Starting phenix.real_space_refine on Sat Jul 4 13:22:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o9v_70264/07_2026/9o9v_70264.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o9v_70264/07_2026/9o9v_70264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9o9v_70264/07_2026/9o9v_70264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o9v_70264/07_2026/9o9v_70264.map" model { file = "/net/cci-nas-00/data/ceres_data/9o9v_70264/07_2026/9o9v_70264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o9v_70264/07_2026/9o9v_70264.cif" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 8 9.91 5 S 108 5.16 5 C 12236 2.51 5 N 3260 2.21 5 O 4742 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s 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: 20354 Number of models: 1 Model: "" Number of chains: 32 Chain: "D" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2951 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "E" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2951 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "F" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2951 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 980 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "I" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 980 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "J" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 980 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "K" Number of atoms: 2951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 383, 2951 Classifications: {'peptide': 383} Link IDs: {'PCIS': 3, 'PTRANS': 19, 'TRANS': 360} Chain: "L" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 103} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "M" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 103} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 103} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "O" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 980 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 859 Classifications: {'peptide': 112} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 103} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 28 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 2 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: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "E" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 154 Classifications: {'water': 154} Link IDs: {None: 153} Chain: "F" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "H" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "I" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "J" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "K" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 139 Classifications: {'water': 139} Link IDs: {None: 138} Chain: "L" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 39 Classifications: {'water': 39} Link IDs: {None: 38} Chain: "N" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 40 Classifications: {'water': 40} Link IDs: {None: 39} Chain: "O" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "P" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Time building chain proxies: 4.39, per 1000 atoms: 0.22 Number of scatterers: 20354 At special positions: 0 Unit cell: (139.83, 137.175, 85.845, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 8 19.99 S 108 16.00 O 4742 8.00 N 3260 7.00 C 12236 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=12, symmetry=0 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 279 " - pdb=" SG CYS D 292 " distance=2.03 Simple disulfide: pdb=" SG CYS D 281 " - pdb=" SG CYS D 290 " distance=2.03 Simple disulfide: pdb=" SG CYS E 124 " - pdb=" SG CYS E 129 " distance=2.02 Simple disulfide: pdb=" SG CYS E 279 " - pdb=" SG CYS E 292 " distance=2.03 Simple disulfide: pdb=" SG CYS E 281 " - pdb=" SG CYS E 290 " distance=2.03 Simple disulfide: pdb=" SG CYS F 124 " - pdb=" SG CYS F 129 " distance=2.04 Simple disulfide: pdb=" SG CYS F 279 " - pdb=" SG CYS F 292 " distance=2.03 Simple disulfide: pdb=" SG CYS F 281 " - pdb=" SG CYS F 290 " distance=2.03 Simple disulfide: pdb=" SG CYS K 124 " - pdb=" SG CYS K 129 " distance=2.03 Simple disulfide: pdb=" SG CYS K 279 " - pdb=" SG CYS K 292 " distance=2.04 Simple disulfide: pdb=" SG CYS K 281 " - pdb=" SG CYS K 290 " 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 BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " NAG-ASN " NAG A 1 " - " ASN D 146 " " NAG B 1 " - " ASN E 146 " " NAG C 1 " - " ASN F 146 " " NAG D 501 " - " ASN D 88 " " NAG D 502 " - " ASN D 235 " " NAG E 501 " - " ASN E 88 " " NAG E 502 " - " ASN E 235 " " NAG F 501 " - " ASN F 88 " " NAG F 502 " - " ASN F 235 " " NAG G 1 " - " ASN K 146 " " NAG K 501 " - " ASN K 88 " " NAG K 502 " - " ASN K 235 " Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 715.1 milliseconds 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4472 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 48 sheets defined 4.5% alpha, 43.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 409 through 414 Processing helix chain 'E' and resid 104 through 109 Processing helix chain 'E' and resid 142 through 146 Processing helix chain 'E' and resid 409 through 414 Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 142 through 146 Processing helix chain 'F' and resid 409 through 414 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.575A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 64 removed outlier: 3.969A pdb=" N LYS I 64 " --> pdb=" O PRO I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 83 through 87 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'K' and resid 104 through 109 Processing helix chain 'K' and resid 142 through 146 Processing helix chain 'K' and resid 409 through 414 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.766A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 83 removed outlier: 3.797A pdb=" N VAL M 83 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 79 through 83 removed outlier: 3.837A pdb=" N VAL N 83 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 87 Processing helix chain 'P' and resid 79 through 83 removed outlier: 3.827A pdb=" N VAL P 83 " --> pdb=" O ALA P 80 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.605A pdb=" N SER D 444 " --> pdb=" O LEU D 100 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N LYS D 102 " --> pdb=" O SER D 442 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N SER D 442 " --> pdb=" O LYS D 102 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 115 through 124 removed outlier: 4.664A pdb=" N PHE D 115 " --> pdb=" O ALA D 138 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ALA D 138 " --> pdb=" O PHE D 115 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N ILE D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N GLN D 136 " --> pdb=" O ILE D 117 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N THR D 157 " --> pdb=" O THR D 135 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N SER D 160 " --> pdb=" O PHE D 174 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N PHE D 174 " --> pdb=" O SER D 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 180 through 185 removed outlier: 3.521A pdb=" N SER D 180 " --> pdb=" O ILE D 195 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP D 214 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N TYR D 208 " --> pdb=" O ILE D 212 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ILE D 212 " --> pdb=" O TYR D 208 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 232 through 234 removed outlier: 6.517A pdb=" N GLU D 259 " --> pdb=" O ILE D 263 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE D 263 " --> pdb=" O GLU D 259 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 277 through 284 removed outlier: 4.788A pdb=" N CYS D 279 " --> pdb=" O VAL D 291 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N VAL D 291 " --> pdb=" O CYS D 279 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N CYS D 281 " --> pdb=" O THR D 289 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N THR D 289 " --> pdb=" O CYS D 281 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLU D 287 " --> pdb=" O PRO D 283 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 350 through 353 removed outlier: 6.669A pdb=" N ASN D 369 " --> pdb=" O GLY D 395 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLY D 395 " --> pdb=" O ASN D 369 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N PHE D 371 " --> pdb=" O ILE D 393 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 96 through 102 removed outlier: 6.617A pdb=" N SER E 444 " --> pdb=" O LEU E 100 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS E 102 " --> pdb=" O SER E 442 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N SER E 442 " --> pdb=" O LYS E 102 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 115 through 124 removed outlier: 4.674A pdb=" N PHE E 115 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N ALA E 138 " --> pdb=" O