Starting phenix.real_space_refine on Thu Feb 5 04:22:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cyj_46046/02_2026/9cyj_46046.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cyj_46046/02_2026/9cyj_46046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cyj_46046/02_2026/9cyj_46046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cyj_46046/02_2026/9cyj_46046.map" model { file = "/net/cci-nas-00/data/ceres_data/9cyj_46046/02_2026/9cyj_46046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cyj_46046/02_2026/9cyj_46046.cif" } resolution = 2.97 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= 0.018 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 4 9.91 5 S 95 5.16 5 C 9036 2.51 5 N 2501 2.21 5 O 3020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14656 Number of models: 1 Model: "" Number of chains: 26 Chain: "C" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2999 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 374} Chain: "H" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 986 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "L" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 848 Classifications: {'peptide': 110} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 104} Chain: "B" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2999 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 374} Chain: "A" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2999 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 374} Chain: "D" Number of atoms: 2999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 2999 Classifications: {'peptide': 388} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 374} Chain: "E" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 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: "S" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 24 Unusual residues: {'FUC': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 94 Unusual residues: {'BMA': 1, 'MAN': 5, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' CA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.32, per 1000 atoms: 0.23 Number of scatterers: 14656 At special positions: 0 Unit cell: (85.55, 113.1, 140.65, 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 4 19.99 S 95 16.00 O 3020 8.00 N 2501 7.00 C 9036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS C 92 " - pdb=" SG CYS C 417 " distance=2.03 Simple disulfide: pdb=" SG CYS C 124 " - pdb=" SG CYS C 129 " distance=2.04 Simple disulfide: pdb=" SG CYS C 175 " - pdb=" SG CYS C 193 " distance=2.02 Simple disulfide: pdb=" SG CYS C 183 " - pdb=" SG CYS C 230 " distance=2.03 Simple disulfide: pdb=" SG CYS C 232 " - pdb=" SG CYS C 237 " distance=2.03 Simple disulfide: pdb=" SG CYS C 278 " - pdb=" SG CYS C 291 " distance=2.03 Simple disulfide: pdb=" SG CYS C 280 " - pdb=" SG CYS C 289 " distance=2.03 Simple disulfide: pdb=" SG CYS C 318 " - pdb=" SG CYS C 337 " distance=2.03 Simple disulfide: pdb=" SG CYS C 421 " - pdb=" SG CYS C 447 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS B 92 " - pdb=" SG CYS B 417 " distance=2.03 Simple disulfide: pdb=" SG CYS B 124 " - pdb=" SG CYS B 129 " distance=2.03 Simple disulfide: pdb=" SG CYS B 175 " - pdb=" SG CYS B 193 " distance=2.03 Simple disulfide: pdb=" SG CYS B 183 " - pdb=" SG CYS B 230 " distance=2.03 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 237 " distance=2.03 Simple disulfide: pdb=" SG CYS B 278 " - pdb=" SG CYS B 291 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 289 " distance=2.03 Simple disulfide: pdb=" SG CYS B 318 " - pdb=" SG CYS B 337 " distance=2.03 Simple disulfide: pdb=" SG CYS B 421 " - pdb=" SG CYS B 447 " distance=2.03 Simple disulfide: pdb=" SG CYS A 92 " - pdb=" SG CYS A 417 " distance=2.03 Simple disulfide: pdb=" SG CYS A 124 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 175 " - pdb=" SG CYS A 193 " distance=2.03 Simple disulfide: pdb=" SG CYS A 183 " - pdb=" SG CYS A 230 " distance=2.03 Simple disulfide: pdb=" SG CYS A 232 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 278 " - pdb=" SG CYS A 291 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 289 " distance=2.03 Simple disulfide: pdb=" SG CYS A 318 " - pdb=" SG CYS A 337 " distance=2.03 Simple disulfide: pdb=" SG CYS A 421 " - pdb=" SG CYS A 447 " distance=2.03 Simple disulfide: pdb=" SG CYS D 92 " - pdb=" SG CYS D 417 " distance=2.03 Simple disulfide: pdb=" SG CYS D 124 " - pdb=" SG CYS D 129 " distance=2.03 Simple disulfide: pdb=" SG CYS D 175 " - pdb=" SG CYS D 193 " distance=2.02 Simple disulfide: pdb=" SG CYS D 183 " - pdb=" SG CYS D 230 " distance=2.03 Simple disulfide: pdb=" SG CYS D 232 " - pdb=" SG CYS D 237 " distance=2.03 Simple disulfide: pdb=" SG CYS D 278 " - pdb=" SG CYS D 291 " distance=2.03 Simple disulfide: pdb=" SG CYS D 280 " - pdb=" SG CYS D 289 " distance=2.03 Simple disulfide: pdb=" SG CYS D 318 " - pdb=" SG CYS D 337 " distance=2.03 Simple disulfide: pdb=" SG CYS D 421 " - pdb=" SG CYS D 447 " 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 ALPHA1-2 " MAN G 4 " - " MAN G 5 " " MAN M 4 " - " MAN M 5 " " MAN P 4 " - " MAN P 5 " " MAN U 4 " - " MAN U 5 " ALPHA1-3 " BMA G 3 " - " MAN G 4 " " MAN G 6 " - " MAN G 7 " " BMA M 3 " - " MAN M 4 " " MAN M 6 " - " MAN M 7 " " BMA P 3 " - " MAN P 4 " " MAN P 6 " - " MAN P 7 " " BMA U 3 " - " MAN U 4 " " MAN U 6 " - " MAN U 7 " ALPHA1-6 " BMA G 3 " - " MAN G 6 " " MAN G 6 " - " MAN G 8 " " BMA M 3 " - " MAN M 6 " " MAN M 6 " - " MAN M 8 " " BMA P 3 " - " MAN P 6 " " MAN P 6 " - " MAN P 8 " " BMA U 3 " - " MAN U 6 " " MAN U 6 " - " MAN U 8 " BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG I 1 " - " NAG I 2 " " NAG K 1 " - " NAG K 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG P 2 " - " BMA P 3 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " " NAG U 2 " - " BMA U 3 " " NAG V 1 " - " NAG V 2 " BETA1-6 " NAG E 1 " - " FUC E 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG J 1 " - " FUC J 2 " " NAG R 1 " - " FUC R 3 " " NAG S 1 " - " FUC S 2 " NAG-ASN " NAG A 502 " - " ASN A 234 " " NAG A 503 " - " ASN A 86 " " NAG B 502 " - " ASN B 234 " " NAG B 503 " - " ASN B 86 " " NAG C 502 " - " ASN C 234 " " NAG C 503 " - " ASN C 86 " " NAG D 502 " - " ASN D 234 " " NAG D 503 " - " ASN D 86 " " NAG E 1 " - " ASN C 245 " " NAG F 1 " - " ASN C 146 " " NAG G 1 " - " ASN C 200 " " NAG I 1 " - " ASN C 367 " " NAG J 1 " - " ASN B 245 " " NAG K 1 " - " ASN B 146 " " NAG M 1 " - " ASN B 200 " " NAG N 1 " - " ASN B 367 " " NAG O 1 " - " ASN A 146 " " NAG P 1 " - " ASN A 200 " " NAG Q 1 " - " ASN A 367 " " NAG R 1 " - " ASN A 245 " " NAG S 1 " - " ASN D 245 " " NAG T 1 " - " ASN D 146 " " NAG U 1 " - " ASN D 200 " " NAG V 1 " - " ASN D 367 " Time building additional restraints: 1.81 Conformation dependent library (CDL) restraints added in 549.0 milliseconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3236 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 31 sheets defined 3.4% alpha, 38.