Starting phenix.real_space_refine on Thu Feb 5 23:07:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9o9v_70264/02_2026/9o9v_70264.cif Found real_map, /net/cci-nas-00/data/ceres_data/9o9v_70264/02_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_70264/02_2026/9o9v_70264.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9o9v_70264/02_2026/9o9v_70264.map" model { file = "/net/cci-nas-00/data/ceres_data/9o9v_70264/02_2026/9o9v_70264.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9o9v_70264/02_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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, 30 Unusual residues: {' CA': 2, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 5.23, per 1000 atoms: 0.26 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: 1.76 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.03 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: 4.98 Time building geometry restraints manager: 2.29 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 2.510 nonbonded pdb=" OD1 ASN D 378 " pdb="CA CA D 504 " model vdw 2.205 2.510 nonbonded pdb=" O ASP F 294 " pdb="CA CA F 503 " model vdw 2.227 2.510 nonbonded pdb=" OD1 ASP F 376 " pdb="CA CA F 504 " model vdw 2.228 2.510 nonbonded pdb=" O ASP K 294 " pdb="CA CA K 503 " model vdw 2.246 2.510 ... (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: 8.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.200 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6215 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 covalent geometry : bond 0.00689 (19940) covalent geometry : angle 1.22797 (27148) SS BOND : bond 0.00404 ( 12) SS BOND : angle 1.35085 ( 24) hydrogen bonds : bond 0.18158 ( 653) hydrogen bonds : angle 8.98113 ( 1737) link_BETA1-4 : bond 0.01619 ( 8) link_BETA1-4 : angle 3.85758 ( 24) link_NAG-ASN : bond 0.00560 ( 12) link_NAG-ASN : angle 3.74948 ( 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 : 0.825 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: 0.6545 time to fit residues: 297.9841 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 : 0.819 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: D 144 HIS E 144 HIS E 189 ASN E 227 GLN 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: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.143949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.116101 restraints weight = 20582.969| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.54 r_work: 0.3242 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.1454 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= 0.116 Angle : 0.644 10.417 27232 Z= 0.334 Chirality : 0.048 0.184 2984 Planarity : 0.005 0.060 3472 Dihedral : 8.915 62.861 3146 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.72 % Favored : 97.11 % Rotamer: Outliers : 2.99 % Allowed : 9.86 % 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: -0.89 (0.16), residues: 2460 helix: -1.94 (0.78), residues: 24 sheet: -0.11 (0.16), residues: 1040 loop : -0.91 (0.15), residues: 1396 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 0.020 0.002 PHE I 78 TRP 0.017 0.002 TRP E 179 HIS 0.004 0.001 HIS O 40 Details of bonding type rmsd covalent geometry : bond 0.00245 (19940) covalent geometry : angle 0.63340 (27148) SS BOND : bond 0.00197 ( 12) SS BOND : angle 0.42008 ( 24) hydrogen bonds : bond 0.04272 ( 653) hydrogen bonds : angle 6.37292 ( 1737) link_BETA1-4 : bond 0.00678 ( 8) link_BETA1-4 : angle 2.50690 ( 24) link_NAG-ASN : bond 0.00199 ( 12) link_NAG-ASN : angle 2.62242 ( 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 353 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 289 time to evaluate : 0.839 Fit side-chains REVERT: D 220 ARG cc_start: 0.8294 (mmt90) cc_final: 0.7272 (mmt90) REVERT: D 243 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8584 (m) REVERT: D 331 LYS cc_start: 0.7900 (pttt) cc_final: 0.7409 (ptpp) REVERT: D 430 ARG cc_start: 0.8066 (mtp85) cc_final: 0.7517 (mtm180) REVERT: E 220 ARG cc_start: 0.8376 (mmt90) cc_final: 0.7499 (mmm160) REVERT: E 260 LYS cc_start: 0.8734 (mttm) cc_final: 0.8468 (mtpt) REVERT: E 378 ASN cc_start: 0.7688 (m110) cc_final: 0.7398 (m110) REVERT: E 462 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6875 (tt0) REVERT: F 220 ARG cc_start: 0.8571 (mmt90) cc_final: 0.7636 (mmm-85) REVERT: F 462 GLU cc_start: 0.7432 (mt-10) cc_final: 0.7231 (tp30) REVERT: H 5 GLN cc_start: 0.7897 (tt0) cc_final: 0.7643 (tp-100) REVERT: I 3 GLN cc_start: 0.8386 (OUTLIER) cc_final: 0.7781 (mp10) REVERT: I 110 THR cc_start: 0.8380 (m) cc_final: 0.8178 (p) REVERT: J 27 GLU cc_start: 0.7887 (mt-10) cc_final: 0.7625 (mt-10) REVERT: K 260 LYS cc_start: 0.8436 (mttm) cc_final: 0.8082 (mtpp) REVERT: K 309 ASN cc_start: 0.8270 (m-40) cc_final: 0.7821 (t0) REVERT: K 331 LYS cc_start: 0.7399 (pttt) cc_final: 0.6600 (ptmt) REVERT: N 10 SER cc_start: 0.8300 (t) cc_final: 0.8079 (t) REVERT: N 67 SER cc_start: 0.8447 (p) cc_final: 0.8183 (t) REVERT: N 100 GLN cc_start: 0.7851 (mm-40) cc_final: 0.7608 (mp10) REVERT: N 103 LYS cc_start: 0.8386 (OUTLIER) cc_final: 0.8083 (tmtm) REVERT: O 5 GLN cc_start: 0.8132 (tt0) cc_final: 0.7736 (tp40) REVERT: O 81 