PHE E 115 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N ILE E 117 " --> pdb=" O GLN E 136 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN E 136 " --> pdb=" O ILE E 117 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N GLU E 119 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU E 134 " --> pdb=" O GLU E 119 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU E 158 " --> pdb=" O GLU E 175 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 180 through 185 removed outlier: 3.538A pdb=" N SER E 180 " --> pdb=" O ILE E 195 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N ALA E 204 " --> pdb=" O THR E 215 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR E 215 " --> pdb=" O ALA E 204 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LEU E 206 " --> pdb=" O THR E 213 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 225 through 226 removed outlier: 3.541A pdb=" N ALA E 232 " --> pdb=" O PHE E 239 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 225 through 226 removed outlier: 3.624A pdb=" N LYS E 265 " --> pdb=" O ARG E 257 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N GLU E 259 " --> pdb=" O ILE E 263 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ILE E 263 " --> pdb=" O GLU E 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 277 through 284 removed outlier: 4.976A pdb=" N CYS E 279 " --> pdb=" O VAL E 291 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL E 291 " --> pdb=" O CYS E 279 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N CYS E 281 " --> pdb=" O THR E 289 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N THR E 289 " --> pdb=" O CYS E 281 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N GLU E 287 " --> pdb=" O PRO E 283 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 350 through 353 removed outlier: 7.417A pdb=" N GLU E 398 " --> pdb=" O GLY E 370 " (cutoff:3.500A) removed outlier: 10.538A pdb=" N GLU E 372 " --> pdb=" O ILE E 396 " (cutoff:3.500A) removed outlier: 11.324A pdb=" N ILE E 396 " --> pdb=" O GLU E 372 " (cutoff:3.500A) removed outlier: 11.563A pdb=" N ILE E 374 " --> pdb=" O VAL E 394 " (cutoff:3.500A) removed outlier: 13.815A pdb=" N VAL E 394 " --> pdb=" O ILE E 374 " (cutoff:3.500A) removed outlier: 14.834A pdb=" N ASP E 376 " --> pdb=" O ASP E 392 " (cutoff:3.500A) removed outlier: 16.017A pdb=" N ASP E 392 " --> pdb=" O ASP E 376 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 96 through 103 removed outlier: 6.681A pdb=" N SER F 444 " --> pdb=" O LEU F 100 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N LYS F 102 " --> pdb=" O SER F 442 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N SER F 442 " --> pdb=" O LYS F 102 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 115 through 124 removed outlier: 5.212A pdb=" N ALA F 138 " --> pdb=" O VAL F 116 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N ARG F 118 " --> pdb=" O GLN F 136 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N GLN F 136 " --> pdb=" O ARG F 118 " (cutoff:3.500A) removed outlier: 7.246A pdb=" N LEU F 134 " --> pdb=" O PRO F 120 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE F 122 " --> pdb=" O PHE F 132 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N PHE F 132 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N CYS F 124 " --> pdb=" O ARG F 130 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ARG F 130 " --> pdb=" O CYS F 124 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR F 157 " --> pdb=" O THR F 135 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N SER F 160 " --> pdb=" O PHE F 174 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N PHE F 174 " --> pdb=" O SER F 160 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 180 through 185 removed outlier: 3.557A pdb=" N SER F 180 " --> pdb=" O ILE F 195 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP F 214 " --> pdb=" O LEU F 206 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N TYR F 208 " --> pdb=" O ILE F 212 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N ILE F 212 " --> pdb=" O TYR F 208 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 232 through 234 removed outlier: 3.567A pdb=" N ALA F 232 " --> pdb=" O PHE F 239 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS F 265 " --> pdb=" O ARG F 257 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N GLU F 259 " --> pdb=" O ILE F 263 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE F 263 " --> pdb=" O GLU F 259 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 277 through 284 removed outlier: 4.839A pdb=" N CYS F 279 " --> pdb=" O VAL F 291 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N VAL F 291 " --> pdb=" O CYS F 279 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N CYS F 281 " --> pdb=" O THR F 289 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR F 289 " --> pdb=" O CYS F 281 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N GLU F 287 " --> pdb=" O PRO F 283 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 350 through 353 removed outlier: 6.678A pdb=" N ASN F 369 " --> pdb=" O GLY F 395 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N GLY F 395 " --> pdb=" O ASN F 369 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N PHE F 371 " --> pdb=" O ILE F 393 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AC3, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.520A pdb=" N TYR H 100E" --> pdb=" O SER H 98 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 57 through 59 removed outlier: 5.374A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N VAL H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'I' and resid 3 through 7 Processing sheet with id=AC6, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.622A pdb=" N GLY I 49 " --> pdb=" O TRP I 36 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG I 38 " --> pdb=" O TRP I 47 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N TRP I 47 " --> pdb=" O ARG I 38 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 11 through 12 removed outlier: 6.803A pdb=" N CYS I 92 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL I 102 " --> pdb=" O CYS I 92 " (cutoff:3.500A) removed outlier: 6.140A pdb=" N ARG I 94 " --> pdb=" O LEU I 100I" (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU I 100I" --> pdb=" O ARG I 94 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N GLY I 96 " --> pdb=" O LEU I 100G" (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR I 100E" --> pdb=" O SER I 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AC9, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.427A pdb=" N ARG J 38 " --> pdb=" O TRP J 47 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N TRP J 47 " --> pdb=" O ARG J 38 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 11 through 12 removed outlier: 6.816A pdb=" N CYS J 92 " --> pdb=" O VAL J 102 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL J 102 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ARG J 94 " --> pdb=" O LEU J 100I" (cutoff:3.500A) removed outlier: 4.329A pdb=" N LEU J 100I" --> pdb=" O ARG J 94 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N GLY J 96 " --> pdb=" O LEU J 100G" (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR J 100E" --> pdb=" O SER J 98 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 96 through 102 removed outlier: 6.508A pdb=" N SER K 444 " --> pdb=" O LEU K 100 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N LYS K 102 " --> pdb=" O SER K 442 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N SER K 442 " --> pdb=" O LYS K 102 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 115 through 124 removed outlier: 4.719A pdb=" N PHE K 115 " --> pdb=" O ALA K 138 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ALA K 138 " --> pdb=" O PHE K 115 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ILE K 117 " --> pdb=" O GLN K 136 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN K 136 " --> pdb=" O ILE K 117 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLU K 119 " --> pdb=" O LEU K 134 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU K 134 " --> pdb=" O GLU K 119 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N THR K 157 " --> pdb=" O THR K 135 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N SER K 160 " --> pdb=" O PHE K 174 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N PHE K 174 " --> pdb=" O SER K 160 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 180 through 185 removed outlier: 3.608A pdb=" N SER K 180 " --> pdb=" O ILE K 195 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA K 204 " --> pdb=" O THR K 215 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR K 215 " --> pdb=" O ALA K 204 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LEU K 206 " --> pdb=" O THR K 213 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 232 through 234 removed outlier: 6.554A pdb=" N GLU K 259 " --> pdb=" O ILE K 263 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE K 263 " --> pdb=" O GLU K 259 