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'C' and resid 104 through 110 removed outlier: 3.858A pdb=" N ALA C 110 " --> pdb=" O ILE C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 146 removed outlier: 3.638A pdb=" N ASN C 146 " --> pdb=" O VAL C 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'B' and resid 104 through 110 removed outlier: 3.711A pdb=" N ALA B 110 " --> pdb=" O ILE B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 146 removed outlier: 3.917A pdb=" N ASN B 146 " --> pdb=" O VAL B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'A' and resid 104 through 110 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'D' and resid 104 through 112 removed outlier: 3.770A pdb=" N ALA D 110 " --> pdb=" O ILE D 106 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLY D 111 " --> pdb=" O ARG D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 146 removed outlier: 3.514A pdb=" N SER D 145 " --> pdb=" O ASN D 142 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ASN D 146 " --> pdb=" O VAL D 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 142 through 146' Processing sheet with id=AA1, first strand: chain 'C' and resid 97 through 102 removed outlier: 6.757A pdb=" N VAL C 445 " --> pdb=" O PHE C 100 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N LYS C 102 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ILE C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 5.863A pdb=" N ARG C 420 " --> pdb=" O GLY C 448 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 115 through 121 removed outlier: 4.713A pdb=" N TRP C 115 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N THR C 138 " --> pdb=" O TRP C 115 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N THR C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLN C 136 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR C 157 " --> pdb=" O GLY C 135 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N LEU C 158 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS C 172 " --> pdb=" O MET C 160 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 179 through 184 removed outlier: 3.586A pdb=" N SER C 179 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASP C 213 " --> pdb=" O PHE C 205 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR C 207 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N LEU C 211 " --> pdb=" O TYR C 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 231 through 233 removed outlier: 3.691A pdb=" N VAL C 231 " --> pdb=" O THR C 238 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 233 " --> pdb=" O THR C 236 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS C 264 " --> pdb=" O PHE C 256 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU C 258 " --> pdb=" O ILE C 262 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE C 262 " --> pdb=" O GLU C 258 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 276 through 281 removed outlier: 5.129A pdb=" N CYS C 278 " --> pdb=" O VAL C 290 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL C 290 " --> pdb=" O CYS C 278 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N CYS C 280 " --> pdb=" O ARG C 288 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ARG C 288 " --> pdb=" O CYS C 280 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER C 311 " --> pdb=" O ASN C 306 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 352 through 356 removed outlier: 4.744A pdb=" N TRP C 352 " --> pdb=" O GLY C 363 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY C 363 " --> pdb=" O TRP C 352 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP C 359 " --> pdb=" O ASP C 356 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LEU C 372 " --> pdb=" O VAL C 398 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N VAL C 398 " --> pdb=" O LEU C 372 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR C 374 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N VAL C 396 " --> pdb=" O TYR C 374 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N THR C 376 " --> pdb=" O ARG C 394 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ARG C 394 " --> pdb=" O THR C 376 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.096A pdb=" N GLU H 10 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.096A pdb=" N GLU H 10 " --> pdb=" O THR H 125 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER H 117 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 18 through 19 removed outlier: 3.546A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 14 removed outlier: 6.792A pdb=" N LEU L 11 " --> pdb=" O GLU L 106 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LYS L 108 " --> pdb=" O LEU L 11 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N LEU L 13 " --> pdb=" O LYS L 108 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.556A pdb=" N GLU L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 96 through 102 removed outlier: 3.535A pdb=" N GLY B 96 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N VAL B 445 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N ARG B 420 " --> pdb=" O GLY B 448 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 121 through 124 removed outlier: 3.956A pdb=" N CYS B 175 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N MET B 160 " --> pdb=" O GLN B 173 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N GLN B 173 " --> pdb=" O MET B 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 179 through 184 removed outlier: 3.556A pdb=" N SER B 179 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASP B 213 " --> pdb=" O PHE B 205 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TYR B 207 " --> pdb=" O LEU B 211 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LEU B 211 " --> pdb=" O TYR B 207 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 231 through 233 removed outlier: 3.522A pdb=" N VAL B 231 " --> pdb=" O THR B 238 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS B 264 " --> pdb=" O PHE B 256 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N GLU B 258 " --> pdb=" O ILE B 262 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE B 262 " --> pdb=" O GLU B 258 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 279 through 281 Processing sheet with id=AB9, first strand: chain 'B' and resid 352 through 355 removed outlier: 4.574A pdb=" N TRP B 352 " --> pdb=" O GLY B 363 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLY B 363 " --> pdb=" O TRP B 352 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ASP B 402 " --> pdb=" O GLY B 373 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N GLU B 375 " --> pdb=" O ARG B 400 " (cutoff:3.500A) removed outlier: 10.682A pdb=" N ARG B 400 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 11.463A pdb=" N PHE B 377 " --> pdb=" O VAL B 398 " (cutoff:3.500A) removed outlier: 13.315A pdb=" N VAL B 398 " --> pdb=" O PHE B 377 " (cutoff:3.500A) removed outlier: 16.222A pdb=" N VAL B 379 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 16.340A pdb=" N VAL B 396 " --> pdb=" O VAL B 379 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 97 through 101 removed outlier: 5.945A pdb=" N CYS A 447 " --> pdb=" O PRO A 99 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N ARG A 420 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 121 through 124 removed outlier: 3.902A