ARG cc_start: 0.7814 (ttp-170) cc_final: 0.7423 (ttp-170) REVERT: O 82 SER cc_start: 0.8257 (m) cc_final: 0.7855 (t) REVERT: O 83 THR cc_start: 0.8137 (t) cc_final: 0.7903 (p) REVERT: P 10 SER cc_start: 0.8487 (t) cc_final: 0.8084 (p) REVERT: P 24 ARG cc_start: 0.8171 (ttm-80) cc_final: 0.7796 (mtt-85) REVERT: P 74 LYS cc_start: 0.8391 (OUTLIER) cc_final: 0.7801 (mtmp) outliers start: 64 outliers final: 31 residues processed: 337 average time/residue: 0.7029 time to fit residues: 266.4850 Evaluate side-chains 276 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 241 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 216 ILE Chi-restraints excluded: chain D residue 243 THR Chi-restraints excluded: chain D residue 297 HIS 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 65 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 K residue 297 HIS 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: 0.9990 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 184 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 144 HIS D 355 ASN D 449 ASN E 227 GLN E 297 HIS F 313 GLN I 39 GLN I 76 ASN N 27 GLN O 76 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.138149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110998 restraints weight = 20565.831| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.47 r_work: 0.3160 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19972 Z= 0.168 Angle : 0.684 9.291 27232 Z= 0.355 Chirality : 0.050 0.186 2984 Planarity : 0.005 0.049 3472 Dihedral : 7.431 58.834 3120 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.58 % Favored : 96.26 % Rotamer: Outliers : 3.22 % Allowed : 11.87 % Favored : 84.91 % 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: -0.51 (0.16), residues: 2460 helix: -1.53 (0.88), residues: 24 sheet: 0.12 (0.16), residues: 1048 loop : -0.63 (0.16), residues: 1388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 368 TYR 0.016 0.002 TYR K 274 PHE 0.025 0.003 PHE H 78 TRP 0.014 0.002 TRP F 179 HIS 0.024 0.002 HIS K 297 Details of bonding type rmsd covalent geometry : bond 0.00385 (19940) covalent geometry : angle 0.67467 (27148) SS BOND : bond 0.00173 ( 12) SS BOND : angle 0.73315 ( 24) hydrogen bonds : bond 0.04446 ( 653) hydrogen bonds : angle 6.18970 ( 1737) link_BETA1-4 : bond 0.00746 ( 8) link_BETA1-4 : angle 2.47710 ( 24) link_NAG-ASN : bond 0.00145 ( 12) link_NAG-ASN : angle 2.50291 ( 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 321 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 252 time to evaluate : 0.828 Fit side-chains REVERT: D 220 ARG cc_start: 0.8357 (mmt90) cc_final: 0.7395 (mmt90) REVERT: D 311 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: D 331 LYS cc_start: 0.7969 (pttt) cc_final: 0.7439 (ptpp) REVERT: D 430 ARG cc_start: 0.8118 (mtp85) cc_final: 0.7595 (mtm180) REVERT: E 220 ARG cc_start: 0.8395 (mmt90) cc_final: 0.7528 (mmm160) REVERT: E 260 LYS cc_start: 0.8760 (mttm) cc_final: 0.8487 (mtpt) REVERT: E 311 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: E 378 ASN cc_start: 0.7872 (m110) cc_final: 0.7647 (m110) REVERT: E 462 GLU cc_start: 0.7383 (mt-10) cc_final: 0.6882 (tt0) REVERT: F 220 ARG cc_start: 0.8620 (mmt90) cc_final: 0.7625 (mmm-85) REVERT: F 411 GLU cc_start: 0.8576 (mp0) cc_final: 0.8331 (mp0) REVERT: H 3 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.7657 (mt0) REVERT: J 27 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7642 (mt-10) REVERT: K 260 LYS cc_start: 0.8714 (mttm) cc_final: 0.8366 (mtpp) REVERT: N 67 SER cc_start: 0.8460 (p) cc_final: 0.8228 (t) REVERT: N 103 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8121 (tmtm) REVERT: O 5 GLN cc_start: 0.8140 (tt0) cc_final: 0.7789 (tp40) REVERT: O 81 ARG cc_start: 0.7893 (ttp-170) cc_final: 0.7528 (ttp-170) REVERT: O 82 SER cc_start: 0.8222 (m) cc_final: 0.7765 (t) REVERT: P 24 ARG cc_start: 0.8119 (ttm-80) cc_final: 0.7732 (mtt-85) REVERT: P 74 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7644 (mtmt) outliers start: 69 outliers final: 43 residues processed: 303 average time/residue: 0.7045 time to fit residues: 240.1539 Evaluate side-chains 282 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 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 110 THR 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 75 ILE 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: 1.9990 chunk 76 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 107 optimal weight: 0.0870 chunk 96 optimal weight: 0.6980 chunk 219 optimal weight: 2.9990 chunk 127 optimal weight: 4.9990 chunk 236 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 100 optimal weight: 0.1980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 449 ASN E 297 HIS F 313 GLN H 76 ASN I 76 ASN K 270 ASN K 449 ASN M 27 GLN ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN P 100 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.141768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.113873 restraints weight = 20650.878| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.52 r_work: 0.3214 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8692 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19972 