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 277 through 284 removed outlier: 4.894A pdb=" N CYS K 279 " --> pdb=" O VAL K 291 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N VAL K 291 " --> pdb=" O CYS K 279 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N CYS K 281 " --> pdb=" O THR K 289 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N THR K 289 " --> pdb=" O CYS K 281 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU K 287 " --> pdb=" O PRO K 283 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'K' and resid 350 through 353 removed outlier: 6.635A pdb=" N ASN K 369 " --> pdb=" O GLY K 395 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N GLY K 395 " --> pdb=" O ASN K 369 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N PHE K 371 " --> pdb=" O ILE K 393 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AD9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.665A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU L 33 " --> pdb=" O SER L 49 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N SER L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.665A pdb=" N GLY L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 4 through 6 Processing sheet with id=AE3, first strand: chain 'M' and resid 10 through 13 removed outlier: 3.514A pdb=" N VAL M 104 " --> pdb=" O GLY M 84 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLY M 84 " --> pdb=" O VAL M 104 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N LEU M 33 " --> pdb=" O SER M 49 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N SER M 49 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP M 35 " --> pdb=" O LEU M 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 4 through 6 Processing sheet with id=AE5, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.531A pdb=" N GLY N 84 " --> pdb=" O VAL N 104 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LEU N 33 " --> pdb=" O SER N 49 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N SER N 49 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N TRP N 35 " --> pdb=" O LEU N 47 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'N' and resid 10 through 13 removed outlier: 3.531A pdb=" N GLY N 84 " --> pdb=" O VAL N 104 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N THR N 97 " --> pdb=" O GLN N 90 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 3 through 7 removed outlier: 3.594A pdb=" N GLN O 5 " --> pdb=" O SER O 23 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 11 through 12 removed outlier: 3.643A pdb=" N GLY O 49 " --> pdb=" O TRP O 36 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ARG O 38 " --> pdb=" O TRP O 47 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N TRP O 47 " --> pdb=" O ARG O 38 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'O' and resid 11 through 12 removed outlier: 6.731A pdb=" N CYS O 92 " --> pdb=" O VAL O 102 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL O 102 " --> pdb=" O CYS O 92 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N ARG O 94 " --> pdb=" O LEU O 100I" (cutoff:3.500A) removed outlier: 4.210A pdb=" N LEU O 100I" --> pdb=" O ARG O 94 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLY O 96 " --> pdb=" O LEU O 100G" (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 4 through 6 Processing sheet with id=AF2, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.541A pdb=" N GLY P 84 " --> pdb=" O VAL P 104 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU P 37 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 5.383A pdb=" N LEU P 46 " --> pdb=" O LEU P 37 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 10 through 13 removed outlier: 3.541A pdb=" N GLY P 84 " --> pdb=" O VAL P 104 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR P 97 " --> pdb=" O GLN P 90 " (cutoff:3.500A) 688 hydrogen bonds defined for protein. 1737 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: 3.61 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5205 1.33 - 1.47: 6283 1.47 - 1.60: 8316 1.60 - 1.74: 1 1.74 - 1.87: 135 Bond restraints: 19940 Sorted by residual: bond pdb=" C GLU E 462 " pdb=" N LEU E 463 " ideal model delta sigma weight residual 1.327 1.423 -0.097 1.71e-02 3.42e+03 3.19e+01 bond pdb=" C PHE N 98 " pdb=" N GLY N 99 " ideal model delta sigma weight residual 1.333 1.289 0.045 1.11e-02 8.12e+03 1.61e+01 bond pdb=" CG TYR E 253 " pdb=" CD1 TYR E 253 " ideal model delta sigma weight residual 1.389 1.469 -0.080 2.10e-02 2.27e+03 1.44e+01 bond pdb=" CE2 TYR O 34 " pdb=" CZ TYR O 34 " ideal model delta sigma weight residual 1.378 1.307 0.071 2.40e-02 1.74e+03 8.70e+00 bond pdb=" CE2 TYR I 100F" pdb=" CZ TYR I 100F" ideal model delta sigma weight residual 1.378 1.310 0.068 2.40e-02 1.74e+03 7.92e+00 ... (remaining 19935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.35: 26779 4.35 - 8.70: 339 8.70 - 13.05: 27 13.05 - 17.40: 1 17.40 - 21.75: 2 Bond angle restraints: 27148 Sorted by residual: angle pdb=" C TRP O 103 " pdb=" N GLY O 104 " pdb=" CA GLY O 104 " ideal model delta sigma weight residual 122.83 113.95 8.88 1.21e+00 6.83e-01 5.39e+01 angle pdb=" CB LEU F 100 " pdb=" CG LEU F 100 " pdb=" CD2 LEU F 100 " ideal model delta sigma weight residual 110.70 88.95 21.75 3.00e+00 1.11e-01 5.26e+01 angle pdb=" N GLY H 44 " pdb=" CA GLY H 44 " pdb=" C GLY H 44 " ideal model delta sigma weight residual 110.87 100.60 10.27 1.54e+00 4.22e-01 4.44e+01 angle pdb=" C ASN E 300 " pdb=" N ARG E 301 " pdb=" CA ARG E 301 " ideal model delta sigma weight residual 122.38 103.13 19.25 2.90e+00 1.19e-01 4.41e+01 angle pdb=" N ASN F 309 " pdb=" CA ASN F 309 " pdb=" C ASN F 309 " ideal model delta sigma weight residual 113.02 106.38 6.64 1.20e+00 6.94e-01 3.06e+01 ... (remaining 27143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.66: 10944 19.66 - 39.32: 747 39.32 - 58.97: 142 58.97 - 78.63: 58 78.63 - 98.29: 21 Dihedral angle restraints: 11912 sinusoidal: 4868 harmonic: 7044 Sorted by residual: dihedral pdb=" CA LYS J 43 " pdb=" C LYS J 43 " pdb=" N GLY J 44 " pdb=" CA GLY J 44 " ideal model delta harmonic sigma weight residual 180.00 118.85 61.15 0 5.00e+00 4.00e-02 1.50e+02 dihedral pdb=" CA ASN E 378 " pdb=" C ASN E 378 " pdb=" N GLY E 379 " pdb=" CA GLY E 379 " ideal model delta harmonic sigma weight residual -180.00 -151.13 -28.87 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA PHE O 78 " pdb=" C PHE O 78 " pdb=" N TYR O 79 " pdb=" CA TYR O 79 " ideal model delta harmonic sigma weight residual -180.00 -151.37 -28.63 0 5.00e+00 4.00e-02 3.28e+01 ... (remaining 11909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.270: 2965 0.270 - 0.540: 15 0.540 - 0.810: 3 0.810 - 1.080: 0 1.080 - 1.350: 1 Chirality restraints: 2984 Sorted by residual: chirality pdb=" CG LEU L 33 " pdb=" CB LEU L 33 " pdb=" CD1 LEU L 33 " pdb=" CD2 LEU L 33 " both_signs ideal model delta sigma weight residual False -2.59 -1.24 -1.35 2.00e-01 2.50e+01 4.56e+01 chirality pdb=" CG LEU J 18 " pdb=" CB LEU J 18 " pdb=" CD1 LEU J 18 " pdb=" CD2 LEU J 18 " both_signs ideal model delta sigma weight residual False -2.59 -1.94 -0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CG LEU E 310 " pdb=" CB LEU E 310 " pdb=" CD1 LEU E 310 " pdb=" CD2 LEU E 310 " both_signs ideal model delta sigma weight residual False -2.59 -1.99 -0.60 2.00e-01 2.50e+01 9.02e+00 ... (remaining 2981 not shown) Planarity restraints: 3484 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 70 " 0.036 2.00e-02 2.50e+03 5.67e-02 6.42e+01 pdb=" CG TYR N 70 " -0.137 2.00e-02 2.50e+03 pdb=" CD1 TYR N 70 " 0.048 2.00e-02 2.50e+03 pdb=" CD2 TYR N 70 " 0.057 2.00e-02 2.50e+03 pdb=" CE1 TYR N 70 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR N 70 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR N 70 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR N 70 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG F 173 " -0.573 9.50e-02 1.11e+02 2.61e-01 6.28e+01 pdb=" NE ARG F 173 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG F 173 " 0.089 2.00e-02 2.50e+03 pdb=" NH1 ARG F 173 " -0.023 2.00e-02 2.50e+03 pdb=" NH2 ARG F 173 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP F 380 " -0.038 2.00e-02 2.50e+03 4.51e-02 5.08e+01 pdb=" CG TRP F 380 " 0.064 2.00e-02 2.50e+03 pdb=" CD1 TRP F 380 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TRP F 380 " 0.038 2.00e-02 2.50e+03 pdb=" NE1 TRP F 380 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 380 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP F 380 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 380 " -0.065 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 380 " -0.055 2.00e-02 2.50e+03 pdb=" CH2 TRP F 380 " 0.073 2.00e-02 2.50e+03 ... (remaining 3481 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1698 2.74 - 3.28: 19104 3.28 - 3.82: 36021 3.82 - 4.36: 48972 4.36 - 4.90: 78141 Nonbonded interactions: 183936 Sorted by model distance: nonbonded pdb=" OD1 ASN F 378 " pdb="CA CA F 504 " model vdw 2.197 3.250 nonbonded pdb=" OD1 ASN D 378 " pdb="CA CA D 504 " model vdw 2.205 3.250 nonbonded pdb=" O ASP F 294 " pdb="CA CA F 503 " model vdw 2.227 3.250 nonbonded pdb=" OD1 ASP F 376 " pdb="CA CA F 504 " model vdw 2.228 3.250 nonbonded pdb=" O ASP K 294 " pdb="CA CA K 503 " model vdw 2.246 3.250 ... (remaining 183931 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 'B' selection = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' } 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: 7.