pdb=" N CYS A 175 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N MET A 160 " --> pdb=" O GLN A 173 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N GLN A 173 " --> pdb=" O MET A 160 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 179 through 184 removed outlier: 3.554A pdb=" N SER A 179 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP A 213 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N TYR A 207 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU A 211 " --> pdb=" O TYR A 207 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 223 through 224 Processing sheet with id=AC5, first strand: chain 'A' and resid 223 through 224 removed outlier: 3.591A pdb=" N HIS A 264 " --> pdb=" O PHE A 256 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N GLU A 258 " --> pdb=" O ILE A 262 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ILE A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'A' and resid 276 through 281 removed outlier: 5.001A pdb=" N CYS A 278 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL A 290 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N CYS A 280 " --> pdb=" O ARG A 288 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ARG A 288 " --> pdb=" O CYS A 280 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 352 through 355 removed outlier: 4.724A pdb=" N TRP A 352 " --> pdb=" O GLY A 363 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 363 " --> pdb=" O TRP A 352 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ASP A 402 " --> pdb=" O GLY A 373 " (cutoff:3.500A) removed outlier: 9.447A pdb=" N GLU A 375 " --> pdb=" O ARG A 400 " (cutoff:3.500A) removed outlier: 10.544A pdb=" N ARG A 400 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 11.450A pdb=" N PHE A 377 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 13.380A pdb=" N VAL A 398 " --> pdb=" O PHE A 377 " (cutoff:3.500A) removed outlier: 15.640A pdb=" N VAL A 379 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 16.099A pdb=" N VAL A 396 " --> pdb=" O VAL A 379 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 97 through 102 removed outlier: 5.563A pdb=" N CYS D 447 " --> pdb=" O PRO D 99 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ARG D 420 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 115 through 125 removed outlier: 4.710A pdb=" N TRP D 115 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N THR D 138 " --> pdb=" O TRP D 115 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N THR D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN D 136 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N LEU D 158 " --> pdb=" O VAL D 174 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS D 172 " --> pdb=" O MET D 160 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 179 through 184 removed outlier: 3.579A pdb=" N SER D 179 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP D 213 " --> pdb=" O PHE D 205 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N TYR D 207 " --> pdb=" O LEU D 211 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU D 211 " --> pdb=" O TYR D 207 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 231 through 233 removed outlier: 3.821A pdb=" N VAL D 231 " --> pdb=" O THR D 238 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLU D 258 " --> pdb=" O ILE D 262 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILE D 262 " --> pdb=" O GLU D 258 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 276 through 281 removed outlier: 5.081A pdb=" N CYS D 278 " --> pdb=" O VAL D 290 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL D 290 " --> pdb=" O CYS D 278 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N CYS D 280 " --> pdb=" O ARG D 288 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ARG D 288 " --> pdb=" O CYS D 280 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 353 through 355 removed outlier: 7.269A pdb=" N ASP D 402 " --> pdb=" O GLY D 373 " (cutoff:3.500A) removed outlier: 9.763A pdb=" N GLU D 375 " --> pdb=" O ARG D 400 " (cutoff:3.500A) removed outlier: 10.454A pdb=" N ARG D 400 " --> pdb=" O GLU D 375 " (cutoff:3.500A) removed outlier: 11.237A pdb=" N PHE D 377 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 13.177A pdb=" N VAL D 398 " --> pdb=" O PHE D 377 " (cutoff:3.500A) removed outlier: 15.999A pdb=" N VAL D 379 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 16.221A pdb=" N VAL D 396 " --> pdb=" O VAL D 379 " (cutoff:3.500A) 381 hydrogen bonds defined for protein. 1023 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.00 Time building geometry restraints manager: 2.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4672 1.34 - 1.47: 3985 1.47 - 1.59: 6192 1.59 - 1.72: 0 1.72 - 1.84: 114 Bond restraints: 14963 Sorted by residual: bond pdb=" C1 NAG F 2 " pdb=" O5 NAG F 2 " ideal model delta sigma weight residual 1.406 1.470 -0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C1 NAG T 2 " pdb=" O5 NAG T 2 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 9.13e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.466 -0.060 2.00e-02 2.50e+03 9.02e+00 bond pdb=" C1 NAG R 1 " pdb=" O5 NAG R 1 " ideal model delta sigma weight residual 1.406 1.450 -0.044 2.00e-02 2.50e+03 4.79e+00 bond pdb=" C4 FUC J 2 " pdb=" C5 FUC J 2 " ideal model delta sigma weight residual 1.531 1.571 -0.040 2.00e-02 2.50e+03 4.09e+00 ... (remaining 14958 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 19349 1.75 - 3.49: 760 3.49 - 5.24: 141 5.24 - 6.98: 41 6.98 - 8.73: 3 Bond angle restraints: 20294 Sorted by residual: angle pdb=" CA CYS C 124 " pdb=" CB CYS C 124 " pdb=" SG CYS C 124 " ideal model delta sigma weight residual 114.40 123.13 -8.73 2.30e+00 1.89e-01 1.44e+01 angle pdb=" N CYS C 124 " pdb=" CA CYS C 124 " pdb=" C CYS C 124 " ideal model delta sigma weight residual 108.79 114.24 -5.45 1.53e+00 4.27e-01 1.27e+01 angle pdb=" N ASN A 245 " pdb=" CA ASN A 245 " pdb=" CB ASN A 245 " ideal model delta sigma weight residual 110.49 115.97 -5.48 1.69e+00 3.50e-01 1.05e+01 angle pdb=" C SER C 123 " pdb=" N CYS C 124 " pdb=" CA CYS C 124 " ideal model delta sigma weight residual 121.62 116.29 5.33 1.83e+00 2.99e-01 8.48e+00 angle pdb=" N ASN A 245 " pdb=" CA ASN A 245 " pdb=" C ASN A 245 " ideal model delta sigma weight residual 110.80 105.30 5.50 2.13e+00 2.20e-01 6.67e+00 ... (remaining 20289 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.11: 9171 25.11 - 50.22: 327 50.22 - 75.33: 70 75.33 - 100.44: 69 100.44 - 125.54: 81 Dihedral angle restraints: 9718 sinusoidal: 4641 harmonic: 5077 Sorted by residual: dihedral pdb=" CA PRO D 282 " pdb=" C PRO D 282 " pdb=" N ARG D 283 " pdb=" CA ARG D 283 " ideal model delta harmonic sigma weight residual 180.00 155.64 24.36 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA PRO B 282 " pdb=" C PRO B 282 " pdb=" N ARG B 283 " pdb=" CA ARG B 283 " ideal model delta harmonic sigma weight residual 180.00 157.40 22.60 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CB CYS C 124 " pdb=" SG CYS C 124 " pdb=" SG CYS C 129 " pdb=" CB CYS C 129 " ideal model delta sinusoidal sigma weight residual 93.00 56.01 36.99 1 1.00e+01 1.00e-02 1.93e+01 ... (remaining 9715 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1842 0.055 - 0.110: 427 0.110 - 0.165: 128 0.165 - 0.220: 4 0.220 - 0.274: 4 Chirality restraints: 2405 Sorted by residual: chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" C5 BMA M 3 " pdb=" C4 BMA M 3 " pdb=" C6 BMA M 3 " pdb=" O5 BMA M 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C5 BMA U 3 " pdb=" C4 BMA U 3 " pdb=" C6 BMA U 3 " pdb=" O5 BMA U 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.52 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 2402 not shown) Planarity restraints: 2547 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP B 125 " 0.051 5.00e-02 4.00e+02 7.71e-02 9.50e+00 pdb=" N PRO B 126 " -0.133 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP C 243 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.74e+00 pdb=" CG ASP C 243 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASP C 243 " 0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP C 243 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP D 125 " -0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO D 126 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO D 126 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 126 " -0.023 5.00e-02 4.00e+02 ... (remaining 2544 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 365 2.67 - 3.22: 14010 3.22 - 3.78: 23134 3.78 - 4.34: 34249 4.34 - 4.90: 57226 Nonbonded interactions: 128984 Sorted by model distance: nonbonded pdb=" OG SER A 217 " pdb=" O SER A 219 " model vdw 2.107 3.040 nonbonded pdb=" NH1 ARG A 428 " pdb=" O ALA A 462 " model vdw 2.218 3.120 nonbonded pdb=" OE1 GLU A 276 " pdb=" ND2 ASN A 294 " model vdw 2.277 3.120 nonbonded pdb=" OG SER A 217 " pdb=" OD2 ASP A 243 " model vdw 2.278 3.040 nonbonded pdb=" O ILE D 222 " pdb=" NH1 ARG D 224 " model vdw 2.330 3.120 ... (remaining 128979 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and resid 1) selection = (chain 'F' and resid 1) selection = (chain 'I' and resid 1) selection = (chain 'J' and resid 1) selection = (chain 'K' and resid 1) selection = (chain 'N' and resid 1) selection = (chain 'O' and resid 1) selection = (chain 'Q' and resid 1) selection = (chain 'S' and resid 1) selection = (chain 'T' and resid 1) selection = (chain 'V' and resid 1) } ncs_group { reference = chain 'G' selection = chain 'M' selection = chain 'P' selection = chain 'U' } 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: 11.010 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: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 15.330 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 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: 0.000 Load rotamer database and sin/cos tables:6.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 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 : 0.006 0.064 15066 Z= 0.258 Angle : 0.860 10.075 20565 Z= 0.398 Chirality : 0.053 0.274 2405 Planarity : 0.004 0.077 2523 Dihedral : 19.709 125.545 6368 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 1.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 0.78 % Allowed : 6.86 % Favored : 92.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.19), residues: 1780 helix: -2.44 (0.68), residues: 48 sheet: -0.76 (0.21), residues: 595 loop : -1.00 (0.17), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 420 TYR 0.016 0.002 TYR L 91 PHE 0.018 0.002 PHE B 354 TRP 0.010 0.001 TRP C 178 HIS 0.006 0.001 HIS D 168 Details of bonding type rmsd covalent geometry : bond 0.00586 (14963) covalent geometry : angle 0.81742 (20294) SS BOND : bond 0.00355 ( 38) SS BOND : angle 1.01298 ( 76) hydrogen bonds : bond 0.23919 ( 375) hydrogen bonds : angle 11.33690 ( 1023) link_ALPHA1-2 : bond 0.00320 ( 4) link_ALPHA1-2 : angle 1.51012 ( 12) link_ALPHA1-3 : bond 0.00327 ( 8) link_ALPHA1-3 : angle 1.80426 ( 24) link_ALPHA1-6 : bond 0.00311 ( 8) link_ALPHA1-6 : angle 1.85790 ( 24) link_BETA1-4 : bond 0.00512 ( 17) link_BETA1-4 : angle 2.51981 ( 51) link_BETA1-6 : bond 0.00839 ( 4) link_BETA1-6 : angle 2.08617 ( 12) link_NAG-ASN : bond 0.00550 ( 24) link_NAG-ASN : angle 3.77234 ( 72) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 220 time to evaluate : 0.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 128 LYS cc_start: 0.8700 (ptmm) cc_final: 0.8353 (ptmm) REVERT: C 344 LYS cc_start: 0.6606 (mmpt) cc_final: 0.6180 (mmpt) REVERT: C 415 LYS cc_start: 0.8943 (tttt) cc_final: 0.8728 (ttpt) REVERT: L 106 GLU cc_start: 0.6788 (tm-30) cc_final: 0.6582 (tm-30) REVERT: B 276 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8186 (mm-30) REVERT: B 355 ASP cc_start: 0.8613 (p0) cc_final: 0.8385 (p0) REVERT: B 435 GLU cc_start: 0.8030 (mp0) cc_final: 0.7802 (mp0) REVERT: A 130 TYR cc_start: 0.8833 (m-80) cc_final: 0.8176 (m-80) REVERT: A 221 ASP cc_start: 0.6679 (m-30) cc_final: 0.6434 (m-30) REVERT: A 339 ASN cc_start: 0.8411 (m-40) cc_final: 0.8180 (m-40) REVERT: A 417 CYS cc_start: 0.6484 (m) cc_final: 0.6100 (m) REVERT: A 432 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7351 (mp0) outliers start: 12 outliers final: 6 residues processed: 232 average time/residue: 0.5392 time to fit residues: 139.1550 Evaluate side-chains 167 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 161 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain D residue 230 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 1.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 336 HIS ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN B 168 HIS B 173 GLN B 264 HIS B 391 GLN B 441 ASN B 468 HIS A 104 ASN A 131 GLN D 131 GLN D 173 GLN D 310 HIS D 358 ASN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.127815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.098706 restraints weight = 18988.277| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.70 r_work: 0.3046 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15066 Z= 0.232 Angle : 0.749 11.315 20565 Z= 0.361 Chirality : 0.051 0.250 2405 Planarity : 0.005 0.071 2523 Dihedral : 18.072 114.807 3246 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.39 % Allowed : 12.04 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.23 (0.19), residues: 1780 helix: -2.77 (0.61), residues: 48 sheet: -0.37 (0.21), residues: 626 loop : -0.98 (0.17), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 150 TYR 0.018 0.002 TYR D 121 PHE 0.019 0.002 PHE B 354 TRP 0.017 0.001 TRP C 178 HIS 0.009 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00544 (14963) covalent geometry : angle 0.69670 (20294) SS BOND : bond 0.00450 ( 38) SS BOND : angle 1.31372 ( 76) hydrogen bonds : bond 0.04828 ( 375) hydrogen bonds : angle 8.05200 ( 1023) link_ALPHA1-2 : bond 0.00444 ( 4) link_ALPHA1-2 : angle 1.93474 ( 12) link_ALPHA1-3 : bond 0.00620 ( 8) link_ALPHA1-3 : angle 2.11877 ( 24) link_ALPHA1-6 : bond 0.00309 ( 8) link_ALPHA1-6 : angle 1.59857 ( 24) link_BETA1-4 : bond 0.00491 ( 17) link_BETA1-4 : angle 2.22019 ( 51) link_BETA1-6 : bond 0.00901 ( 4) link_BETA1-6 : angle 2.23332 ( 12) link_NAG-ASN : bond 0.00517 ( 24) link_NAG-ASN : angle 3.80544 ( 72) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 160 