Z= 0.101 Angle : 0.574 9.517 27232 Z= 0.296 Chirality : 0.046 0.183 2984 Planarity : 0.004 0.041 3472 Dihedral : 6.243 57.667 3118 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.48 % Favored : 97.36 % Rotamer: Outliers : 2.99 % Allowed : 12.57 % Favored : 84.44 % 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: -0.13 (0.17), residues: 2460 helix: -1.42 (0.88), residues: 24 sheet: 0.40 (0.16), residues: 1036 loop : -0.39 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 430 TYR 0.011 0.001 TYR K 274 PHE 0.017 0.002 PHE J 78 TRP 0.012 0.001 TRP F 179 HIS 0.006 0.001 HIS K 297 Details of bonding type rmsd covalent geometry : bond 0.00217 (19940) covalent geometry : angle 0.56662 (27148) SS BOND : bond 0.00160 ( 12) SS BOND : angle 0.35557 ( 24) hydrogen bonds : bond 0.03469 ( 653) hydrogen bonds : angle 5.85223 ( 1737) link_BETA1-4 : bond 0.00479 ( 8) link_BETA1-4 : angle 2.04052 ( 24) link_NAG-ASN : bond 0.00209 ( 12) link_NAG-ASN : angle 2.11084 ( 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 316 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 252 time to evaluate : 0.787 Fit side-chains REVERT: D 220 ARG cc_start: 0.8328 (mmt90) cc_final: 0.7340 (mmt90) REVERT: D 331 LYS cc_start: 0.7998 (pttt) cc_final: 0.7457 (ptpp) REVERT: D 430 ARG cc_start: 0.8135 (mtp85) cc_final: 0.7617 (mtm180) REVERT: E 220 ARG cc_start: 0.8353 (mmt90) cc_final: 0.7392 (mmm160) REVERT: E 260 LYS cc_start: 0.8766 (mttm) cc_final: 0.8482 (mttt) REVERT: E 311 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8131 (mt-10) REVERT: E 462 GLU cc_start: 0.7417 (mt-10) cc_final: 0.6874 (tt0) REVERT: F 220 ARG cc_start: 0.8609 (mmt90) cc_final: 0.7601 (mmm-85) REVERT: J 81 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7402 (ttt-90) REVERT: J 100 GLU cc_start: 0.7854 (mp0) cc_final: 0.7470 (mp0) REVERT: K 260 LYS cc_start: 0.8700 (mttm) cc_final: 0.8348 (mtpp) REVERT: N 67 SER cc_start: 0.8390 (p) cc_final: 0.8156 (t) REVERT: N 103 LYS cc_start: 0.8533 (OUTLIER) cc_final: 0.8062 (tmtm) REVERT: O 5 GLN cc_start: 0.8094 (tt0) cc_final: 0.7769 (tp40) REVERT: O 82 SER cc_start: 0.8125 (m) cc_final: 0.7707 (t) REVERT: P 10 SER cc_start: 0.8464 (t) cc_final: 0.8105 (p) REVERT: P 24 ARG cc_start: 0.8153 (ttm-80) cc_final: 0.7776 (mtt-85) REVERT: P 74 LYS cc_start: 0.8320 (OUTLIER) cc_final: 0.7596 (mtmt) outliers start: 64 outliers final: 36 residues processed: 301 average time/residue: 0.6894 time to fit residues: 233.7129 Evaluate side-chains 271 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 231 time to evaluate : 0.825 ------------------------------------------------------------------------------- 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 434 ASN 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 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 35 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain J residue 81 ARG Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain K residue 297 HIS 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 75 ILE 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 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: 4.9990 chunk 236 optimal weight: 2.9990 chunk 208 optimal weight: 2.9990 chunk 232 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 50 optimal weight: 0.0980 chunk 15 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 151 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 369 ASN E 297 HIS F 369 ASN I 76 ASN K 449 ASN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3597 r_free = 0.3597 target = 0.135703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.108661 restraints weight = 20488.014| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.56 r_work: 0.3119 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 19972 Z= 0.254 Angle : 0.747 8.851 27232 Z= 0.389 Chirality : 0.053 0.211 2984 Planarity : 0.006 0.054 3472 Dihedral : 6.930 59.500 3116 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.37 % Favored : 96.46 % Rotamer: Outliers : 4.11 % Allowed : 12.52 % Favored : 83.36 % 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: -0.27 (0.16), residues: 2460 helix: -1.73 (0.87), residues: 24 sheet: 0.31 (0.16), residues: 960 loop : -0.45 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 368 TYR 0.018 0.002 TYR O 91 PHE 0.026 0.003 PHE I 78 TRP 0.017 0.003 TRP F 179 HIS 0.013 0.002 HIS K 297 Details of bonding type rmsd covalent geometry : bond 0.00599 (19940) covalent geometry : angle 0.73826 (27148) SS BOND : bond 0.00201 ( 12) SS BOND : angle 1.06527 ( 24) hydrogen bonds : bond 0.04776 ( 653) hydrogen bonds : angle 6.18333 ( 1737) link_BETA1-4 : bond 0.00716 ( 8) link_BETA1-4 : angle 2.22036 ( 24) link_NAG-ASN : bond 0.00277 ( 12) link_NAG-ASN : angle 2.61078 ( 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 323 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 235 time to evaluate : 0.834 Fit side-chains REVERT: D 220 ARG cc_start: 0.8444 (mmt90) cc_final: 0.7488 (mmt90) REVERT: D 311 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: D 331 LYS cc_start: 0.8091 (pttt) cc_final: 0.7385 (ptpp) REVERT: D 430 ARG cc_start: 0.8151 (mtp85) cc_final: 