Starting phenix.real_space_refine on Thu Mar 5 06:18:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pzw_20538/03_2026/6pzw_20538.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pzw_20538/03_2026/6pzw_20538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6pzw_20538/03_2026/6pzw_20538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pzw_20538/03_2026/6pzw_20538.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pzw_20538/03_2026/6pzw_20538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pzw_20538/03_2026/6pzw_20538.map" } resolution = 3.0 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= 0.143 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 124 5.16 5 C 12304 2.51 5 N 3379 2.21 5 O 3971 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19778 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3054 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 366} Chain: "I" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "K" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 118} Chain: "D" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3054 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 366} Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "F" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 118} Chain: "G" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "J" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 118} Chain: "C" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3054 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 366} Chain: "B" Number of atoms: 3054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3054 Classifications: {'peptide': 388} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 366} Chain: "L" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 790 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 957 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 118} Chain: "M" 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: "N" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "S" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 105 Unusual residues: {'BMA': 1, 'MAN': 6, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 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: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.63, per 1000 atoms: 0.23 Number of scatterers: 19778 At special positions: 0 Unit cell: (167.89, 167.89, 88.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 124 16.00 O 3971 8.00 N 3379 7.00 C 12304 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=1.82 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=2.04 Simple disulfide: pdb=" SG CYS D 175 " - pdb=" SG CYS D 193 " distance=2.03 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=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=1.82 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Simple disulfide: pdb=" SG CYS J 22 " - pdb=" SG CYS J 92 " distance=1.82 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=2.03 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=2.04 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=2.04 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=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=1.82 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 N 4 " - " MAN N 5 " " MAN N 5 " - " MAN N 6 " " MAN P 4 " - " MAN P 5 " " MAN P 5 " - " MAN P 6 " " MAN R 4 " - " MAN R 5 " " MAN R 5 " - " MAN R 6 " " MAN S 4 " - " MAN S 5 " " MAN S 5 " - " MAN S 6 " ALPHA1-3 " BMA N 3 " - " MAN N 4 " " MAN N 7 " - " MAN N 8 " " BMA P 3 " - " MAN P 4 " " MAN P 7 " - " MAN P 8 " " BMA R 3 " - " MAN R 4 " " MAN R 7 " - " MAN R 8 " " BMA S 3 " - " MAN S 4 " " MAN S 7 " - " MAN S 8 " ALPHA1-6 " BMA N 3 " - " MAN N 7 " " MAN N 7 " - " MAN N 9 " " BMA P 3 " - " MAN P 7 " " MAN P 7 " - " MAN P 9 " " BMA R 3 " - " MAN R 7 " " MAN R 7 " - " MAN R 9 " " BMA S 3 " - " MAN S 7 " " MAN S 7 " - " MAN S 9 " BETA1-4 " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG N 2 " - " BMA N 3 " " 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 R 2 " - " BMA R 3 " " NAG S 1 " - " NAG S 2 " " NAG S 2 " - " BMA S 3 " " NAG T 1 " - " NAG T 2 " NAG-ASN " NAG B1301 " - " ASN B 86 " " NAG C1301 " - " ASN C 86 " " NAG D1301 " - " ASN D 86 " " NAG M 1 " - " ASN A 146 " " NAG N 1 " - " ASN A 200 " " NAG O 1 " - " ASN D 146 " " NAG P 1 " - " ASN D 200 " " NAG Q 1 " - " ASN C 146 " " NAG R 1 " - " ASN C 200 " " NAG S 1 " - " ASN B 200 " " NAG T 1 " - " ASN B 146 " Time building additional restraints: 1.65 Conformation dependent library (CDL) restraints added in 954.1 milliseconds 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4496 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 52 sheets defined 6.0% alpha, 44.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 104 through 109 Processing helix chain 'A' and resid 110 through 112 No H-bonds generated for 'chain 'A' and resid 110 through 112' Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 463 through 468 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'K' and resid 28 through 30 No H-bonds generated for 'chain 'K' and resid 28 through 30' Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'D' and resid 104 through 109 Processing helix chain 'D' and resid 110 through 112 No H-bonds generated for 'chain 'D' and resid 110 through 112' Processing helix chain 'D' and resid 142 through 146 Processing helix chain 'D' and resid 463 through 468 Processing helix chain 'E' and resid 79 through 83 Processing helix chain 'F' and resid 28 through 30 No H-bonds generated for 'chain 'F' and resid 28 through 30' Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 79 through 83 Processing helix chain 'J' and resid 28 through 30 No H-bonds