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 128 LYS cc_start: 0.8648 (ptmm) cc_final: 0.8325 (ptmt) REVERT: C 415 LYS cc_start: 0.9117 (tttt) cc_final: 0.8857 (ttmm) REVERT: L 106 GLU cc_start: 0.7063 (tm-30) cc_final: 0.6805 (tm-30) REVERT: B 128 LYS cc_start: 0.8593 (ptpp) cc_final: 0.8238 (ptmt) REVERT: B 258 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7920 (mp0) REVERT: B 355 ASP cc_start: 0.8929 (p0) cc_final: 0.8652 (p0) REVERT: B 413 GLU cc_start: 0.8342 (OUTLIER) cc_final: 0.8030 (tt0) REVERT: B 435 GLU cc_start: 0.8228 (mp0) cc_final: 0.7837 (mp0) REVERT: A 103 ASP cc_start: 0.8601 (t70) cc_final: 0.8276 (t0) REVERT: A 294 ASN cc_start: 0.6614 (OUTLIER) cc_final: 0.6121 (m-40) REVERT: A 339 ASN cc_start: 0.8469 (m-40) cc_final: 0.8259 (m-40) REVERT: A 400 ARG cc_start: 0.8630 (ttp80) cc_final: 0.8401 (ttp-110) REVERT: A 432 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7287 (mp0) outliers start: 37 outliers final: 13 residues processed: 187 average time/residue: 0.4817 time to fit residues: 101.3915 Evaluate side-chains 167 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 152 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 399 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 158 optimal weight: 1.9990 chunk 143 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 294 ASN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN D 358 ASN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.122382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.093896 restraints weight = 19213.159| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.72 r_work: 0.2989 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15066 Z= 0.219 Angle : 0.702 11.451 20565 Z= 0.339 Chirality : 0.048 0.175 2405 Planarity : 0.004 0.070 2523 Dihedral : 14.818 108.947 3246 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.39 % Allowed : 14.17 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.19 (0.19), residues: 1780 helix: -2.98 (0.58), residues: 48 sheet: -0.29 (0.21), residues: 626 loop : -0.98 (0.17), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 150 TYR 0.014 0.002 TYR D 121 PHE 0.016 0.002 PHE H 64 TRP 0.017 0.001 TRP C 178 HIS 0.007 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00514 (14963) covalent geometry : angle 0.64560 (20294) SS BOND : bond 0.00465 ( 38) SS BOND : angle 1.16150 ( 76) hydrogen bonds : bond 0.04140 ( 375) hydrogen bonds : angle 7.44652 ( 1023) link_ALPHA1-2 : bond 0.00654 ( 4) link_ALPHA1-2 : angle 2.25147 ( 12) link_ALPHA1-3 : bond 0.00702 ( 8) link_ALPHA1-3 : angle 1.93490 ( 24) link_ALPHA1-6 : bond 0.00313 ( 8) link_ALPHA1-6 : angle 1.58065 ( 24) link_BETA1-4 : bond 0.00560 ( 17) link_BETA1-4 : angle 2.31337 ( 51) link_BETA1-6 : bond 0.01094 ( 4) link_BETA1-6 : angle 1.97780 ( 12) link_NAG-ASN : bond 0.00528 ( 24) link_NAG-ASN : angle 3.79567 ( 72) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 159 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 ASP cc_start: 0.8493 (t0) cc_final: 0.8284 (t0) REVERT: C 128 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8257 (ptmt) REVERT: C 359 ASP cc_start: 0.8030 (m-30) cc_final: 0.7564 (m-30) REVERT: C 415 LYS cc_start: 0.9160 (tttt) cc_final: 0.8866 (ttmm) REVERT: L 106 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6811 (tm-30) REVERT: B 258 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7969 (mp0) REVERT: B 413 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8081 (tt0) REVERT: B 435 GLU cc_start: 0.8223 (mp0) cc_final: 0.7693 (mp0) REVERT: A 103 ASP cc_start: 0.8600 (t70) cc_final: 0.8166 (t0) REVERT: A 294 ASN cc_start: 0.6772 (OUTLIER) cc_final: 0.6306 (m-40) REVERT: A 359 ASP cc_start: 0.7816 (m-30) cc_final: 0.7529 (m-30) REVERT: D 258 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8242 (mt-10) REVERT: D 390 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8736 (tt) outliers start: 37 outliers final: 19 residues processed: 186 average time/residue: 0.4579 time to fit residues: 96.6299 Evaluate side-chains 171 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 399 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 85 optimal weight: 1.9990 chunk 173 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 145 optimal weight: 0.2980 chunk 56 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 129 optimal weight: 1.9990 chunk 98 optimal weight: 0.6980 chunk 160 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 112 ASN L 6 GLN B 173 GLN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 468 HIS A 104 ASN A 273 GLN A 347 HIS ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.125108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.097380 restraints weight = 19094.076| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.67 r_work: 0.3014 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15066 Z= 0.164 Angle : 0.675 11.214 20565 Z= 0.321 Chirality : 0.047 0.185 2405 Planarity : 0.004 0.064 2523 Dihedral : 13.464 105.602 3246 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.33 % Allowed : 16.12 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.19), residues: 1780 helix: -2.93 (0.59), residues: 48 sheet: -0.25 (0.22), residues: 598 loop : -0.93 (0.17), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 150 TYR 0.012 0.002 TYR D 121 PHE 0.013 0.002 PHE H 64 TRP 0.014 0.001 TRP C 178 HIS 0.005 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00379 (14963) covalent geometry : angle 0.61776 (20294) SS BOND : bond 0.00372 ( 38) SS BOND : angle 1.06232 ( 76) hydrogen bonds : bond 0.03636 ( 375) hydrogen bonds : angle 7.10282 ( 1023) link_ALPHA1-2 : bond 0.00718 ( 4) link_ALPHA1-2 : angle 2.40387 ( 12) link_ALPHA1-3 : bond 0.00826 ( 8) link_ALPHA1-3 : angle 1.80943 ( 24) link_ALPHA1-6 : bond 0.00357 ( 8) link_ALPHA1-6 : angle 1.53575 ( 24) link_BETA1-4 : bond 0.00594 ( 17) link_BETA1-4 : angle 2.36445 ( 51) link_BETA1-6 : bond 0.01261 ( 4) link_BETA1-6 : angle 2.46651 ( 12) link_NAG-ASN : bond 0.00482 ( 24) link_NAG-ASN : angle 3.66893 ( 72) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 ASP cc_start: 0.8497 (t0) cc_final: 0.8052 (t0) REVERT: C 105 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8149 (m) REVERT: C 128 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8247 (ptmt) REVERT: C 359 ASP cc_start: 0.8031 (OUTLIER) cc_final: 0.7525 (m-30) REVERT: C 415 LYS cc_start: 0.9170 (tttt) cc_final: 0.8872 (ttmm) REVERT: H 38 ARG cc_start: 0.8331 (ttp80) cc_final: 0.8089 (ttp80) REVERT: L 106 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6794 (tm-30) REVERT: B 258 GLU cc_start: 0.8261 (mt-10) cc_final: 0.8005 (mp0) REVERT: B 277 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8039 (pt0) REVERT: B 413 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7888 (tt0) REVERT: B 435 GLU cc_start: 0.8161 (mp0) cc_final: 0.7568 (mp0) REVERT: A 103 ASP cc_start: 0.8563 (t70) cc_final: 0.8071 (t0) REVERT: A 130 TYR cc_start: 0.9073 (m-80) cc_final: 0.8305 (m-80) REVERT: D 390 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8751 (tt) outliers start: 36 outliers final: 19 residues processed: 181 average time/residue: 0.4212 time to fit residues: 