0.7630 (mtm180) REVERT: E 220 ARG cc_start: 0.8415 (mmt90) cc_final: 0.7448 (mmm160) REVERT: E 260 LYS cc_start: 0.8781 (mttm) cc_final: 0.8528 (mtpt) REVERT: E 311 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8154 (mt-10) REVERT: E 462 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7044 (tt0) REVERT: F 220 ARG cc_start: 0.8667 (mmt90) cc_final: 0.7661 (mmm160) REVERT: H 3 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7749 (mt0) REVERT: I 66 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8380 (mtp180) REVERT: J 27 GLU cc_start: 0.8025 (mt-10) cc_final: 0.7581 (pt0) REVERT: J 81 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7532 (ttt-90) REVERT: K 260 LYS cc_start: 0.8791 (mttm) cc_final: 0.8474 (mttt) REVERT: M 9 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.8040 (mp) REVERT: M 39 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8227 (mttt) REVERT: N 103 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8041 (tmtm) REVERT: O 3 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7817 (mm-40) REVERT: O 5 GLN cc_start: 0.8259 (tt0) cc_final: 0.7852 (tp40) REVERT: O 82 SER cc_start: 0.8297 (m) cc_final: 0.7818 (t) REVERT: P 10 SER cc_start: 0.8559 (t) cc_final: 0.8191 (p) REVERT: P 22 SER cc_start: 0.8972 (OUTLIER) cc_final: 0.8758 (m) REVERT: P 24 ARG cc_start: 0.8157 (ttm-80) cc_final: 0.7757 (mtt-85) REVERT: P 74 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7683 (mtmt) outliers start: 88 outliers final: 55 residues processed: 295 average time/residue: 0.6506 time to fit residues: 215.8760 Evaluate side-chains 291 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 225 time to evaluate : 0.875 ------------------------------------------------------------------------------- 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 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 243 THR Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 441 SER Chi-restraints excluded: chain E residue 450 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 266 SER Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 450 SER 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 66 ARG Chi-restraints excluded: chain I residue 83 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 63 SER Chi-restraints excluded: chain L residue 65 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 22 SER Chi-restraints excluded: chain M residue 39 LYS 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 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 9 LEU Chi-restraints excluded: chain P residue 22 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 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: 0.2980 chunk 214 optimal weight: 0.0970 chunk 91 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 229 optimal weight: 0.8980 chunk 186 optimal weight: 0.9980 chunk 239 optimal weight: 3.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 297 HIS H 76 ASN I 76 ASN K 449 ASN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.140529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.112576 restraints weight = 20416.035| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.51 r_work: 0.3195 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.12 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 19972 Z= 0.106 Angle : 0.580 10.157 27232 Z= 0.299 Chirality : 0.046 0.184 2984 Planarity : 0.004 0.036 3472 Dihedral : 6.178 59.973 3116 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.68 % Favored : 97.15 % Rotamer: Outliers : 2.94 % Allowed : 13.79 % Favored : 83.27 % 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: -0.02 (0.17), residues: 2460 helix: -1.50 (0.88), residues: 24 sheet: 0.42 (0.16), residues: 1016 loop : -0.24 (0.16), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 430 TYR 0.011 0.001 TYR O 91 PHE 0.018 0.002 PHE J 78 TRP 0.014 0.001 TRP F 179 HIS 0.002 0.001 HIS D 297 Details of bonding type rmsd covalent geometry : bond 0.00229 (19940) covalent geometry : angle 0.57326 (27148) SS BOND : bond 0.00160 ( 12) SS BOND : angle 0.34728 ( 24) hydrogen bonds : bond 0.03544 ( 653) hydrogen bonds : angle 5.82601 ( 1737) link_BETA1-4 : bond 0.00539 ( 8) link_BETA1-4 : angle 1.73810 ( 24) link_NAG-ASN : bond 0.00384 ( 12) link_NAG-ASN : angle 2.11706 ( 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 303 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 240 time to evaluate : 0.831 Fit side-chains revert: symmetry clash REVERT: D 220 ARG cc_start: 0.8389 (mmt90) cc_final: 0.7416 (mmt90) REVERT: D 311 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7591 (mp0) REVERT: D 430 ARG cc_start: 0.8120 (mtp85) cc_final: 0.7616 (mtm180) REVERT: E 220 ARG cc_start: 0.8361 (mmt90) cc_final: 0.7376 (mmm160) REVERT: E 260 LYS cc_start: 0.8766 (mttm) cc_final: 0.8556 (mtpt) REVERT: E 311 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: E 462 GLU cc_start: 0.7604 (mt-10) cc_final: 0.6964 (tt0) REVERT: F 220 ARG cc_start: 0.8627 (mmt90) cc_final: 0.7652 (mmm-85) REVERT: I 66 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8332 (mtp180) REVERT: J 27 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7653 (pt0) REVERT: J 100 GLU cc_start: 0.7967 (mp0) cc_final: 0.7558 (mp0) REVERT: K 260 LYS cc_start: 0.8719 (mttm) cc_final: 0.8428 (mttt) REVERT: M 100 GLN cc_start: 0.7863 (mp10) cc_final: 0.7628 (mp10) REVERT: N 67 SER cc_start: 0.8407 (p) cc_final: 0.8147 (t) REVERT: N 103 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8199 (tptm) REVERT: O 3 GLN cc_start: 0.8221 (OUTLIER) cc_final: 0.7783 (mm-40) REVERT: O 5 GLN cc_start: 0.8164 (tt0) cc_final: 0.7851 (tp40) REVERT: O 82 SER cc_start: 0.8256 (m) cc_final: 0.7788 (t) REVERT: P 10 SER cc_start: 0.8490 (t) cc_final: 0.8163 (p) REVERT: P 22 SER cc_start: 0.8980 (OUTLIER) cc_final: 0.8777 (m) REVERT: P 24 ARG cc_start: 0.8141 (ttm-80) cc_final: 0.7769 (mtt-85) outliers start: 63 outliers final: 40 residues processed: 287 average time/residue: 0.6411 time to fit residues: 207.1757 Evaluate side-chains 272 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 226 time to evaluate : 0.651 ------------------------------------------------------------------------------- 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 434 ASN Chi-restraints excluded: chain E residue 173 ARG 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 216 ILE 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 66 ARG Chi-restraints excluded: chain I residue 112 SER Chi-restraints excluded: chain J residue 2 VAL 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 K residue 297 HIS 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 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 22 SER Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 50 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 242 optimal weight: 4.9990 chunk 67 optimal weight: 0.2980 chunk 79 optimal weight: 0.8980 chunk 223 optimal weight: 0.8980 chunk 115 optimal weight: 8.9990 chunk 170 optimal weight: 6.9990 chunk 31 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 63 optimal weight: 0.9980 chunk 225 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 297 HIS I 76 ASN K 270 ASN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 100 GLN 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 = 0.3644 r_free = 0.3644 target = 0.139772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.111658 restraints weight = 20517.828| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.52 r_work: 0.3187 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2474 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= 0.118 Angle : 0.588 9.791 27232 Z= 0.304 Chirality : 0.046 0.184 2984 Planarity : 0.004 0.035 3472 Dihedral : 6.022 59.877 3116 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.25 % Favored : 96.59 % Rotamer: Outliers : 3.13 % Allowed : 13.79 % Favored : 83.08 % 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: 0.07 (0.17), residues: 2460 helix: -1.38 (0.92), residues: 24 sheet: 0.48 (0.17), residues: 972 loop : -0.16 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 368 TYR 0.011 0.001 TYR K 274 PHE 0.020 0.002 PHE H 78 TRP 0.012 0.001 TRP I 47 HIS 0.002 0.001 HIS E 297 Details of bonding type rmsd covalent geometry : bond 0.00264 (19940) covalent geometry : angle 0.58209 (27148) SS BOND : bond 0.00139 ( 12) SS BOND : angle 0.49431 ( 24) hydrogen bonds : bond 0.03632 ( 653) hydrogen bonds : angle 5.77653 ( 1737) link_BETA1-4 : bond 0.00579 ( 8) link_BETA1-4 : angle 1.63700 ( 24) link_NAG-ASN : bond 0.00308 ( 12) link_NAG-ASN : angle 2.07690 ( 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 303 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 236 time to evaluate : 0.872 Fit side-chains REVERT: D 220 ARG cc_start: 0.8381 (mmt90) cc_final: 0.7422 (mmt90) REVERT: D 311 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7554 (mp0) REVERT: D 331 LYS cc_start: 0.8062 (pttt) cc_final: 0.7354 (ptpp) REVERT: D 430 ARG cc_start: 0.8086 (mtp85) cc_final: 0.7526 (mtm180) REVERT: E 220 ARG cc_start: 0.8361 (mmt90) cc_final: 0.7371 (mmm160) REVERT: E 260 LYS cc_start: 0.8776 (mttm) cc_final: 0.8560 (mtpt) REVERT: E 311 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8093 (mt-10) REVERT: E 462 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7016 (tt0) REVERT: F 220 ARG cc_start: 0.8633 (mmt90) cc_final: 0.7677 (mmm-85) REVERT: J 100 GLU cc_start: 0.7957 (mp0) cc_final: 0.7558 (mp0) REVERT: K 260 LYS cc_start: 0.8748 (mttm) cc_final: 0.8445 (mttt) REVERT: N 67 SER cc_start: 0.8403 (p) cc_final: 0.8133 (t) REVERT: N 103 LYS cc_start: 0.8454 (OUTLIER) cc_final: 0.8179 (tptm) REVERT: O 3 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7793 (mm-40) REVERT: O 5 GLN cc_start: 0.8175 (tt0) cc_final: 0.7854 (tp40) REVERT: O 82 SER cc_start: 0.8240 (m) cc_final: 0.7758 (t) REVERT: P 10 SER cc_start: 0.8530 (t) cc_final: 0.8228 (p) REVERT: P 24 ARG cc_start: 0.8144 (ttm-80) cc_final: 0.7775 (mtt-85) outliers start: 67 outliers final: 47 residues processed: 284 average time/residue: 0.7017 time to fit residues: 223.7782 Evaluate side-chains 278 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 227 time to evaluate : 0.771 ------------------------------------------------------------------------------- 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 