generated for 'chain 'J' and resid 28 through 30' Processing helix chain 'J' and resid 61 through 64 Processing helix chain 'J' and resid 83 through 87 Processing helix chain 'C' and resid 104 through 109 Processing helix chain 'C' and resid 110 through 112 No H-bonds generated for 'chain 'C' and resid 110 through 112' Processing helix chain 'C' and resid 142 through 146 Processing helix chain 'C' and resid 463 through 468 Processing helix chain 'B' and resid 104 through 109 Processing helix chain 'B' and resid 110 through 112 No H-bonds generated for 'chain 'B' and resid 110 through 112' Processing helix chain 'B' and resid 142 through 146 Processing helix chain 'B' and resid 463 through 468 Processing helix chain 'L' and resid 79 through 83 Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 83 through 87 Processing sheet with id=AA1, first strand: chain 'A' and resid 90 through 91 removed outlier: 6.905A pdb=" N GLY A 90 " --> pdb=" O TYR A 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 102 removed outlier: 6.713A pdb=" N SER A 445 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS A 102 " --> pdb=" O ILE A 443 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE A 443 " --> pdb=" O LYS A 102 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA A 420 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 115 through 125 removed outlier: 4.579A pdb=" N LEU A 115 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N THR A 138 " --> pdb=" O LEU A 115 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR A 117 " --> pdb=" O GLN A 136 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN A 136 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLU A 119 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU A 134 " --> pdb=" O GLU A 119 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU A 158 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 179 through 184 removed outlier: 5.645A pdb=" N TYR A 207 " --> pdb=" O PRO A 211 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 236 through 244 removed outlier: 7.492A pdb=" N THR A 252 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER A 267 " --> pdb=" O THR A 252 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 254 " --> pdb=" O TRP A 265 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TRP A 265 " --> pdb=" O ILE A 254 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR A 256 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 283 removed outlier: 4.605A pdb=" N CYS A 278 " --> pdb=" O THR A 290 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR A 290 " --> pdb=" O CYS A 278 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N CYS A 280 " --> pdb=" O THR A 288 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR A 288 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY A 282 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 354 removed outlier: 6.894A pdb=" N SER A 372 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU A 399 " --> pdb=" O SER A 372 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR A 374 " --> pdb=" O ILE A 397 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN A 393 " --> pdb=" O LYS A 378 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 9 through 13 removed outlier: 3.822A pdb=" N GLY I 13 " --> pdb=" O THR I 105 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP I 35 " --> pdb=" O MET I 47 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 9 through 13 removed outlier: 3.822A pdb=" N GLY I 13 " --> pdb=" O THR I 105 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR I 95A" --> pdb=" O THR I 92 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 19 through 24 Processing sheet with id=AB2, first strand: chain 'K' and resid 3 through 7 Processing sheet with id=AB3, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.481A pdb=" N GLY K 10 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY K 33 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL K 50 " --> pdb=" O MET K 34 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP K 36 " --> pdb=" O VAL K 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 10 through 11 removed outlier: 6.481A pdb=" N GLY K 10 " --> pdb=" O THR K 110 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS K 92 " --> pdb=" O TRP K 103 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TRP K 103 " --> pdb=" O CYS K 92 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS K 94 " --> pdb=" O ASP K 101 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 90 through 91 removed outlier: 6.905A pdb=" N GLY D 90 " --> pdb=" O TYR D 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 96 through 102 removed outlier: 6.713A pdb=" N SER D 445 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS D 102 " --> pdb=" O ILE D 443 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE D 443 " --> pdb=" O LYS D 102 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA D 420 " --> pdb=" O SER D 448 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 115 through 125 removed outlier: 4.579A pdb=" N LEU D 115 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N THR D 138 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR D 117 " --> pdb=" O GLN D 136 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN D 136 " --> pdb=" O THR D 117 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLU D 119 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU D 134 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU D 158 " --> pdb=" O GLU D 174 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 179 through 184 removed outlier: 5.645A pdb=" N TYR D 207 " --> pdb=" O PRO D 211 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 