86.2564 Evaluate side-chains 166 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 413 GLU Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 399 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 78 optimal weight: 0.9990 chunk 93 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 126 optimal weight: 0.7980 chunk 120 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 123 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 151 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN B 441 ASN B 468 HIS A 104 ASN A 347 HIS ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN D 441 ASN D 468 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.125627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.098182 restraints weight = 19129.140| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.66 r_work: 0.3018 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 15066 Z= 0.158 Angle : 0.667 11.272 20565 Z= 0.315 Chirality : 0.047 0.197 2405 Planarity : 0.004 0.061 2523 Dihedral : 12.534 102.371 3246 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.85 % Allowed : 17.28 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.10 (0.19), residues: 1780 helix: -2.92 (0.58), residues: 48 sheet: -0.22 (0.21), residues: 599 loop : -0.91 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 150 TYR 0.012 0.002 TYR D 121 PHE 0.012 0.002 PHE B 354 TRP 0.013 0.001 TRP C 178 HIS 0.005 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00362 (14963) covalent geometry : angle 0.61104 (20294) SS BOND : bond 0.00358 ( 38) SS BOND : angle 0.97105 ( 76) hydrogen bonds : bond 0.03470 ( 375) hydrogen bonds : angle 6.87453 ( 1023) link_ALPHA1-2 : bond 0.00769 ( 4) link_ALPHA1-2 : angle 2.58565 ( 12) link_ALPHA1-3 : bond 0.00837 ( 8) link_ALPHA1-3 : angle 1.74874 ( 24) link_ALPHA1-6 : bond 0.00384 ( 8) link_ALPHA1-6 : angle 1.52471 ( 24) link_BETA1-4 : bond 0.00603 ( 17) link_BETA1-4 : angle 2.32797 ( 51) link_BETA1-6 : bond 0.01362 ( 4) link_BETA1-6 : angle 2.09779 ( 12) link_NAG-ASN : bond 0.00487 ( 24) link_NAG-ASN : angle 3.66577 ( 72) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 151 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 ASP cc_start: 0.8467 (t0) cc_final: 0.8022 (t0) REVERT: C 105 SER cc_start: 0.8564 (OUTLIER) cc_final: 0.8125 (m) REVERT: C 128 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8307 (ptmt) REVERT: C 359 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7487 (m-30) REVERT: C 415 LYS cc_start: 0.9167 (tttt) cc_final: 0.8865 (ttmm) REVERT: H 38 ARG cc_start: 0.8365 (ttp80) cc_final: 0.8044 (ttp80) REVERT: L 106 GLU cc_start: 0.7104 (tm-30) cc_final: 0.6775 (tm-30) REVERT: B 258 GLU cc_start: 0.8239 (mt-10) cc_final: 0.7998 (mp0) REVERT: B 309 ASP cc_start: 0.8120 (m-30) cc_final: 0.7914 (p0) REVERT: B 435 GLU cc_start: 0.8175 (mp0) cc_final: 0.7543 (mp0) REVERT: A 103 ASP cc_start: 0.8538 (t70) cc_final: 0.8076 (t0) REVERT: A 130 TYR cc_start: 0.9059 (m-80) cc_final: 0.8299 (m-80) REVERT: A 294 ASN cc_start: 0.6615 (OUTLIER) cc_final: 0.6248 (m-40) REVERT: D 390 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8746 (tt) REVERT: D 399 ASP cc_start: 0.8123 (OUTLIER) cc_final: 0.7892 (m-30) outliers start: 44 outliers final: 25 residues processed: 183 average time/residue: 0.4332 time to fit residues: 90.0934 Evaluate side-chains 169 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 138 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 390 LEU Chi-restraints excluded: chain D residue 399 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 27 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 67 optimal weight: 3.9990 chunk 174 optimal weight: 0.9980 chunk 137 optimal weight: 0.2980 chunk 41 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 104 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 HIS ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.125307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.096944 restraints weight = 19003.291| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.72 r_work: 0.3030 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15066 Z= 0.138 Angle : 0.652 11.798 20565 Z= 0.307 Chirality : 0.047 0.198 2405 Planarity : 0.004 0.059 2523 Dihedral : 11.785 98.912 3246 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.78 % Allowed : 18.25 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.19), residues: 1780 helix: -2.89 (0.58), residues: 48 sheet: -0.16 (0.21), residues: 599 loop : -0.88 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG C 150 TYR 0.013 0.001 TYR C 121 PHE 0.012 0.001 PHE C 354 TRP 0.013 0.001 TRP C 178 HIS 0.004 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00312 (14963) covalent geometry : angle 0.59704 (20294) SS BOND : bond 0.00351 ( 38) SS BOND : angle 0.90135 ( 76) hydrogen bonds : bond 0.03315 ( 375) hydrogen bonds : angle 6.68614 ( 1023) link_ALPHA1-2 : bond 0.00850 ( 4) link_ALPHA1-2 : angle 2.75345 ( 12) link_ALPHA1-3 : bond 0.00908 ( 8) link_ALPHA1-3 : angle 1.66468 ( 24) link_ALPHA1-6 : bond 0.00455 ( 8) link_ALPHA1-6 : angle 1.50471 ( 24) link_BETA1-4 : bond 0.00618 ( 17) link_BETA1-4 : angle 2.26580 ( 51) link_BETA1-6 : bond 0.01275 ( 4) link_BETA1-6 : angle 1.93860 ( 12) link_NAG-ASN : bond 0.00471 ( 24) link_NAG-ASN : angle 3.61127 ( 72) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 148 time to evaluate : 0.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 ASP cc_start: 0.8449 (t0) cc_final: 0.7982 (t0) REVERT: C 105 SER cc_start: 0.8557 (OUTLIER) cc_final: 0.8116 (m) REVERT: C 128 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.8267 (ptmt) REVERT: C 359 ASP cc_start: 0.8011 (OUTLIER) cc_final: 0.7481 (m-30) REVERT: C 415 LYS cc_start: 0.9165 (tttt) cc_final: 0.8862 (ttmm) REVERT: L 106 GLU cc_start: 0.7081 (tm-30) cc_final: 0.6737 (tm-30) REVERT: B 258 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7940 (mp0) REVERT: B 435 GLU cc_start: 0.8185 (mp0) cc_final: 0.7540 (mp0) REVERT: A 103 ASP cc_start: 0.8526 (t70) cc_final: 0.8012 (t0) REVERT: A 130 TYR cc_start: 0.9045 (m-80) cc_final: 0.8273 (m-80) REVERT: D 399 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7903 (m-30) outliers start: 43 outliers final: 20 residues processed: 181 average time/residue: 0.4449 time to fit residues: 91.3647 Evaluate side-chains 161 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 137 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 399 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 30 optimal weight: 0.0070 chunk 173 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.0570 chunk 6 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 HIS ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 ASN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.126092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.097696 restraints weight = 18960.174| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.71 r_work: 0.3049 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15066 Z= 0.144 Angle : 0.656 11.973 20565 Z= 0.308 Chirality : 0.047 0.209 2405 Planarity : 0.004 0.060 2523 Dihedral : 11.220 96.159 3246 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.52 % Allowed : 19.03 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.20 % 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: -0.99 (0.19), residues: 1780 helix: -2.84 (0.58), residues: 48 sheet: -0.12 (0.21), residues: 599 loop : -0.85 (0.17), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 150 TYR 0.011 0.001 TYR D 121 PHE 0.012 0.001 PHE C 354 TRP 0.012 0.001 TRP C 178 HIS 0.004 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00328 (14963) covalent geometry : angle 0.59905 (20294) SS BOND : bond 0.00379 ( 38) SS BOND : angle 0.91336 ( 76) hydrogen bonds : bond 0.03269 ( 375) hydrogen bonds : angle 6.54442 ( 1023) link_ALPHA1-2 : bond 0.00896 ( 4) link_ALPHA1-2 : angle 2.90755 ( 12) link_ALPHA1-3 : bond 0.00892 ( 8) link_ALPHA1-3 : angle 1.65864 ( 24) link_ALPHA1-6 : bond 0.00459 ( 8) link_ALPHA1-6 : angle 1.51180 ( 24) link_BETA1-4 : bond 0.00621 ( 17) link_BETA1-4 : angle 2.30010 ( 51) link_BETA1-6 : bond 0.01249 ( 4) link_BETA1-6 : angle 1.60726 ( 12) link_NAG-ASN : bond 0.00478 ( 24) link_NAG-ASN : angle 3.66907 ( 72) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 ASP cc_start: 0.8453 (t0) cc_final: 0.7996 (t0) REVERT: C 105 SER cc_start: 0.8573 (OUTLIER) cc_final: 0.8118 (m) REVERT: C 128 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8226 (ptmt) REVERT: C 359 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7524 (m-30) REVERT: C 415 LYS cc_start: 0.9174 (tttt) cc_final: 0.8867 (ttmm) REVERT: L 106 GLU cc_start: 0.7126 (tm-30) cc_final: 0.6708 (tm-30) REVERT: B 258 GLU cc_start: 0.8232 (mt-10) cc_final: 0.7979 (mp0) REVERT: B 277 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8096 (pt0) REVERT: B 435 GLU cc_start: 0.8196 (mp0) cc_final: 0.7569 (mp0) REVERT: A 103 ASP cc_start: 0.8500 (t70) cc_final: 0.8032 (t0) REVERT: A 130 TYR cc_start: 0.9041 (m-80) cc_final: 0.8280 (m-80) REVERT: D 399 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7908 (m-30) outliers start: 39 outliers final: 27 residues processed: 174 average time/residue: 0.4365 time to fit residues: 86.2888 Evaluate side-chains 170 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 138 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 399 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 70 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 144 optimal weight: 5.9990 chunk 21 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 159 optimal weight: 0.8980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 168 HIS ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.123885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.095375 restraints weight = 19001.476| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.72 r_work: 0.3016 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 15066 Z= 0.214 Angle : 0.693 12.120 20565 Z= 0.328 Chirality : 0.048 0.233 2405 Planarity : 0.004 0.063 2523 Dihedral : 11.254 97.255 3246 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.11 % Allowed : 18.96 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.19), residues: 1780 helix: -2.98 (0.56), residues: 48 sheet: -0.07 (0.21), residues: 591 loop : -0.90 (0.17), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 150 TYR 0.015 0.002 TYR C 121 PHE 0.017 0.002 PHE B 354 TRP 0.014 0.001 TRP C 178 HIS 0.004 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00504 (14963) covalent geometry : angle 0.63477 (20294) SS BOND : bond 0.00421 ( 38) SS BOND : angle 1.09326 ( 76) hydrogen bonds : bond 0.03476 ( 375) hydrogen bonds : angle 6.63156 ( 1023) link_ALPHA1-2 : bond 0.00803 ( 4) link_ALPHA1-2 : angle 2.99417 ( 12) link_ALPHA1-3 : bond 0.00781 ( 8) link_ALPHA1-3 : angle 1.87297 ( 24) link_ALPHA1-6 : bond 0.00339 ( 8) link_ALPHA1-6 : angle 1.59107 ( 24) link_BETA1-4 : bond 0.00549 ( 17) link_BETA1-4 : angle 2.42012 ( 51) link_BETA1-6 : bond 0.01168 ( 4) link_BETA1-6 : angle 1.59686 ( 12) link_NAG-ASN : bond 0.00531 ( 24) link_NAG-ASN : angle 3.77615 ( 72) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 137 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 ASP cc_start: 0.8456 (t0) cc_final: 0.7982 (t0) REVERT: C 105 SER cc_start: 0.8566 (OUTLIER) cc_final: 0.8053 (m) REVERT: C 128 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8241 (ptmt) REVERT: C 359 ASP cc_start: 0.8075 (OUTLIER) cc_final: 0.7558 (m-30) REVERT: C 415 LYS cc_start: 0.9202 (tttt) cc_final: 0.8877 (ttmm) REVERT: L 106 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6840 (tm-30) REVERT: B 258 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8055 (mp0) REVERT: B 435 GLU cc_start: 0.8218 (mp0) cc_final: 0.7662 (mp0) REVERT: A 103 ASP cc_start: 0.8521 (t70) cc_final: 0.8023 (t0) REVERT: A 130 TYR cc_start: 0.9065 (m-80) cc_final: 0.8347 (m-80) REVERT: D 273 GLN cc_start: 0.7852 (tm130) cc_final: 0.7650 (tm-30) REVERT: D 399 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7936 (m-30) outliers start: 48 outliers final: 31 residues processed: 175 average time/residue: 0.4461 time to fit residues: 88.3239 Evaluate side-chains 170 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 344 LYS Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 399 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 137 optimal weight: 0.1980 chunk 124 optimal weight: 0.9980 chunk 123 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 142 optimal weight: 0.7980 chunk 38 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 HIS ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.126230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.097762 restraints weight = 18957.020| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.72 r_work: 0.3050 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15066 Z= 0.136 Angle : 0.657 12.053 20565 Z= 0.309 Chirality : 0.046 0.211 2405 Planarity : 0.004 0.060 2523 Dihedral : 10.617 92.342 3246 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.78 % Allowed : 19.61 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.20 % 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: -0.92 (0.19), residues: 1780 helix: -2.93 (0.57), residues: 48 sheet: -0.12 (0.21), residues: 627 loop : -0.78 (0.18), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 150 TYR 0.010 0.001 TYR D 121 PHE 0.012 0.001 PHE C 354 TRP 0.012 0.001 TRP B 178 HIS 0.003 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00306 (14963) covalent geometry : angle 0.60123 (20294) SS BOND : bond 0.00347 ( 38) SS BOND : angle 0.94224 ( 76) hydrogen bonds : bond 0.03225 ( 375) hydrogen bonds : angle 6.45643 ( 1023) link_ALPHA1-2 : bond 0.01089 ( 4) link_ALPHA1-2 : angle 2.98113 ( 12) link_ALPHA1-3 : bond 0.00948 ( 8) link_ALPHA1-3 : angle 1.64038 ( 24) link_ALPHA1-6 : bond 0.00457 ( 8) link_ALPHA1-6 : angle 1.50809 ( 24) link_BETA1-4 : bond 0.00613 ( 17) link_BETA1-4 : angle 2.25340 ( 51) link_BETA1-6 : bond 0.01215 ( 4) link_BETA1-6 : angle 1.57404 ( 12) link_NAG-ASN : bond 0.00487 ( 24) link_NAG-ASN : angle 3.66870 ( 72) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 145 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 ASP cc_start: 0.8454 (t0) cc_final: 0.7977 (t0) REVERT: C 105 SER cc_start: 0.8551 (OUTLIER) cc_final: 