434 ASN Chi-restraints excluded: chain E residue 173 ARG 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 E residue 450 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 35 THR Chi-restraints excluded: chain J residue 65 THR Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain K residue 297 HIS 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 63 SER Chi-restraints excluded: chain N residue 92 VAL 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 56 SER Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 33 LEU 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: 0.7980 chunk 64 optimal weight: 0.9990 chunk 222 optimal weight: 7.9990 chunk 92 optimal weight: 4.9990 chunk 137 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 218 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 297 HIS I 76 ASN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 HIS 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 = 0.3595 r_free = 0.3595 target = 0.136185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.109002 restraints weight = 20612.316| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.45 r_work: 0.3138 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8724 moved from start: 0.2507 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= 0.124 Angle : 0.592 9.539 27232 Z= 0.305 Chirality : 0.047 0.182 2984 Planarity : 0.004 0.035 3472 Dihedral : 5.982 59.372 3116 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.93 % Favored : 96.91 % Rotamer: Outliers : 2.90 % Allowed : 14.25 % Favored : 82.85 % 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: -1.38 (0.91), residues: 24 sheet: 0.49 (0.17), residues: 972 loop : -0.13 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 368 TYR 0.011 0.001 TYR O 91 PHE 0.020 0.002 PHE H 78 TRP 0.012 0.001 TRP F 179 HIS 0.003 0.001 HIS E 297 Details of bonding type rmsd covalent geometry : bond 0.00278 (19940) covalent geometry : angle 0.58626 (27148) SS BOND : bond 0.00149 ( 12) SS BOND : angle 0.48566 ( 24) hydrogen bonds : bond 0.03648 ( 653) hydrogen bonds : angle 5.76935 ( 1737) link_BETA1-4 : bond 0.00582 ( 8) link_BETA1-4 : angle 1.60013 ( 24) link_NAG-ASN : bond 0.00284 ( 12) link_NAG-ASN : angle 2.09068 ( 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 294 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 232 time to evaluate : 0.816 Fit side-chains REVERT: D 220 ARG cc_start: 0.8382 (mmt90) cc_final: 0.7406 (mmt90) REVERT: D 311 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7563 (mp0) REVERT: D 331 LYS cc_start: 0.8081 (pttt) cc_final: 0.7381 (ptpp) REVERT: D 430 ARG cc_start: 0.8081 (mtp85) cc_final: 0.7452 (mtm180) REVERT: E 220 ARG cc_start: 0.8419 (mmt90) cc_final: 0.7356 (mmm160) REVERT: E 260 LYS cc_start: 0.8753 (mttm) cc_final: 0.8536 (mtpt) REVERT: E 293 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.7966 (ttm170) REVERT: E 311 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8093 (mt-10) REVERT: E 462 GLU cc_start: 0.7611 (mt-10) cc_final: 0.6922 (tt0) REVERT: F 220 ARG cc_start: 0.8637 (mmt90) cc_final: 0.7598 (mmm-85) REVERT: H 27 GLU cc_start: 0.7885 (mt-10) cc_final: 0.6932 (pt0) REVERT: J 100 GLU cc_start: 0.7992 (mp0) cc_final: 0.7578 (mp0) REVERT: K 260 LYS cc_start: 0.8743 (mttm) cc_final: 0.8415 (mttt) REVERT: M 13 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.7842 (t) REVERT: N 103 LYS cc_start: 0.8409 (OUTLIER) cc_final: 0.8136 (tptm) REVERT: O 5 GLN cc_start: 0.8128 (tt0) cc_final: 0.7802 (tp40) REVERT: O 82 SER cc_start: 0.8260 (m) cc_final: 0.7798 (t) REVERT: P 10 SER cc_start: 0.8559 (t) cc_final: 0.8256 (p) REVERT: P 24 ARG cc_start: 0.8165 (ttm-80) cc_final: 0.7810 (mtt-85) REVERT: P 38 GLN cc_start: 0.8689 (OUTLIER) cc_final: 0.6449 (tp40) outliers start: 62 outliers final: 49 residues processed: 279 average time/residue: 0.6309 time to fit residues: 197.9323 Evaluate side-chains 283 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 228 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 434 ASN Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 441 SER Chi-restraints excluded: chain E residue 450 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 266 SER 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 173 ARG Chi-restraints excluded: chain K residue 216 ILE Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain K residue 297 HIS Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 33 LEU 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 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 33 LEU Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 50 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 208 optimal weight: 2.9990 chunk 213 optimal weight: 1.9990 chunk 200 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 115 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 449 ASN E 297 HIS E 449 ASN I 76 ASN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 93 GLN N 100 GLN 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 = 0.3600 r_free = 0.3600 target = 0.136693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.109366 restraints weight = 20620.087| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 