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 16.830 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 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:8.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6363 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 19972 Z= 0.320 Angle : 1.240 21.751 27232 Z= 0.663 Chirality : 0.073 1.350 2984 Planarity : 0.014 0.261 3472 Dihedral : 15.246 98.291 7404 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.69 % Allowed : 4.88 % Favored : 94.43 % Rotamer: Outliers : 4.39 % Allowed : 7.06 % Favored : 88.55 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.95 (0.15), residues: 2460 helix: -1.96 (0.93), residues: 24 sheet: -0.76 (0.16), residues: 1024 loop : -1.73 (0.14), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.088 0.004 ARG J 100C TYR 0.137 0.008 TYR N 70 PHE 0.094 0.006 PHE E 465 TRP 0.100 0.010 TRP F 455 HIS 0.060 0.008 HIS K 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00689 / 0.32 (19940) covalent geometry : angle 1.22797 / 0.66 (27148) SS BOND : bond 0.00404 / 0.21 ( 12) SS BOND : angle 1.35085 / 0.79 ( 24) hydrogen bonds : bond 0.18158 / 12.12 ( 653) hydrogen bonds : angle 8.98113 / 6.22 ( 1737) link_BETA1-4 : bond 0.01619 / 0.75 ( 8) link_BETA1-4 : angle 3.85758 / 2.24 ( 24) link_NAG-ASN : bond 0.00560 / 0.35 ( 12) link_NAG-ASN : angle 3.74948 / 2.36 ( 36) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 323 time to evaluate : 0.608 Fit side-chains REVERT: D 220 ARG cc_start: 0.6263 (mmt90) cc_final: 0.4672 (mmt90) REVERT: D 277 GLU cc_start: 0.7388 (mt-10) cc_final: 0.7053 (mt-10) REVERT: D 311 GLU cc_start: 0.6212 (mt-10) cc_final: 0.5597 (mp0) REVERT: D 331 LYS cc_start: 0.6193 (pttt) cc_final: 0.5567 (ptpp) REVERT: D 430 ARG cc_start: 0.7207 (mtp85) cc_final: 0.6030 (mtm180) REVERT: D 434 ASN cc_start: 0.6981 (m110) cc_final: 0.6770 (t0) REVERT: D 462 GLU cc_start: 0.6515 (mt-10) cc_final: 0.5952 (mm-30) REVERT: E 173 ARG cc_start: 0.6032 (ptt-90) cc_final: 0.5810 (ptt180) REVERT: E 220 ARG cc_start: 0.6029 (mmt90) cc_final: 0.4582 (mmm160) REVERT: E 260 LYS cc_start: 0.6360 (mttm) cc_final: 0.5750 (mtpt) REVERT: E 309 ASN cc_start: 0.6985 (m-40) cc_final: 0.6680 (m-40) REVERT: E 311 GLU cc_start: 0.6742 (mt-10) cc_final: 0.6192 (mp0) REVERT: E 313 GLN cc_start: 0.6840 (mt0) cc_final: 0.6273 (mt0) REVERT: E 335 CYS cc_start: 0.6246 (p) cc_final: 0.5460 (m) REVERT: E 367 SER cc_start: 0.7207 (m) cc_final: 0.6705 (t) REVERT: E 378 ASN cc_start: 0.5809 (m110) cc_final: 0.5445 (m110) REVERT: E 462 GLU cc_start: 0.5930 (mt-10) cc_final: 0.5014 (tt0) REVERT: F 123 SER cc_start: 0.8142 (OUTLIER) cc_final: 0.7787 (t) REVERT: F 150 LYS cc_start: 0.6520 (tttt) cc_final: 0.6172 (tttt) REVERT: F 220 ARG cc_start: 0.6404 (mmt90) cc_final: 0.4759 (mmm-85) REVERT: F 228 GLU cc_start: 0.6472 (mm-30) cc_final: 0.6130 (mm-30) REVERT: F 462 GLU cc_start: 0.5870 (mt-10) cc_final: 0.5211 (tp30) REVERT: H 5 GLN cc_start: 0.6789 (tt0) cc_final: 0.6519 (tt0) REVERT: H 7 SER cc_start: 0.7643 (p) cc_final: 0.7238 (m) REVERT: H 76 ASN cc_start: 0.7404 (m-40) cc_final: 0.7068 (m110) REVERT: H 81 ARG cc_start: 0.7227 (ttp-170) cc_final: 0.6969 (ttp-170) REVERT: H 100 GLU cc_start: 0.5756 (mm-30) cc_final: 0.5546 (mt-10) REVERT: H 105 GLN cc_start: 0.7365 (mm110) cc_final: 0.7149 (mm110) REVERT: I 5 GLN cc_start: 0.6939 (tt0) cc_final: 0.6612 (tt0) REVERT: I 15 SER cc_start: 0.7169 (OUTLIER) cc_final: 0.6834 (p) REVERT: I 46 GLU cc_start: 0.7199 (tt0) cc_final: 0.6637 (tm-30) REVERT: I 76 ASN cc_start: 0.7318 (m-40) cc_final: 0.6941 (m110) REVERT: I 105 GLN cc_start: 0.7212 (mm110) cc_final: 0.7000 (mp-120) REVERT: I 110 THR cc_start: 0.7852 (m) cc_final: 0.7505 (p) REVERT: J 5 GLN cc_start: 0.6430 (tt0) cc_final: 0.5849 (tp40) REVERT: J 27 GLU cc_start: 0.6973 (mt-10) cc_final: 0.6301 (mt-10) REVERT: J 76 ASN cc_start: 0.7389 (m-40) cc_final: 0.6777 (m-40) REVERT: K 111 LYS cc_start: 0.6691 (tttp) cc_final: 0.6483 (tttm) REVERT: K 184 CYS cc_start: 0.7435 (OUTLIER) cc_final: 0.6850 (t) REVERT: K 260 LYS cc_start: 0.6128 (mttm) cc_final: 0.5363 (mtpp) REVERT: K 309 ASN cc_start: 0.6580 (m-40) cc_final: 0.5560 (t0) REVERT: K 313 GLN cc_start: 0.6974 (mt0) cc_final: 0.6492 (mt0) REVERT: K 331 LYS cc_start: 0.5741 (pttt) cc_final: 0.4714 (ptmt) REVERT: K 430 ARG cc_start: 0.6886 (mtp85) cc_final: 0.6617 (mtp180) REVERT: K 449 ASN cc_start: 0.7133 (t0) cc_final: 0.6918 (m-40) REVERT: K 462 GLU cc_start: 0.6399 (mp0) cc_final: 0.5327 (mm-30) REVERT: L 54 ARG cc_start: 0.7129 (ttp-110) cc_final: 0.6858 (ttp80) REVERT: L 77 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6899 (ptm160) REVERT: M 24 ARG cc_start: 0.7022 (ttm-80) cc_final: 0.6566 (ttm110) REVERT: M 27 GLN cc_start: 0.6800 (mt0) cc_final: 0.6186 (tt0) REVERT: M 52 SER cc_start: 0.7212 (m) cc_final: 0.6927 (p) REVERT: M 54 ARG cc_start: 0.7170 (ttp-110) cc_final: 0.6603 (ttp80) REVERT: M 74 LYS cc_start: 0.7281 (mttt) cc_final: 0.6720 (mtpp) REVERT: M 100 GLN cc_start: 0.6360 (mm-40) cc_final: 0.5738 (mp10) REVERT: N 38 GLN cc_start: 0.8066 (tt0) cc_final: 0.7735 (tt0) REVERT: N 45 GLN cc_start: 0.7504 (pt0) cc_final: 0.7010 (pt0) REVERT: N 54 ARG cc_start: 0.7696 (ttp-110) cc_final: 0.7160 (ttp-110) REVERT: N 67 SER cc_start: 0.6816 (p) cc_final: 0.6471 (t) REVERT: N 74 LYS cc_start: 0.7058 (mttt) cc_final: 0.6580 (mttt) REVERT: N 100 GLN cc_start: 0.7080 (mm-40) cc_final: 0.6350 (mp10) REVERT: O 5 GLN cc_start: 0.7055 (tt0) cc_final: 0.6217 (tp40) REVERT: O 81 ARG cc_start: 0.7131 (ttp-170) cc_final: 0.6375 (ttp-170) REVERT: O 82 SER cc_start: 0.7974 (m) cc_final: 0.7746 (t) REVERT: P 24 ARG cc_start: 0.7076 (ttm-80) cc_final: 0.6665 (mtt-85) REVERT: P 45 GLN cc_start: 0.7424 (pt0) cc_final: 0.7110 (pt0) REVERT: P 82 ASP cc_start: 0.6761 (m-30) cc_final: 0.6367 (m-30) REVERT: P 100 GLN cc_start: 0.7032 (mm-40) cc_final: 0.6746 (mp10) outliers start: 94 outliers final: 28 residues processed: 404 average time/residue: 0.5602 time to fit residues: 256.0819 Evaluate side-chains 284 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 252 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 297 HIS Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 253 TYR Chi-restraints excluded: chain F residue 123 SER Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain I residue 15 SER Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 94 VAL Chi-restraints excluded: chain K residue 184 CYS Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 77 ARG Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 14 THR Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 40 PRO Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 94 THR Chi-restraints excluded: chain O residue 35 THR Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 94 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 216 optimal weight: 0.0670 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 227 optimal weight: 3.9990 chunk 107 optimal weight: 0.2980 chunk 10 optimal weight: 0.0970 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 235 optimal weight: 7.9990 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 144 HIS E 144 HIS E 189 ASN E 227 GLN E 297 HIS E 369 ASN E 386 ASN F 144 HIS F 200 ASN H 5 GLN K 144 HIS K 270 ASN K 297 HIS K 369 ASN L 6 GLN L 93 GLN M 6 GLN N 6 GLN O 5 GLN O 76 ASN P 6 GLN P 38 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.143930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.116042 restraints weight = 20467.602| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 1.54 r_work: 0.3239 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19972 Z= 0.117 Angle : 0.653 10.441 27232 Z= 0.339 Chirality : 0.048 0.181 2984 Planarity : 0.005 0.059 3472 Dihedral : 9.023 64.099 3146 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.97 % Favored : 96.87 % Rotamer: Outliers : 2.85 % Allowed : 10.00 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.95 (0.16), residues: 2460 helix: -1.94 (0.79), residues: 24 sheet: -0.19 (0.16), residues: 1012 loop : -0.91 (0.15), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 430 TYR 0.014 0.001 TYR K 274 PHE 0.019 0.002 PHE H 78 TRP 0.018 0.001 TRP E 179 HIS 0.003 0.001 HIS K 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (19940) covalent geometry : angle 0.64228 / 0.34 (27148) SS BOND : bond 0.00217 / 0.13 ( 12) SS BOND : angle 0.48043 / 0.30 ( 24) hydrogen bonds : bond 0.04353 / 2.94 ( 653) hydrogen bonds : angle 6.38093 / 4.43 ( 1737) link_BETA1-4 : bond 0.00692 / 0.35 ( 8) link_BETA1-4 : angle 2.49503 / 1.57 ( 24) link_NAG-ASN : bond 0.00173 / 0.08 ( 