0.8073 (m) REVERT: C 128 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8257 (ptmt) REVERT: C 160 MET cc_start: 0.9200 (ttp) cc_final: 0.8873 (ttp) REVERT: C 359 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7523 (m-30) REVERT: C 415 LYS cc_start: 0.9170 (tttt) cc_final: 0.8857 (ttmm) REVERT: H 43 GLN cc_start: 0.7135 (mm110) cc_final: 0.6897 (tm-30) REVERT: L 106 GLU cc_start: 0.7185 (tm-30) cc_final: 0.6719 (tm-30) REVERT: B 258 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7979 (mp0) REVERT: B 355 ASP cc_start: 0.9023 (p0) cc_final: 0.8612 (p0) REVERT: B 435 GLU cc_start: 0.8216 (mp0) cc_final: 0.7650 (mp0) REVERT: A 103 ASP cc_start: 0.8485 (t70) cc_final: 0.8014 (t0) REVERT: A 130 TYR cc_start: 0.9042 (m-80) cc_final: 0.8272 (m-80) REVERT: D 103 ASP cc_start: 0.8612 (t70) cc_final: 0.8328 (t70) REVERT: D 390 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8714 (tt) outliers start: 43 outliers final: 30 residues processed: 178 average time/residue: 0.4533 time to fit residues: 91.4308 Evaluate side-chains 172 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 138 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 359 ASP Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 338 LEU Chi-restraints excluded: chain D residue 390 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 160 optimal weight: 0.8980 chunk 111 optimal weight: 0.6980 chunk 162 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 161 optimal weight: 0.7980 chunk 49 optimal weight: 0.7980 chunk 67 optimal weight: 0.6980 chunk 152 optimal weight: 5.9990 chunk 20 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 HIS ** D 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.126464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.098045 restraints weight = 18902.890| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.72 r_work: 0.3052 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15066 Z= 0.144 Angle : 0.657 12.015 20565 Z= 0.307 Chirality : 0.046 0.217 2405 Planarity : 0.004 0.060 2523 Dihedral : 9.819 87.202 3246 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.52 % Allowed : 20.32 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.20 % 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: -0.85 (0.19), residues: 1780 helix: -2.89 (0.57), residues: 48 sheet: 0.05 (0.21), residues: 610 loop : -0.80 (0.18), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 150 TYR 0.013 0.001 TYR C 121 PHE 0.012 0.001 PHE B 354 TRP 0.013 0.001 TRP C 178 HIS 0.003 0.001 HIS D 274 Details of bonding type rmsd covalent geometry : bond 0.00327 (14963) covalent geometry : angle 0.60183 (20294) SS BOND : bond 0.00367 ( 38) SS BOND : angle 0.92934 ( 76) hydrogen bonds : bond 0.03193 ( 375) hydrogen bonds : angle 6.38503 ( 1023) link_ALPHA1-2 : bond 0.01288 ( 4) link_ALPHA1-2 : angle 2.84199 ( 12) link_ALPHA1-3 : bond 0.00865 ( 8) link_ALPHA1-3 : angle 1.69098 ( 24) link_ALPHA1-6 : bond 0.00470 ( 8) link_ALPHA1-6 : angle 1.50593 ( 24) link_BETA1-4 : bond 0.00605 ( 17) link_BETA1-4 : angle 2.31300 ( 51) link_BETA1-6 : bond 0.01346 ( 4) link_BETA1-6 : angle 1.36683 ( 12) link_NAG-ASN : bond 0.00475 ( 24) link_NAG-ASN : angle 3.62869 ( 72) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 103 ASP cc_start: 0.8438 (t0) cc_final: 0.7949 (t0) REVERT: C 105 SER cc_start: 0.8539 (OUTLIER) cc_final: 0.8048 (m) REVERT: C 128 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8197 (ptmt) REVERT: C 160 MET cc_start: 0.9196 (ttp) cc_final: 0.8789 (ttp) REVERT: C 359 ASP cc_start: 0.8040 (OUTLIER) cc_final: 0.7517 (m-30) REVERT: C 415 LYS cc_start: 0.9171 (tttt) cc_final: 0.8865 (ttmt) REVERT: L 106 GLU cc_start: 0.7202 (tm-30) cc_final: 0.6736 (tm-30) REVERT: B 258 GLU cc_start: 0.8222 (mt-10) cc_final: 0.7971 (mp0) REVERT: B 277 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8133 (pt0) REVERT: B 435 GLU cc_start: 0.8229 (mp0) cc_final: 0.7676 (mp0) REVERT: A 103 ASP cc_start: 0.8487 (t70) cc_final: 0.8009 (t0) REVERT: A 130 TYR cc_start: 0.9036 (m-80) cc_final: 0.8278 (m-80) REVERT: D 103 ASP cc_start: 0.8587 (t70) cc_final: 0.8305 (t70) outliers start: 39 outliers final: 29 residues processed: 175 average time/residue: 0.4844 time to fit residues: 95.8808 Evaluate side-chains 176 residues out of total 1545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 143 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 CYS Chi-restraints excluded: chain C residue 105 SER Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 128 LYS Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 325 THR Chi-restraints excluded: chain C residue 359 ASP Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 455 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 69 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 169 LEU Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 277 GLU Chi-restraints excluded: chain B residue 362 MET Chi-restraints excluded: chain B residue 400 ARG Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 271 SER Chi-restraints excluded: chain D residue 275 VAL Chi-restraints excluded: chain D residue 329 THR Chi-restraints excluded: chain D residue 338 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 97 optimal weight: 3.9990 chunk 167 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 142 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 173 GLN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 ASN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 468 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.124214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.095718 restraints weight = 18987.600| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.72 r_work: 0.3020 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 15066 Z= 0.198 Angle : 0.693 12.210 20565 Z= 0.328 Chirality : 0.048 0.241 2405 Planarity : 0.004 0.062 2523 Dihedral : 9.738 86.860 3246 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.59 % Allowed : 20.39 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.20 % 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: -0.98 (0.19), residues: 1780 helix: -2.98 (0.57), residues: 48 sheet: -0.01 (0.21), residues: 590 loop : -0.90 (0.17), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C 150 TYR 0.013 0.002 TYR D 121 PHE 0.016 0.002 PHE B 354 TRP 0.015 0.001 TRP D 295 HIS 0.003 0.001 HIS A 184 Details of bonding type rmsd covalent geometry : bond 0.00463 (14963) covalent geometry : angle 0.63484 (20294) SS BOND : bond 0.00414 ( 38) SS BOND : angle 1.10520 ( 76) hydrogen bonds : bond 0.03381 ( 375) hydrogen bonds : angle 6.51487 ( 1023) link_ALPHA1-2 : bond 0.01247 ( 4) link_ALPHA1-2 : angle 2.73763 ( 12) link_ALPHA1-3 : bond 0.00759 ( 8) link_ALPHA1-3 : angle 1.89419 ( 24) link_ALPHA1-6 : bond 0.00342 ( 8) link_ALPHA1-6 : angle 1.60019 ( 24) link_BETA1-4 : bond 0.00551 ( 17) link_BETA1-4 : angle 2.44983 ( 51) link_BETA1-6 : bond 0.01226 ( 4) link_BETA1-6 : angle 1.29268 ( 12) link_NAG-ASN : bond 0.00521 ( 24) link_NAG-ASN : angle 3.79677 ( 72) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4582.25 seconds wall clock time: 79 minutes 21.54 seconds (4761.54 seconds total)