1.46 r_work: 0.3144 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19972 Z= 0.117 Angle : 0.580 9.418 27232 Z= 0.299 Chirality : 0.046 0.181 2984 Planarity : 0.004 0.035 3472 Dihedral : 5.857 58.795 3116 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.13 % Favored : 96.71 % Rotamer: Outliers : 3.13 % Allowed : 14.07 % Favored : 82.80 % 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: 0.15 (0.17), residues: 2460 helix: -1.38 (0.92), residues: 24 sheet: 0.52 (0.17), residues: 972 loop : -0.10 (0.16), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 368 TYR 0.011 0.001 TYR O 91 PHE 0.019 0.002 PHE H 78 TRP 0.012 0.001 TRP J 47 HIS 0.003 0.001 HIS E 297 Details of bonding type rmsd covalent geometry : bond 0.00262 (19940) covalent geometry : angle 0.57389 (27148) SS BOND : bond 0.00152 ( 12) SS BOND : angle 0.47032 ( 24) hydrogen bonds : bond 0.03564 ( 653) hydrogen bonds : angle 5.72879 ( 1737) link_BETA1-4 : bond 0.00573 ( 8) link_BETA1-4 : angle 1.51977 ( 24) link_NAG-ASN : bond 0.00272 ( 12) link_NAG-ASN : angle 2.04233 ( 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 302 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 235 time to evaluate : 0.794 Fit side-chains REVERT: D 220 ARG cc_start: 0.8377 (mmt90) cc_final: 0.7398 (mmt90) REVERT: D 311 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7572 (mp0) REVERT: D 331 LYS cc_start: 0.8075 (pttt) cc_final: 0.7364 (ptpp) REVERT: D 430 ARG cc_start: 0.8098 (mtp85) cc_final: 0.7432 (mtm180) REVERT: E 220 ARG cc_start: 0.8415 (mmt90) cc_final: 0.7443 (mmm160) REVERT: E 260 LYS cc_start: 0.8740 (mttm) cc_final: 0.8532 (mtpt) REVERT: E 293 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.7871 (ttm170) REVERT: E 311 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8094 (mt-10) REVERT: E 462 GLU cc_start: 0.7589 (mt-10) cc_final: 0.6929 (tt0) REVERT: F 220 ARG cc_start: 0.8634 (mmt90) cc_final: 0.7627 (mmm-85) REVERT: H 27 GLU cc_start: 0.7878 (mt-10) cc_final: 0.6959 (pt0) REVERT: J 27 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7804 (pt0) REVERT: J 100 GLU cc_start: 0.7986 (mp0) cc_final: 0.7552 (mp0) REVERT: K 260 LYS cc_start: 0.8720 (mttm) cc_final: 0.8393 (mttt) REVERT: K 390 LYS cc_start: 0.8471 (ttpt) cc_final: 0.8195 (tmmt) REVERT: M 13 VAL cc_start: 0.8264 (OUTLIER) cc_final: 0.7841 (t) REVERT: N 103 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8130 (tptm) REVERT: O 3 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.7623 (tm-30) REVERT: O 5 GLN cc_start: 0.8131 (tt0) cc_final: 0.7780 (tp40) REVERT: O 82 SER cc_start: 0.8227 (m) cc_final: 0.7714 (t) REVERT: P 10 SER cc_start: 0.8555 (t) cc_final: 0.8265 (p) REVERT: P 24 ARG cc_start: 0.8169 (ttm-80) cc_final: 0.7815 (mtt-85) outliers start: 67 outliers final: 50 residues processed: 285 average time/residue: 0.6539 time to fit residues: 208.5915 Evaluate side-chains 286 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 230 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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 434 ASN Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 293 ARG Chi-restraints excluded: chain E residue 311 GLU Chi-restraints excluded: chain E residue 441 SER Chi-restraints excluded: chain E residue 450 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 266 SER Chi-restraints excluded: chain F residue 339 SER Chi-restraints excluded: chain F residue 421 CYS 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 2 VAL 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 216 ILE Chi-restraints excluded: chain K residue 273 ASN Chi-restraints excluded: chain K residue 297 HIS Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 33 LEU 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 50 PHE Chi-restraints excluded: chain N residue 63 SER Chi-restraints excluded: chain N residue 92 VAL 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 56 SER Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 50 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 244 random chunks: chunk 114 optimal weight: 10.0000 chunk 130 optimal weight: 0.2980 chunk 56 optimal weight: 0.0270 chunk 21 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 182 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 187 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 297 HIS E 449 ASN I 76 ASN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 93 GLN N 100 GLN 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 = 0.3614 r_free = 0.3614 target = 0.137853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.110603 restraints weight = 20771.771| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.47 r_work: 0.3152 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19972 Z= 0.099 Angle : 0.562 9.457 27232 Z= 0.288 Chirality : 0.045 0.182 2984 Planarity : 0.004 0.041 3472 Dihedral : 5.673 58.997 3115 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.80 % Favored : 97.03 % Rotamer: Outliers : 2.62 % Allowed : 14.86 % Favored : 82.52 % 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: 0.20 (0.17), residues: 2460 helix: -1.34 (0.92), residues: 24 sheet: 0.52 (0.16), residues: 