12) link_NAG-ASN : angle 2.63097 / 1.66 ( 36) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 289 time to evaluate : 0.778 Fit side-chains REVERT: D 220 ARG cc_start: 0.8314 (mmt90) cc_final: 0.7289 (mmt90) REVERT: D 243 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8591 (m) REVERT: D 331 LYS cc_start: 0.7894 (pttt) cc_final: 0.7407 (ptpp) REVERT: D 430 ARG cc_start: 0.8064 (mtp85) cc_final: 0.7516 (mtm180) REVERT: E 220 ARG cc_start: 0.8364 (mmt90) cc_final: 0.7490 (mmm160) REVERT: E 260 LYS cc_start: 0.8738 (mttm) cc_final: 0.8465 (mtpt) REVERT: E 378 ASN cc_start: 0.7671 (m110) cc_final: 0.7373 (m110) REVERT: E 462 GLU cc_start: 0.7236 (mt-10) cc_final: 0.6846 (tt0) REVERT: F 220 ARG cc_start: 0.8550 (mmt90) cc_final: 0.7578 (mmm-85) REVERT: F 462 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7231 (tp30) REVERT: H 5 GLN cc_start: 0.7879 (tt0) cc_final: 0.7634 (tp-100) REVERT: I 3 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.7802 (mp10) REVERT: I 110 THR cc_start: 0.8392 (m) cc_final: 0.8191 (p) REVERT: J 27 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7631 (mt-10) REVERT: K 260 LYS cc_start: 0.8432 (mttm) cc_final: 0.8074 (mtpp) REVERT: K 309 ASN cc_start: 0.8271 (m-40) cc_final: 0.7814 (t0) REVERT: K 331 LYS cc_start: 0.7396 (pttt) cc_final: 0.6598 (ptmt) REVERT: N 10 SER cc_start: 0.8318 (t) cc_final: 0.8054 (t) REVERT: N 54 ARG cc_start: 0.8213 (ttp-110) cc_final: 0.7777 (ttp-110) REVERT: N 67 SER cc_start: 0.8468 (p) cc_final: 0.8194 (t) REVERT: N 100 GLN cc_start: 0.7857 (mm-40) cc_final: 0.7579 (mp10) REVERT: N 103 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.8086 (tmtm) REVERT: O 5 GLN cc_start: 0.8124 (tt0) cc_final: 0.7736 (tp40) REVERT: O 81 ARG cc_start: 0.7801 (ttp-170) cc_final: 0.7440 (ttp-170) REVERT: O 82 SER cc_start: 0.8281 (m) cc_final: 0.7888 (t) REVERT: O 83 THR cc_start: 0.8159 (t) cc_final: 0.7911 (p) REVERT: P 10 SER cc_start: 0.8488 (t) cc_final: 0.8085 (p) REVERT: P 24 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7801 (mtt-85) REVERT: P 74 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.7839 (mtmp) outliers start: 61 outliers final: 28 residues processed: 335 average time/residue: 0.5662 time to fit residues: 214.4688 Evaluate side-chains 272 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 240 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain E residue 117 ILE Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 243 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 67 SER Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 27 SER Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 74 LYS Chi-restraints excluded: chain P residue 92 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 1 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 78 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 144 HIS D 355 ASN D 369 ASN D 449 ASN E 227 GLN E 297 HIS F 313 GLN F 369 ASN H 76 ASN I 39 GLN I 76 ASN K 386 ASN O 76 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.137376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.110482 restraints weight = 20449.783| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.38 r_work: 0.3155 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.02 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8901 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19972 Z= 0.201 Angle : 0.725 9.852 27232 Z= 0.377 Chirality : 0.052 0.182 2984 Planarity : 0.006 0.051 3472 Dihedral : 7.697 59.365 3118 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.78 % Favored : 96.06 % Rotamer: Outliers : 3.46 % Allowed : 11.73 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.16), residues: 2460 helix: -1.70 (0.85), residues: 24 sheet: 0.07 (0.16), residues: 1052 loop : -0.67 (0.16), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 368 TYR 0.017 0.002 TYR H 91 PHE 0.025 0.003 PHE H 78 TRP 0.015 0.002 TRP F 179 HIS 0.005 0.001 HIS F 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (19940) covalent geometry : angle 0.71512 / 0.37 (27148) SS BOND : bond 0.00200 / 0.11 ( 12) SS BOND : angle 0.84330 / 0.55 ( 24) hydrogen bonds : bond 0.04712 / 3.18 ( 653) hydrogen bonds : angle 6.28299 / 4.38 ( 1737) link_BETA1-4 : bond 0.00710 / 0.31 ( 8) link_BETA1-4 : angle 2.54519 / 1.64 ( 24) link_NAG-ASN : bond 0.00167 / 0.10 ( 12) link_NAG-ASN : angle 2.63994 / 1.67 ( 36) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 249 time to evaluate : 0.678 Fit side-chains REVERT: D 220 ARG cc_start: 0.8377 (mmt90) cc_final: 0.7429 (mmt90) REVERT: D 311 GLU cc_start: 0.8141 (OUTLIER) cc_final: 0.7576 (mp0) REVERT: D 331 LYS cc_start: 0.7980 (pttt) cc_final: 0.7428 (ptpp) REVERT: D 430 ARG cc_start: 0.8147 (mtp85) cc_final: 0.7602 (mtm180) REVERT: E 220 ARG cc_start: 0.8381 (mmt90) cc_final: 0.7535 (mmm160) REVERT: E 260 LYS cc_start: 0.8756 (mttm) cc_final: 0.8484 (mtpt) REVERT: E 311 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8159 (mt-10) REVERT: E 378 ASN cc_start: 0.7901 (m110) cc_final: 0.7666 (m110) REVERT: E 462 GLU cc_start: 0.7463 (mt-10) cc_final: 0.6941 (tt0) REVERT: F 220 ARG cc_start: 0.8648 (mmt90) cc_final: 0.7634 (mmm160) REVERT: F 411 GLU cc_start: 0.8572 (mp0) cc_final: 0.8326 (mp0) REVERT: H 3 GLN cc_start: 0.8287 (OUTLIER) cc_final: 0.7654 (mt0) REVERT: I 110 THR cc_start: 0.8450 (m) cc_final: 0.8241 (p) REVERT: J 27 GLU cc_start: 0.7922 (mt-10) cc_final: 0.7680 (mt-10) REVERT: K 260 LYS cc_start: 0.8727 (mttm) cc_final: 0.8372 (mtpp) REVERT: N 67 SER cc_start: 0.8475 (p) cc_final: 0.8229 (t) REVERT: N 103 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8100 (tmtm) REVERT: O 5 GLN cc_start: 0.8155 (tt0) cc_final: 0.7765 (tp40) REVERT: O 81 ARG cc_start: 0.7883 (ttp-170) cc_final: 0.7557 (ttp-170) REVERT: O 82 SER cc_start: 0.8245 (m) cc_final: 0.7809 (t) REVERT: P 10 SER cc_start: 0.8580 (t) cc_final: 0.8179 (p) REVERT: P 24 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7729 (mtt-85) REVERT: P 74 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.7630 (mtmt) outliers start: 74 outliers final: 46 residues processed: 302 average time/residue: 0.5483 time to fit residues: 188.2218 Evaluate side-chains 280 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 229 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain D residue 297 HIS Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 434 ASN Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 441 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain H residue 3 GLN Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 117 ILE Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 74 LYS Chi-restraints excluded: chain P residue 92 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 83 optimal weight: 0.5980 chunk 76 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 219 optimal weight: 3.9990 chunk 127 optimal weight: 0.9980 chunk 236 optimal weight: 0.8980 chunk 77 optimal weight: 0.9980 chunk 100 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 449 ASN E 297 HIS F 313 GLN H 76 ASN I 76 ASN I 105 GLN K 270 ASN K 386 ASN K 449 ASN M 27 GLN ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN O 105 GLN P 100 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.139630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.111136 restraints weight = 20407.964| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.53 r_work: 0.3179 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8875 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19972 Z= 0.126 Angle : 0.621 10.366 27232 Z= 0.320 Chirality : 0.048 0.184 2984 Planarity : 0.004 0.042 3472 Dihedral : 6.714 57.016 3118 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.09 % Favored : 96.75 % Rotamer: Outliers : 2.99 % Allowed : 13.04 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.16), residues: 2460 helix: -1.51 (0.87), residues: 24 sheet: 0.37 (0.16), residues: 1020 loop : -0.49 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 368 TYR 0.013 0.001 TYR K 274 PHE 0.020 0.002 PHE H 78 TRP 0.014 0.002 TRP F 179 HIS 0.002 0.001 HIS P 27D Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (19940) covalent geometry : angle 0.61256 / 0.32 (27148) SS BOND : bond 0.00187 / 0.10 ( 12) SS BOND : angle 0.48618 / 0.32 ( 24) hydrogen bonds : bond 0.03839 / 2.60 ( 653) hydrogen bonds : angle 5.99080 / 4.17 ( 1737) link_BETA1-4 : bond 0.00612 / 0.28 ( 8) link_BETA1-4 : angle 2.23782 / 1.45 ( 24) link_NAG-ASN : bond 0.00185 / 0.11 ( 12) link_NAG-ASN : angle 2.29326 / 1.45 ( 36) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 243 time to evaluate : 0.649 Fit side-chains REVERT: D 220 ARG cc_start: 0.8386 (mmt90) cc_final: 0.7412 (mmt90) REVERT: D 311 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: D 331 LYS cc_start: 0.8076 (pttt) cc_final: 0.7518 (ptpp) REVERT: D 430 ARG cc_start: 0.8163 (mtp85) cc_final: 0.7628 (mtm180) REVERT: E 220 ARG cc_start: 0.8390 (mmt90) cc_final: 0.7433 (mmm160) REVERT: E 260 LYS cc_start: 0.8740 (mttm) cc_final: 0.8497 (mtpt) REVERT: E 311 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8164 (mt-10) REVERT: E 378 ASN cc_start: 0.7838 (m110) cc_final: 0.7604 (m110) REVERT: E 462 GLU cc_start: 0.7527 (mt-10) cc_final: 0.6960 (tt0) REVERT: F 220 ARG cc_start: 0.8642 (mmt90) cc_final: 0.7628 (mmm-85) REVERT: J 100 GLU cc_start: 0.7940 (mp0) cc_final: 0.7667 (mp0) REVERT: K 260 LYS cc_start: 0.8717 (mttm) cc_final: 0.8376 (mtpp) REVERT: M 100 GLN cc_start: 0.7934 (pm20) cc_final: 0.7633 (mp10) REVERT: N 67 SER cc_start: 0.8413 (p) cc_final: 0.8162 (t) REVERT: N 103 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8110 (tmtm) REVERT: O 3 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7719 (mm-40) REVERT: O 5 GLN cc_start: 0.8178 (tt0) cc_final: 0.7818 (tp40) REVERT: O 81 ARG cc_start: 0.7773 (ttp-170) cc_final: 0.7418 (ttp-170) REVERT: O 82 SER cc_start: 0.8180 (m) cc_final: 0.7777 (t) REVERT: P 10 SER cc_start: 0.8496 (t) cc_final: 0.8126 (p) REVERT: P 24 ARG cc_start: 0.8132 (ttm-80) cc_final: 0.7763 (mtt-85) REVERT: P 74 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7609 (mtmt) outliers start: 64 outliers final: 38 residues processed: 290 average time/residue: 0.5986 time to fit residues: 195.7295 Evaluate side-chains 274 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 231 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain D residue 297 HIS Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 434 ASN Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 441 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 74 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 90 optimal weight: 0.9990 chunk 236 optimal weight: 0.9980 chunk 208 optimal weight: 4.9990 chunk 232 optimal weight: 4.9990 chunk 194 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 101 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 297 HIS I 76 ASN J 40 HIS K 270 ASN K 449 ASN ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN P 100 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.139528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.111061 restraints weight = 20245.712| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 1.52 r_work: 0.3178 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8876 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19972 Z= 0.127 Angle : 0.611 10.443 27232 Z= 0.315 Chirality : 0.047 0.183 2984 Planarity : 0.004 0.036 3472 Dihedral : 6.460 58.079 3118 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.13 % Favored : 96.71 % Rotamer: Outliers : 3.36 % Allowed : 12.90 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.17), residues: 2460 helix: -1.40 (0.91), residues: 24 sheet: 0.38 (0.16), residues: 996 loop : -0.32 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 368 TYR 0.012 0.001 TYR K 274 PHE 0.020 0.002 PHE H 78 TRP 0.013 0.002 TRP F 179 HIS 0.003 0.001 HIS E 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (19940) covalent geometry : angle 0.60370 / 0.31 (27148) SS BOND : bond 0.00157 / 0.09 ( 12) SS BOND : angle 0.49877 / 0.32 ( 24) hydrogen bonds : bond 0.03767 / 2.56 ( 653) hydrogen bonds : angle 5.84639 / 4.08 ( 1737) link_BETA1-4 : bond 0.00600 / 0.27 ( 8) link_BETA1-4 : angle 1.94192 / 1.25 ( 24) link_NAG-ASN : bond 0.00274 / 0.19 ( 12) link_NAG-ASN : angle 2.22313 / 1.41 ( 36) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 236 time to evaluate : 0.667 Fit side-chains REVERT: D 220 ARG cc_start: 0.8373 (mmt90) cc_final: 0.7413 (mmt90) REVERT: D 311 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7616 (mp0) REVERT: D 331 LYS cc_start: 0.8053 (pttt) cc_final: 0.7446 (ptpp) REVERT: D 430 ARG cc_start: 0.8108 (mtp85) cc_final: 0.7610 (mtm180) REVERT: E 220 ARG cc_start: 0.8369 (mmt90) cc_final: 0.7409 (mmm160) REVERT: E 260 LYS cc_start: 0.8743 (mttm) cc_final: 0.8523 (mtpt) REVERT: E 311 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8118 (mt-10) REVERT: E 378 ASN cc_start: 0.7778 (m110) cc_final: 0.7569 (m110) REVERT: E 430 ARG cc_start: 0.8594 (mtm110) cc_final: 0.8382 (mmm160) REVERT: E 462 GLU cc_start: 0.7519 (mt-10) cc_final: 0.6932 (tt0) REVERT: F 220 ARG cc_start: 0.8613 (mmt90) cc_final: 0.7644 (mmm-85) REVERT: J 81 ARG cc_start: 0.8004 (OUTLIER) cc_final: 0.7460 (ttt-90) REVERT: J 100 GLU cc_start: 0.7881 (mp0) cc_final: 0.7452 (mp0) REVERT: K 260 LYS cc_start: 0.8724 (mttm) cc_final: 0.8383 (mtpp) REVERT: M 100 GLN cc_start: 0.7984 (pm20) cc_final: 0.7661 (mp10) REVERT: N 67 SER cc_start: 0.8445 (p) cc_final: 0.8174 (t) REVERT: N 103 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.8185 (tptm) REVERT: O 3 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7788 (mm-40) REVERT: O 5 GLN cc_start: 0.8195 (tt0) cc_final: 0.7823 (tp40) REVERT: O 82 SER cc_start: 0.8171 (m) cc_final: 0.7731 (t) REVERT: P 10 SER cc_start: 0.8515 (t) cc_final: 0.8178 (p) REVERT: P 24 ARG cc_start: 0.8124 (ttm-80) cc_final: 0.7759 (mtt-85) REVERT: P 74 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7599 (mtmt) outliers start: 72 outliers final: 49 residues processed: 289 average time/residue: 0.5615 time to fit residues: 183.9746 Evaluate side-chains 282 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 227 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain D residue 297 HIS Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 335 CYS Chi-restraints excluded: chain D residue 434 ASN Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 441 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 92 VAL Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 74 LYS Chi-restraints excluded: chain P residue 94 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 211 optimal weight: 8.9990 chunk 214 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 186 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 297 HIS I 76 ASN K 449 ASN N 100 GLN O 76 ASN O 105 GLN P 100 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.135912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.109126 restraints weight = 20417.597| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.38 r_work: 0.3132 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 19972 Z= 0.253 Angle : 0.746 9.485 27232 Z= 0.388 Chirality : 0.053 0.210 2984 Planarity : 0.005 0.051 3472 Dihedral : 7.012 59.362 3118 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.58 % Favored : 96.26 % Rotamer: Outliers : 3.69 % Allowed : 12.94 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.16), residues: 2460 helix: -1.74 (0.87), residues: 24 sheet: 0.30 (0.16), residues: 1008 loop : -0.37 (0.16), residues: 1428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 368 TYR 0.016 0.002 TYR O 91 PHE 0.025 0.003 PHE I 78 TRP 0.016 0.003 TRP F 179 HIS 0.006 0.002 HIS P 27D Details of bonding type rmsd/Z covalent geometry : bond 0.00599 / 0.25 (19940) covalent geometry : angle 0.73805 / 0.39 (27148) SS BOND : bond 0.00212 / 0.11 ( 12) SS BOND : angle 1.05571 / 0.67 ( 24) hydrogen bonds : bond 0.04711 / 3.19 ( 653) hydrogen bonds : angle 6.14699 / 4.30 ( 1737) link_BETA1-4 : bond 0.00726 / 0.28 ( 8) link_BETA1-4 : angle 2.12308 / 1.38 ( 24) link_NAG-ASN : bond 0.00341 / 0.20 ( 12) link_NAG-ASN : angle 2.61948 / 1.66 ( 36) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 222 time to evaluate : 0.707 Fit side-chains REVERT: D 220 ARG cc_start: 0.8442 (mmt90) cc_final: 0.7489 (mmt90) REVERT: D 311 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: D 331 LYS cc_start: 0.8074 (pttt) cc_final: 0.7392 (ptpp) REVERT: D 430 ARG cc_start: 0.8173 (mtp85) cc_final: 0.7622 (mtm180) REVERT: E 220 ARG cc_start: 0.8408 (mmt90) cc_final: 0.7469 (mmm160) REVERT: E 260 LYS cc_start: 0.8765 (mttm) cc_final: 0.8533 (mtpt) REVERT: E 311 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: E 462 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7107 (tt0) REVERT: F 220 ARG cc_start: 0.8671 (mmt90) cc_final: 0.7671 (mmm160) REVERT: I 66 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8387 (mtp180) REVERT: J 81 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7556 (ttt-90) REVERT: J 100 GLU cc_start: 0.7973 (mp0) cc_final: 0.7697 (mp0) REVERT: K 260 LYS cc_start: 0.8779 (mttm) cc_final: 0.8478 (mttt) REVERT: M 9 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8129 (mp) REVERT: M 100 GLN cc_start: 0.8106 (pm20) cc_final: 0.7767 (mp10) REVERT: N 103 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8204 (tptm) REVERT: O 3 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7717 (mm-40) REVERT: O 5 GLN cc_start: 0.8175 (tt0) cc_final: 0.7818 (tp40) REVERT: O 46 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8503 (tt0) REVERT: O 82 SER cc_start: 0.8342 (m) cc_final: 0.7863 (t) REVERT: P 10 SER cc_start: 0.8560 (t) cc_final: 0.8225 (p) REVERT: P 24 ARG cc_start: 0.8152 (ttm-80) cc_final: 0.7763 (mtt-85) REVERT: P 74 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.7928 (mtmp) outliers start: 79 outliers final: 53 residues processed: 275 average time/residue: 0.5744 time to fit residues: 178.4733 Evaluate side-chains 279 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 217 