 0.6616 (mp0) REVERT: M 35 TYR cc_start: 0.8834 (m-80) cc_final: 0.7967 (m-80) REVERT: M 79 LYS cc_start: 0.8011 (mmtt) cc_final: 0.7721 (mmtp) REVERT: D 68 ASP cc_start: 0.7963 (p0) cc_final: 0.6727 (m-30) REVERT: D 336 SER cc_start: 0.8164 (OUTLIER) cc_final: 0.7823 (p) REVERT: N 6 GLU cc_start: 0.7260 (mp0) cc_final: 0.6579 (mp0) REVERT: N 56 LYS cc_start: 0.7091 (tttm) cc_final: 0.6681 (tptp) REVERT: O 35 TYR cc_start: 0.8704 (m-80) cc_final: 0.7921 (m-80) REVERT: O 79 LYS cc_start: 0.7968 (mmtt) cc_final: 0.7633 (mmtp) REVERT: G 35 ARG cc_start: 0.6837 (OUTLIER) cc_final: 0.3631 (tmm160) REVERT: G 105 LYS cc_start: 0.8303 (mtpt) cc_final: 0.7984 (mttt) REVERT: G 336 SER cc_start: 0.8068 (OUTLIER) cc_final: 0.7691 (p) REVERT: S 6 GLU cc_start: 0.7111 (mp0) cc_final: 0.6659 (mp0) REVERT: S 58 ARG cc_start: 0.6606 (mtm-85) cc_final: 0.6317 (mtm-85) REVERT: T 35 TYR cc_start: 0.8848 (m-80) cc_final: 0.8064 (m-80) REVERT: T 79 LYS cc_start: 0.7884 (mmtt) cc_final: 0.7571 (mmtp) REVERT: P 105 LYS cc_start: 0.8292 (mtpt) cc_final: 0.7997 (mtpp) REVERT: P 253 SER cc_start: 0.8554 (t) cc_final: 0.8060 (m) outliers start: 59 outliers final: 53 residues processed: 284 average time/residue: 0.2958 time to fit residues: 129.8693 Evaluate side-chains 292 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 236 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 170 TYR Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 336 SER Chi-restraints excluded: chain G residue 348 MET Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain T residue 23 CYS Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 148 CYS Chi-restraints excluded: chain P residue 170 TYR Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 220 ILE Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 268 VAL Chi-restraints excluded: chain P residue 295 ILE Chi-restraints excluded: chain P residue 306 SER Chi-restraints excluded: chain P residue 348 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 106 optimal weight: 2.9990 chunk 204 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 210 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 231 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.151245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.135888 restraints weight = 58721.547| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 1.00 r_work: 0.3125 rms_B_bonded: 1.04 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 1.83 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19900 Z= 0.209 Angle : 0.583 5.319 27092 Z= 0.310 Chirality : 0.048 0.200 2952 Planarity : 0.005 0.074 3460 Dihedral : 6.006 50.363 2900 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.81 % Allowed : 12.29 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.97 (0.16), residues: 2464 helix: -3.73 (0.37), residues: 72 sheet: -0.60 (0.16), residues: 940 loop : -1.70 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 58 TYR 0.018 0.002 TYR O 54 PHE 0.020 0.002 PHE S 70 TRP 0.021 0.002 TRP H 39 HIS 0.004 0.001 HIS A 30 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.21 (19860) covalent geometry : angle 0.57844 / 0.31 (27004) SS BOND : bond 0.00250 / 0.17 ( 32) SS BOND : angle 0.92019 / 0.61 ( 64) hydrogen bonds : bond 0.03308 / 2.22 ( 639) hydrogen bonds : angle 5.56639 / 3.86 ( 1824) link_NAG-ASN : bond 0.00572 / 0.28 ( 8) link_NAG-ASN : angle 2.26929 / 1.33 ( 24) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 243 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.7176 (mp0) cc_final: 0.6374 (mp0) REVERT: L 35 TYR cc_start: 0.8817 (m-80) cc_final: 0.8051 (m-80) REVERT: A 105 LYS cc_start: 0.8292 (mtpt) cc_final: 0.7932 (mttt) REVERT: I 6 GLU cc_start: 0.7239 (mp0) cc_final: 0.6701 (mp0) REVERT: M 35 TYR cc_start: 0.8861 (m-80) cc_final: 0.7947 (m-80) REVERT: M 79 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7752 (mmtp) REVERT: D 68 ASP cc_start: 0.8011 (p0) cc_final: 0.6790 (m-30) REVERT: D 336 SER cc_start: 0.8179 (OUTLIER) cc_final: 0.7851 (p) REVERT: D 354 GLU cc_start: 0.7801 (mp0) cc_final: 0.7434 (pm20) REVERT: N 6 GLU cc_start: 0.7293 (mp0) cc_final: 0.6573 (mp0) REVERT: N 56 LYS cc_start: 0.7176 (tttm) cc_final: 0.6710 (tptp) REVERT: O 35 TYR cc_start: 0.8723 (m-80) cc_final: 0.7894 (m-80) REVERT: O 79 LYS cc_start: 0.8003 (mmtt) cc_final: 0.7663 (mmtp) REVERT: G 105 LYS cc_start: 0.8327 (mtpt) cc_final: 0.7995 (mttt) REVERT: G 128 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7257 (ptm) REVERT: G 336 SER cc_start: 0.8208 (OUTLIER) cc_final: 0.7843 (p) REVERT: G 354 GLU cc_start: 0.7806 (mp0) cc_final: 0.7469 (pm20) REVERT: S 6 GLU cc_start: 0.7182 (mp0) cc_final: 0.6735 (mp0) REVERT: T 35 TYR cc_start: 0.8857 (m-80) cc_final: 0.8113 (m-80) REVERT: T 79 LYS cc_start: 0.7915 (mmtt) cc_final: 0.7595 (mmtp) REVERT: P 68 ASP cc_start: 0.8106 (p0) cc_final: 0.7018 (m-30) REVERT: P 105 LYS cc_start: 0.8303 (mtpt) cc_final: 0.8005 (mtpp) REVERT: P 216 MET cc_start: 0.7848 (ptp) cc_final: 0.7361 (ptp) REVERT: P 253 SER cc_start: 0.8529 (t) cc_final: 0.8017 (m) outliers start: 60 outliers final: 56 residues processed: 285 average time/residue: 0.3355 time to fit residues: 148.0544 Evaluate side-chains 297 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 238 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 336 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain D residue 295 ILE Chi-restraints excluded: chain D residue 306 SER Chi-restraints excluded: chain D residue 336 SER Chi-restraints excluded: chain N residue 72 LEU Chi-restraints excluded: chain N residue 90 VAL Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 128 MET Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 170 TYR Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 306 SER Chi-restraints excluded: chain G residue 336 SER Chi-restraints excluded: chain G residue 348 MET Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 90 VAL Chi-restraints excluded: chain T residue 23 CYS Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 148 CYS Chi-restraints excluded: chain P residue 170 TYR Chi-restraints excluded: chain P residue 195 GLU Chi-restraints excluded: chain P residue 220 ILE Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 268 VAL Chi-restraints excluded: chain P residue 295 ILE Chi-restraints excluded: chain P residue 306 SER Chi-restraints excluded: chain P residue 348 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 156 optimal weight: 0.0970 chunk 171 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 155 optimal weight: 0.9980 chunk 1 optimal weight: 0.1980 chunk 145 optimal weight: 0.9980 chunk 70 optimal weight: 0.2980 chunk 144 optimal weight: 0.9990 chunk 192 optimal weight: 1.9990 chunk 162 optimal weight: 0.5980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.154923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.139406 restraints weight = 57918.329| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 1.01 r_work: 0.3169 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.3068 rms_B_bonded: 1.88 restraints_weight: 0.2500 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 19900 Z= 0.097 Angle : 0.512 5.365 27092 Z= 0.268 Chirality : 0.046 0.154 2952 Planarity : 0.004 0.075 3460 Dihedral : 5.687 49.584 2900 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.30 % Allowed : 12.85 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.74 (0.16), residues: 2464 helix: -3.57 (0.40), residues: 72 sheet: -0.51 (0.16), residues: 948 loop : -1.50 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 58 TYR 0.009 0.001 TYR P 156 PHE 0.015 0.001 PHE S 70 TRP 0.015 0.001 TRP H 39 HIS 0.002 0.000 HIS D 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 (19860) covalent geometry : angle 0.50747 / 0.27 (27004) SS BOND : bond 0.00144 / 0.10 ( 32) SS BOND : angle 0.73964 / 0.49 ( 64) hydrogen bonds : bond 0.02830 / 1.91 ( 639) hydrogen bonds : angle 5.28394 / 3.67 ( 1824) link_NAG-ASN : bond 0.00211 / 0.11 ( 8) link_NAG-ASN : angle 2.07506 / 1.20 ( 24) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4928 Ramachandran restraints generated. 2464 Oldfield, 0 Emsley, 2464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 243 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 6 GLU cc_start: 0.7149 (mp0) cc_final: 0.6327 (mp0) REVERT: L 35 TYR cc_start: 0.8781 (m-80) cc_final: 0.7987 (m-80) REVERT: A 105 LYS cc_start: 0.8256 (mtpt) cc_final: 0.7894 (mttt) REVERT: A 266 TYR cc_start: 0.8403 (t80) cc_final: 0.8196 (t80) REVERT: I 6 GLU cc_start: 0.7188 (mp0) cc_final: 0.6634 (mp0) REVERT: M 35 TYR cc_start: 0.8836 (m-80) cc_final: 0.7900 (m-80) REVERT: M 79 LYS cc_start: 0.8042 (mmtt) cc_final: 0.7743 (mmtp) REVERT: D 68 ASP cc_start: 0.7937 (p0) cc_final: 0.6758 (m-30) REVERT: D 224 ASP cc_start: 0.8177 (p0) cc_final: 0.7932 (p0) REVERT: D 336 SER cc_start: 0.8034 (m) cc_final: 0.7762 (p) REVERT: N 6 GLU cc_start: 0.7271 (mp0) cc_final: 0.6492 (mp0) REVERT: N 56 LYS cc_start: 0.7146 (tttm) cc_final: 0.6777 (tptp) REVERT: O 35 TYR cc_start: 0.8699 (m-80) cc_final: 0.7911 (m-80) REVERT: O 79 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7596 (mmtp) REVERT: G 35 ARG cc_start: 0.6679 (OUTLIER) cc_final: 0.3655 (tmm160) REVERT: G 105 LYS cc_start: 0.8292 (mtpt) cc_final: 0.7949 (mttt) REVERT: G 128 MET cc_start: 0.7435 (OUTLIER) cc_final: 0.7198 (ptm) REVERT: G 179 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6891 (mtt) REVERT: G 336 SER cc_start: 0.8139 (m) cc_final: 0.7800 (p) REVERT: S 6 GLU cc_start: 0.7210 (mp0) cc_final: 0.6760 (mp0) REVERT: T 35 TYR cc_start: 0.8811 (m-80) cc_final: 0.8029 (m-80) REVERT: T 79 LYS cc_start: 0.7860 (mmtt) cc_final: 0.7554 (mmtp) REVERT: P 105 LYS cc_start: 0.8304 (mtpt) cc_final: 0.8001 (mtpp) REVERT: P 216 MET cc_start: 0.7726 (ptp) cc_final: 0.7227 (ptp) REVERT: P 253 SER cc_start: 0.8461 (t) cc_final: 0.7973 (m) REVERT: P 336 SER cc_start: 0.7960 (t) cc_final: 0.7524 (p) outliers start: 49 outliers final: 43 residues processed: 279 average time/residue: 0.3231 time to fit residues: 139.4904 Evaluate side-chains 285 residues out of total 2132 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 239 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 90 VAL Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 148 CYS Chi-restraints excluded: chain A residue 170 TYR Chi-restraints excluded: chain A residue 179 MET Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 295 ILE Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 348 MET Chi-restraints excluded: chain I residue 90 VAL Chi-restraints excluded: chain M residue 23 CYS Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 18 SER Chi-restraints excluded: chain D residue 148 CYS Chi-restraints excluded: chain D residue 170 TYR Chi-restraints excluded: chain D residue 195 GLU Chi-restraints excluded: chain D residue 197 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 268 VAL Chi-restraints excluded: chain O residue 4 MET Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain O residue 80 ILE Chi-restraints excluded: chain G residue 35 ARG Chi-restraints excluded: chain G residue 128 MET Chi-restraints excluded: chain G residue 148 CYS Chi-restraints excluded: chain G residue 170 TYR Chi-restraints excluded: chain G residue 179 MET Chi-restraints excluded: chain G residue 195 GLU Chi-restraints excluded: chain G residue 197 SER Chi-restraints excluded: chain G residue 231 VAL Chi-restraints excluded: chain G residue 268 VAL Chi-restraints excluded: chain G residue 348 MET Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 72 LEU Chi-restraints excluded: chain T residue 23 CYS Chi-restraints excluded: chain P residue 12 SER Chi-restraints excluded: chain P residue 35 ARG Chi-restraints excluded: chain P residue 148 CYS Chi-restraints excluded: chain P residue 170 TYR Chi-restraints excluded: chain P residue 220 ILE Chi-restraints excluded: chain P residue 231 VAL Chi-restraints excluded: chain P residue 306 SER Chi-restraints excluded: chain P residue 348 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 35 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 94 optimal weight: 0.4980 chunk 118 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 242 optimal weight: 0.5980 chunk 156 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.154133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.138626 restraints weight = 58107.583| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.01 r_work: 0.3160 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 1.87 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19900 Z= 0.122 Angle : 0.517 5.283 27092 Z= 0.271 Chirality : 0.046 0.148 2952 Planarity : 0.004 0.076 3460 Dihedral : 5.627 49.170 2900 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.49 % Allowed : 12.85 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -1.72 (0.16), residues: 2464 helix: -3.52 (0.40), residues: 72 sheet: -0.49 (0.16), residues: 948 loop : -1.48 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 58 TYR 0.013 0.001 TYR O 54 PHE 0.016 0.001 PHE H 70 TRP 0.016 0.001 TRP H 39 HIS 0.002 0.001 HIS A 124 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (19860) covalent geometry : angle 0.51252 / 0.27 (27004) SS BOND : bond 0.00176 / 0.13 ( 32) SS BOND : angle 0.75459 / 0.51 ( 64) hydrogen bonds : bond 0.02891 / 1.94 ( 639) hydrogen bonds : angle 5.25473 / 3.65 ( 1824) link_NAG-ASN : bond 0.00254 / 0.14 ( 8) link_NAG-ASN : angle 2.02630 / 1.18 ( 24) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7958.34 seconds wall clock time: 135 minutes 51.52 seconds (8151.52 seconds total)