1016 loop : -0.05 (0.17), residues: 1420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 118 TYR 0.010 0.001 TYR O 91 PHE 0.017 0.002 PHE J 78 TRP 0.012 0.001 TRP F 179 HIS 0.002 0.001 HIS K 297 Details of bonding type rmsd covalent geometry : bond 0.00216 (19940) covalent geometry : angle 0.55617 (27148) SS BOND : bond 0.00139 ( 12) SS BOND : angle 0.37388 ( 24) hydrogen bonds : bond 0.03359 ( 653) hydrogen bonds : angle 5.65812 ( 1737) link_BETA1-4 : bond 0.00523 ( 8) link_BETA1-4 : angle 1.45663 ( 24) link_NAG-ASN : bond 0.00254 ( 12) link_NAG-ASN : angle 1.96447 ( 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 290 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 234 time to evaluate : 0.571 Fit side-chains revert: symmetry clash REVERT: D 220 ARG cc_start: 0.8364 (mmt90) cc_final: 0.7375 (mmt90) REVERT: D 311 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: D 430 ARG cc_start: 0.8092 (mtp85) cc_final: 0.7445 (mtm180) REVERT: E 220 ARG cc_start: 0.8405 (mmt90) cc_final: 0.7410 (mmm160) REVERT: E 260 LYS cc_start: 0.8732 (mttm) cc_final: 0.8528 (mtpt) REVERT: E 293 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.7890 (ttm170) REVERT: E 311 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8120 (mt-10) REVERT: E 462 GLU cc_start: 0.7580 (mt-10) cc_final: 0.6874 (tt0) REVERT: F 220 ARG cc_start: 0.8623 (mmt90) cc_final: 0.7613 (mmm-85) REVERT: H 27 GLU cc_start: 0.7883 (mt-10) cc_final: 0.6901 (pt0) REVERT: J 27 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7767 (pt0) REVERT: J 100 GLU cc_start: 0.7980 (mp0) cc_final: 0.7558 (mp0) REVERT: K 260 LYS cc_start: 0.8712 (mttm) cc_final: 0.8384 (mttt) REVERT: K 390 LYS cc_start: 0.8478 (ttpt) cc_final: 0.8221 (tmmt) REVERT: M 13 VAL cc_start: 0.8244 (OUTLIER) cc_final: 0.7824 (t) REVERT: N 103 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8128 (tptm) REVERT: O 3 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.7648 (tm-30) REVERT: O 5 GLN cc_start: 0.8180 (tt0) cc_final: 0.7789 (tp40) REVERT: O 82 SER cc_start: 0.8167 (m) cc_final: 0.7647 (t) REVERT: P 10 SER cc_start: 0.8542 (t) cc_final: 0.8245 (p) REVERT: P 24 ARG cc_start: 0.8159 (ttm-80) cc_final: 0.7806 (mtt-85) outliers start: 56 outliers final: 44 residues processed: 277 average time/residue: 0.6565 time to fit residues: 203.9398 Evaluate side-chains 278 residues out of total 2144 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 228 time to evaluate : 0.480 ------------------------------------------------------------------------------- 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 434 ASN Chi-restraints excluded: chain E residue 173 ARG Chi-restraints excluded: chain E residue 243 THR Chi-restraints excluded: chain E residue 293 ARG 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 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 2 VAL 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 K residue 297 HIS Chi-restraints excluded: chain L residue 33 LEU 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 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 9 LEU Chi-restraints excluded: chain P residue 23 CYS Chi-restraints excluded: chain P residue 33 LEU Chi-restraints excluded: chain P residue 50 PHE 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: 0.0270 chunk 58 optimal weight: 5.9990 chunk 87 optimal weight: 0.0980 chunk 187 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 141 optimal weight: 2.9990 chunk 164 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 236 optimal weight: 0.9990 chunk 170 optimal weight: 0.7980 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 297 HIS E 449 ASN I 76 ASN ** M 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 93 GLN N 100 GLN 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 = 0.3594 r_free = 0.3594 target = 0.136193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.109135 restraints weight = 20792.823| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.40 r_work: 0.3145 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19972 Z= 0.129 Angle : 0.595 9.146 27232 Z= 0.307 Chirality : 0.047 0.181 2984 Planarity : 0.004 0.046 3472 Dihedral : 5.822 58.088 3114 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.17 % Favored : 96.67 % Rotamer: Outliers : 2.85 % Allowed : 14.67 % Favored : 82.48 % 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: 0.14 (0.17), residues: 2460 helix: -1.32 (0.94), residues: 24 sheet: 0.55 (0.17), residues: 948 loop : -0.13 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 118 TYR 0.011 0.001 TYR H 91 PHE 0.019 0.002 PHE O 78 TRP 0.012 0.002 TRP F 179 HIS 0.003 0.001 HIS P 27D Details of bonding type rmsd covalent geometry : bond 0.00293 (19940) covalent geometry : angle 0.58960 (27148) SS BOND : bond 0.00132 ( 12) SS BOND : angle 0.50700 ( 24) hydrogen bonds : bond 0.03674 ( 653) hydrogen bonds : angle 5.74584 ( 1737) link_BETA1-4 : bond 0.00558 ( 8) link_BETA1-4 : angle 1.50183 ( 24) link_NAG-ASN : bond 0.00258 ( 12) link_NAG-ASN : angle 2.09225 ( 36) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7660.56 seconds wall clock time: 131 minutes 28.42 seconds (7888.42 seconds total)