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 335 CYS Chi-restraints excluded: chain D residue 434 ASN Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 441 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 66 ARG Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 173 ARG Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 46 GLU Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 74 LYS Chi-restraints excluded: chain P residue 94 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 242 optimal weight: 0.9980 chunk 67 optimal weight: 0.0570 chunk 79 optimal weight: 0.9990 chunk 223 optimal weight: 0.0060 chunk 115 optimal weight: 7.9990 chunk 170 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 162 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 225 optimal weight: 0.3980 overall best weight: 0.4314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 297 HIS H 76 ASN I 76 ASN N 90 GLN ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN P 100 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.137852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.110421 restraints weight = 20584.863| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.47 r_work: 0.3150 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 19972 Z= 0.100 Angle : 0.572 10.935 27232 Z= 0.295 Chirality : 0.046 0.181 2984 Planarity : 0.004 0.036 3472 Dihedral : 6.139 59.291 3118 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.80 % Favored : 97.03 % Rotamer: Outliers : 2.62 % Allowed : 14.67 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.17), residues: 2460 helix: -1.40 (0.91), residues: 24 sheet: 0.42 (0.16), residues: 992 loop : -0.15 (0.16), residues: 1444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 430 TYR 0.011 0.001 TYR N 87 PHE 0.021 0.002 PHE N 98 TRP 0.014 0.001 TRP F 179 HIS 0.003 0.001 HIS E 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.10 (19940) covalent geometry : angle 0.56545 / 0.29 (27148) SS BOND : bond 0.00165 / 0.09 ( 12) SS BOND : angle 0.33975 / 0.23 ( 24) hydrogen bonds : bond 0.03436 / 2.34 ( 653) hydrogen bonds : angle 5.74743 / 4.01 ( 1737) link_BETA1-4 : bond 0.00589 / 0.27 ( 8) link_BETA1-4 : angle 1.64595 / 1.04 ( 24) link_NAG-ASN : bond 0.00240 / 0.15 ( 12) link_NAG-ASN : angle 2.07223 / 1.30 ( 36) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 235 time to evaluate : 0.617 Fit side-chains REVERT: D 220 ARG cc_start: 0.8365 (mmt90) cc_final: 0.7370 (mmt90) REVERT: D 311 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7514 (mp0) REVERT: D 331 LYS cc_start: 0.8031 (pttt) cc_final: 0.7365 (ptpp) REVERT: D 430 ARG cc_start: 0.8095 (mtp85) cc_final: 0.7519 (mtm180) REVERT: E 220 ARG cc_start: 0.8369 (mmt90) cc_final: 0.7421 (mmm160) REVERT: E 260 LYS cc_start: 0.8736 (mttm) cc_final: 0.8520 (mtpt) REVERT: E 311 GLU cc_start: 0.8557 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: E 462 GLU cc_start: 0.7610 (mt-10) cc_final: 0.6964 (tt0) REVERT: F 220 ARG cc_start: 0.8631 (mmt90) cc_final: 0.7616 (mmm-85) REVERT: H 27 GLU cc_start: 0.7951 (mt-10) cc_final: 0.7067 (pt0) REVERT: J 100 GLU cc_start: 0.7981 (mp0) cc_final: 0.7537 (mp0) REVERT: K 260 LYS cc_start: 0.8710 (mttm) cc_final: 0.8384 (mttt) REVERT: M 100 GLN cc_start: 0.8039 (pm20) cc_final: 0.7735 (mp10) REVERT: N 103 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8122 (tptm) REVERT: O 3 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.7529 (tm-30) REVERT: O 5 GLN cc_start: 0.8207 (tt0) cc_final: 0.7829 (tp40) REVERT: O 82 SER cc_start: 0.8248 (m) cc_final: 0.7735 (t) REVERT: P 10 SER cc_start: 0.8552 (t) cc_final: 0.8204 (p) REVERT: P 24 ARG cc_start: 0.8185 (ttm-80) cc_final: 0.7823 (mtt-85) outliers start: 56 outliers final: 36 residues processed: 274 average time/residue: 0.5765 time to fit residues: 178.3279 Evaluate side-chains 267 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 227 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 434 ASN Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 441 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 421 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 50 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 53 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 222 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 218 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 201 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 297 HIS I 76 ASN K 270 ASN N 93 GLN N 100 GLN O 40 HIS O 76 ASN P 100 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.132270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.104368 restraints weight = 20556.207| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.47 r_work: 0.3074 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 19972 Z= 0.266 Angle : 0.757 9.401 27232 Z= 0.394 Chirality : 0.054 0.204 2984 Planarity : 0.006 0.051 3472 Dihedral : 6.911 59.724 3118 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.70 % Favored : 96.14 % Rotamer: Outliers : 3.27 % Allowed : 14.25 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.16), residues: 2460 helix: -1.79 (0.86), residues: 24 sheet: 0.35 (0.17), residues: 912 loop : -0.40 (0.15), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 368 TYR 0.016 0.002 TYR O 91 PHE 0.026 0.003 PHE I 78 TRP 0.016 0.003 TRP O 35A HIS 0.007 0.002 HIS P 27D Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.27 (19940) covalent geometry : angle 0.74890 / 0.39 (27148) SS BOND : bond 0.00220 / 0.11 ( 12) SS BOND : angle 1.10995 / 0.70 ( 24) hydrogen bonds : bond 0.04789 / 3.24 ( 653) hydrogen bonds : angle 6.12877 / 4.29 ( 1737) link_BETA1-4 : bond 0.00719 / 0.28 ( 8) link_BETA1-4 : angle 2.03025 / 1.32 ( 24) link_NAG-ASN : bond 0.00389 / 0.22 ( 12) link_NAG-ASN : angle 2.63318 / 1.67 ( 36) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 222 time to evaluate : 0.731 Fit side-chains REVERT: D 220 ARG cc_start: 0.8448 (mmt90) cc_final: 0.7477 (mmt90) REVERT: D 311 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.7749 (mp0) REVERT: D 430 ARG cc_start: 0.8211 (mtp85) cc_final: 0.7584 (mtm180) REVERT: E 220 ARG cc_start: 0.8482 (mmt90) cc_final: 0.7463 (mmm160) REVERT: E 260 LYS cc_start: 0.8772 (mttm) cc_final: 0.8540 (mtpt) REVERT: E 311 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: E 462 GLU cc_start: 0.7704 (mt-10) cc_final: 0.7069 (tt0) REVERT: F 220 ARG cc_start: 0.8649 (mmt90) cc_final: 0.7613 (mmm160) REVERT: J 81 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7546 (ttt-90) REVERT: J 100 GLU cc_start: 0.8056 (mp0) cc_final: 0.7579 (mp0) REVERT: K 260 LYS cc_start: 0.8792 (mttm) cc_final: 0.8459 (mttt) REVERT: K 390 LYS cc_start: 0.8676 (tttp) cc_final: 0.8467 (ttpt) REVERT: M 9 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8099 (mp) REVERT: N 103 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8124 (tptm) REVERT: O 3 GLN cc_start: 0.8196 (OUTLIER) cc_final: 0.7786 (mm-40) REVERT: O 5 GLN cc_start: 0.8179 (tt0) cc_final: 0.7816 (tp40) REVERT: O 82 SER cc_start: 0.8363 (m) cc_final: 0.7877 (t) REVERT: P 10 SER cc_start: 0.8620 (t) cc_final: 0.8294 (p) REVERT: P 24 ARG cc_start: 0.8203 (ttm-80) cc_final: 0.7817 (mtt-85) outliers start: 70 outliers final: 46 residues processed: 271 average time/residue: 0.5925 time to fit residues: 181.1309 Evaluate side-chains 267 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 215 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 335 CYS Chi-restraints excluded: chain D residue 434 ASN Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 441 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 65 SER Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain O residue 2 VAL Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 94 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 208 optimal weight: 3.9990 chunk 213 optimal weight: 0.6980 chunk 200 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 449 ASN E 297 HIS I 76 ASN J 40 HIS K 270 ASN N 93 GLN N 100 GLN O 76 ASN P 100 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.136163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.108608 restraints weight = 20326.860| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 1.45 r_work: 0.3125 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19972 Z= 0.120 Angle : 0.603 10.461 27232 Z= 0.310 Chirality : 0.047 0.183 2984 Planarity : 0.004 0.035 3472 Dihedral : 6.244 59.916 3118 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.21 % Favored : 96.63 % Rotamer: Outliers : 2.62 % Allowed : 15.19 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.17), residues: 2460 helix: -1.53 (0.90), residues: 24 sheet: 0.42 (0.16), residues: 964 loop : -0.25 (0.16), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 368 TYR 0.012 0.001 TYR O 91 PHE 0.018 0.002 PHE J 78 TRP 0.014 0.002 TRP F 179 HIS 0.003 0.001 HIS P 27D Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (19940) covalent geometry : angle 0.59593 / 0.31 (27148) SS BOND : bond 0.00177 / 0.10 ( 12) SS BOND : angle 0.46478 / 0.31 ( 24) hydrogen bonds : bond 0.03678 / 2.50 ( 653) hydrogen bonds : angle 5.83286 / 4.07 ( 1737) link_BETA1-4 : bond 0.00559 / 0.25 ( 8) link_BETA1-4 : angle 1.65066 / 1.06 ( 24) link_NAG-ASN : bond 0.00259 / 0.15 ( 12) link_NAG-ASN : angle 2.20452 / 1.39 ( 36) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 228 time to evaluate : 0.711 Fit side-chains REVERT: D 220 ARG cc_start: 0.8392 (mmt90) cc_final: 0.7409 (mmt90) REVERT: D 311 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7613 (mp0) REVERT: D 430 ARG cc_start: 0.8113 (mtp85) cc_final: 0.7536 (mtm180) REVERT: E 220 ARG cc_start: 0.8410 (mmt90) cc_final: 0.7345 (mmm160) REVERT: E 260 LYS cc_start: 0.8744 (mttm) cc_final: 0.8542 (mtpt) REVERT: E 311 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8076 (mt-10) REVERT: E 462 GLU cc_start: 0.7633 (mt-10) cc_final: 0.6999 (tt0) REVERT: F 220 ARG cc_start: 0.8625 (mmt90) cc_final: 0.7598 (mmm-85) REVERT: J 27 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7945 (pt0) REVERT: J 100 GLU cc_start: 0.8040 (mp0) cc_final: 0.7571 (mp0) REVERT: K 260 LYS cc_start: 0.8717 (mttm) cc_final: 0.8386 (mttt) REVERT: L 24 ARG cc_start: 0.7790 (mtt-85) cc_final: 0.7420 (mtp85) REVERT: M 13 VAL cc_start: 0.8266 (OUTLIER) cc_final: 0.7840 (t) REVERT: N 103 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8117 (tptm) REVERT: O 5 GLN cc_start: 0.8132 (tt0) cc_final: 0.7769 (tp40) REVERT: O 82 SER cc_start: 0.8259 (m) cc_final: 0.7727 (t) REVERT: P 10 SER cc_start: 0.8580 (t) cc_final: 0.8257 (p) REVERT: P 24 ARG cc_start: 0.8176 (ttm-80) cc_final: 0.7807 (mtt-85) outliers start: 56 outliers final: 43 residues processed: 269 average time/residue: 0.6394 time to fit residues: 193.5490 Evaluate side-chains 268 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 335 CYS Chi-restraints excluded: chain D residue 434 ASN Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 441 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 421 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 173 ARG Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 114 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 56 optimal weight: 0.2980 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 182 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 187 optimal weight: 0.9990 chunk 52 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 297 HIS I 76 ASN K 270 ASN N 93 GLN N 100 GLN O 76 ASN O 105 GLN P 100 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.136454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.108979 restraints weight = 20518.872| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 1.45 r_work: 0.3128 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8870 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19972 Z= 0.120 Angle : 0.598 10.168 27232 Z= 0.308 Chirality : 0.047 0.184 2984 Planarity : 0.004 0.033 3472 Dihedral : 6.130 59.451 3118 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.21 % Favored : 96.63 % Rotamer: Outliers : 2.62 % Allowed : 15.23 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.17), residues: 2460 helix: -1.44 (0.91), residues: 24 sheet: 0.41 (0.17), residues: 920 loop : -0.13 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 368 TYR 0.011 0.001 TYR O 91 PHE 0.018 0.002 PHE H 78 TRP 0.014 0.002 TRP J 47 HIS 0.002 0.001 HIS P 27D Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (19940) covalent geometry : angle 0.59137 / 0.31 (27148) SS BOND : bond 0.00152 / 0.08 ( 12) SS BOND : angle 0.45762 / 0.30 ( 24) hydrogen bonds : bond 0.03642 / 2.47 ( 653) hydrogen bonds : angle 5.79596 / 4.05 ( 1737) link_BETA1-4 : bond 0.00552 / 0.24 ( 8) link_BETA1-4 : angle 1.60527 / 1.03 ( 24) link_NAG-ASN : bond 0.00225 / 0.13 ( 12) link_NAG-ASN : angle 2.15629 / 1.35 ( 36) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4920 Ramachandran restraints generated. 2460 Oldfield, 0 Emsley, 2460 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 223 time to evaluate : 0.652 Fit side-chains REVERT: D 220 ARG cc_start: 0.8388 (mmt90) cc_final: 0.7407 (mmt90) REVERT: D 311 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: D 398 GLU cc_start: 0.8510 (OUTLIER) cc_final: 0.7962 (mm-30) REVERT: D 430 ARG cc_start: 0.8112 (mtp85) cc_final: 0.7544 (mtm180) REVERT: E 220 ARG cc_start: 0.8408 (mmt90) cc_final: 0.7338 (mmm160) REVERT: E 311 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8077 (mt-10) REVERT: E 462 GLU cc_start: 0.7634 (mt-10) cc_final: 0.7003 (tt0) REVERT: F 220 ARG cc_start: 0.8609 (mmt90) cc_final: 0.7590 (mmm-85) REVERT: J 27 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7924 (pt0) REVERT: J 100 GLU cc_start: 0.8035 (mp0) cc_final: 0.7608 (mp0) REVERT: K 260 LYS cc_start: 0.8739 (mttm) cc_final: 0.8405 (mttt) REVERT: L 24 ARG cc_start: 0.7768 (mtt-85) cc_final: 0.7410 (mtp85) REVERT: M 13 VAL cc_start: 0.8278 (OUTLIER) cc_final: 0.7852 (t) REVERT: N 103 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.7884 (tmtm) REVERT: O 3 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7561 (tm-30) REVERT: O 5 GLN cc_start: 0.8161 (tt0) cc_final: 0.7788 (tp40) REVERT: O 82 SER cc_start: 0.8241 (m) cc_final: 0.7695 (t) REVERT: P 10 SER cc_start: 0.8615 (t) cc_final: 0.8293 (p) REVERT: P 24 ARG cc_start: 0.8194 (ttm-80) cc_final: 0.7825 (mtt-85) outliers start: 56 outliers final: 44 residues processed: 263 average time/residue: 0.6419 time to fit residues: 190.0099 Evaluate side-chains 270 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 220 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 117 ILE Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 273 ASN Chi-restraints excluded: chain D residue 311 GLU Chi-restraints excluded: chain D residue 335 CYS Chi-restraints excluded: chain D residue 398 GLU Chi-restraints excluded: chain D residue 434 ASN Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 441 SER Chi-restraints excluded: chain F residue 173 ARG Chi-restraints excluded: chain F residue 216 ILE Chi-restraints excluded: chain F residue 240 THR Chi-restraints excluded: chain F residue 243 THR Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 421 CYS Chi-restraints excluded: chain H residue 35 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 3 GLN Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 2 VAL Chi-restraints excluded: chain J residue 3 GLN Chi-restraints excluded: chain J residue 35 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 110 THR Chi-restraints excluded: chain K residue 153 SER Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 94 THR Chi-restraints excluded: chain M residue 13 VAL Chi-restraints excluded: chain M residue 50 PHE Chi-restraints excluded: chain M residue 92 VAL Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain N residue 23 CYS Chi-restraints excluded: chain N residue 50 PHE Chi-restraints excluded: chain N residue 100 GLN Chi-restraints excluded: chain N residue 103 LYS Chi-restraints excluded: chain O residue 3 GLN Chi-restraints excluded: chain O residue 56 SER Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 50 PHE Chi-restraints excluded: chain P residue 94 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 235 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 187 optimal weight: 0.5980 chunk 180 optimal weight: 4.9990 chunk 141 optimal weight: 2.9990 chunk 164 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 236 optimal weight: 0.7980 chunk 170 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 76 ASN N 93 GLN N 100 GLN O 76 ASN P 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.134814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107706 restraints weight = 20358.614| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.43 r_work: 0.3115 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8886 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 19972 Z= 0.165 Angle : 0.644 10.116 27232 Z= 0.333 Chirality : 0.048 0.182 2984 Planarity : 0.005 0.033 3472 Dihedral : 6.306 58.559 3118 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.17 % Favored : 96.67 % Rotamer: Outliers : 2.71 % Allowed : 15.23 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.57 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.17), residues: 2460 helix: -1.52 (0.91), residues: 24 sheet: 0.46 (0.16), residues: 952 loop : -0.23 (0.16), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 368 TYR 0.013 0.001 TYR O 91 PHE 0.022 0.002 PHE H 78 TRP 0.014 0.002 TRP J 47 HIS 0.004 0.001 HIS P 27D Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.16 (19940) covalent geometry : angle 0.63786 / 0.33 (27148) SS BOND : bond 0.00167 / 0.09 ( 12) SS BOND : angle 0.66639 / 0.43 ( 24) hydrogen bonds : bond 0.04012 / 2.72 ( 653) hydrogen bonds : angle 5.88205 / 4.11 ( 1737) link_BETA1-4 : bond 0.00582 / 0.24 ( 8) link_BETA1-4 : angle 1.66058 / 1.07 ( 24) link_NAG-ASN : bond 0.00285 / 0.16 ( 12) link_NAG-ASN : angle 2.27993 / 1.43 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6588.50 seconds wall clock time: 113 minutes 17.00 seconds (6797.00 seconds total)