236 through 244 removed outlier: 7.492A pdb=" N THR D 252 " --> pdb=" O SER D 267 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER D 267 " --> pdb=" O THR D 252 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE D 254 " --> pdb=" O TRP D 265 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TRP D 265 " --> pdb=" O ILE D 254 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR D 256 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 276 through 283 removed outlier: 4.605A pdb=" N CYS D 278 " --> pdb=" O THR D 290 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR D 290 " --> pdb=" O CYS D 278 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N CYS D 280 " --> pdb=" O THR D 288 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR D 288 " --> pdb=" O CYS D 280 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY D 282 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY D 286 " --> pdb=" O GLY D 282 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 353 through 354 removed outlier: 6.894A pdb=" N SER D 372 " --> pdb=" O LEU D 399 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU D 399 " --> pdb=" O SER D 372 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR D 374 " --> pdb=" O ILE D 397 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN D 393 " --> pdb=" O LYS D 378 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 9 through 13 removed outlier: 3.822A pdb=" N GLY E 13 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP E 35 " --> pdb=" O MET E 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 9 through 13 removed outlier: 3.822A pdb=" N GLY E 13 " --> pdb=" O THR E 105 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR E 95A" --> pdb=" O THR E 92 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 19 through 24 Processing sheet with id=AC6, first strand: chain 'F' and resid 3 through 7 Processing sheet with id=AC7, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.481A pdb=" N GLY F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY F 33 " --> pdb=" O ASP F 95 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL F 50 " --> pdb=" O MET F 34 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP F 36 " --> pdb=" O VAL F 48 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 10 through 11 removed outlier: 6.481A pdb=" N GLY F 10 " --> pdb=" O THR F 110 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 9 through 13 removed outlier: 3.822A pdb=" N GLY G 13 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP G 35 " --> pdb=" O MET G 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 9 through 13 removed outlier: 3.822A pdb=" N GLY G 13 " --> pdb=" O THR G 105 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR G 95A" --> pdb=" O THR G 92 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 19 through 24 Processing sheet with id=AD3, first strand: chain 'J' and resid 3 through 7 Processing sheet with id=AD4, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.481A pdb=" N GLY J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY J 33 " --> pdb=" O ASP J 95 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET J 34 " --> pdb=" O VAL J 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL J 50 " --> pdb=" O MET J 34 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP J 36 " --> pdb=" O VAL J 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 10 through 11 removed outlier: 6.481A pdb=" N GLY J 10 " --> pdb=" O THR J 110 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS J 92 " --> pdb=" O TRP J 103 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TRP J 103 " --> pdb=" O CYS J 92 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS J 94 " --> pdb=" O ASP J 101 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 90 through 91 removed outlier: 6.905A pdb=" N GLY C 90 " --> pdb=" O TYR C 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'C' and resid 96 through 102 removed outlier: 6.713A pdb=" N SER C 445 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS C 102 " --> pdb=" O ILE C 443 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE C 443 " --> pdb=" O LYS C 102 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA C 420 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 115 through 125 removed outlier: 4.579A pdb=" N LEU C 115 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N THR C 138 " --> pdb=" O LEU C 115 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR C 117 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN C 136 " --> pdb=" O THR C 117 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLU C 119 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU C 134 " --> pdb=" O GLU C 119 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU C 158 " --> pdb=" O GLU C 174 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 179 through 184 removed outlier: 5.645A pdb=" N TYR C 207 " --> pdb=" O PRO C 211 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 236 through 244 removed outlier: 7.492A pdb=" N THR C 252 " --> pdb=" O SER C 267 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER C 267 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE C 254 " --> pdb=" O TRP C 265 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TRP C 265 " --> pdb=" O ILE C 254 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR C 256 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 276 through 283 removed outlier: 4.605A pdb=" N CYS C 278 " --> pdb=" O THR C 290 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR C 290 " --> pdb=" O CYS C 278 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N CYS C 280 " --> pdb=" O THR C 288 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR C 288 " --> pdb=" O CYS C 280 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY C 282 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 353 through 354 removed outlier: 6.894A pdb=" N SER C 372 " --> pdb=" O LEU C 399 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU C 399 " --> pdb=" O SER C 372 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR C 374 " --> pdb=" O ILE C 397 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN C 393 " --> pdb=" O LYS C 378 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 90 through 91 removed outlier: 6.905A pdb=" N GLY B 90 " --> pdb=" O TYR B 418 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'B' and resid 96 through 102 removed outlier: 6.713A pdb=" N SER B 445 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS B 102 " --> pdb=" O ILE B 443 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE B 443 " --> pdb=" O LYS B 102 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA B 420 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 115 through 125 removed outlier: 4.579A pdb=" N LEU B 115 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N THR B 138 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N THR B 117 " --> pdb=" O GLN B 136 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLN B 136 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N GLU B 119 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU B 134 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N LEU B 158 " --> pdb=" O GLU B 174 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 179 through 184 removed outlier: 5.645A pdb=" N TYR B 207 " --> pdb=" O PRO B 211 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 236 through 244 removed outlier: 7.492A pdb=" N THR B 252 " --> pdb=" O SER B 267 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N SER B 267 " --> pdb=" O THR B 252 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 254 " --> pdb=" O TRP B 265 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N TRP B 265 " --> pdb=" O ILE B 254 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N TYR B 256 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 276 through 283 removed outlier: 4.605A pdb=" N CYS B 278 " --> pdb=" O THR B 290 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR B 290 " --> pdb=" O CYS B 278 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N CYS B 280 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N THR B 288 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY B 282 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLY B 286 " --> pdb=" O GLY B 282 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'B' and resid 353 through 354 removed outlier: 6.894A pdb=" N SER B 372 " --> pdb=" O LEU B 399 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU B 399 " --> pdb=" O SER B 372 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N TYR B 374 " --> pdb=" O ILE B 397 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN B 393 " --> pdb=" O LYS B 378 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.822A pdb=" N GLY L 13 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'L' and resid 9 through 13 removed outlier: 3.822A pdb=" N GLY L 13 " --> pdb=" O THR L 105 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR L 95A" --> pdb=" O THR L 92 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'L' and resid 19 through 24 Processing sheet with id=AF5, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AF6, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.481A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N GLY H 33 " --> pdb=" O ASP H 95 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 10 through 11 removed outlier: 6.481A pdb=" N GLY H 10 " --> pdb=" O THR H 110 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N CYS H 92 " --> pdb=" O TRP H 103 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TRP H 103 " --> pdb=" O CYS H 92 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS H 94 " --> pdb=" O ASP H 101 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 1620 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: 3.82 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 4736 1.32 - 1.46: 6456 1.46 - 1.59: 8906 1.59 - 1.73: 16 1.73 - 1.86: 144 Bond restraints: 20258 Sorted by residual: bond pdb=" C1 NAG D1301 " pdb=" O5 NAG D1301 " ideal model delta sigma weight residual 1.406 1.544 -0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C1 NAG B1301 " pdb=" O5 NAG B1301 " ideal model delta sigma weight residual 1.406 1.544 -0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C1 NAG C1301 " pdb=" O5 NAG C1301 " ideal model delta sigma weight residual 1.406 1.544 -0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C1 NAG Q 2 " pdb=" O5 NAG Q 2 " ideal model delta sigma weight residual 1.406 1.542 -0.136 2.00e-02 2.50e+03 4.65e+01 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.542 -0.136 2.00e-02 2.50e+03 4.65e+01 ... (remaining 20253 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 22959 2.24 - 4.48: 3932 4.48 - 6.72: 570 6.72 - 8.97: 84 8.97 - 11.21: 12 Bond angle restraints: 27557 Sorted by residual: angle pdb=" C ASP D 330 " pdb=" N PRO D 331 " pdb=" CA PRO D 331 " ideal model delta sigma weight residual 120.52 128.51 -7.99 9.90e-01 1.02e+00 6.51e+01 angle pdb=" C ASP B 330 " pdb=" N PRO B 331 " pdb=" CA PRO B 331 " ideal model delta sigma weight residual 120.52 128.51 -7.99 9.90e-01 1.02e+00 6.51e+01 angle pdb=" C ASP C 330 " pdb=" N PRO C 331 " pdb=" CA PRO C 331 " ideal model delta sigma weight residual 120.52 128.51 -7.99 9.90e-01 1.02e+00 6.51e+01 angle pdb=" C ASP A 330 " pdb=" N PRO A 331 " pdb=" CA PRO A 331 " ideal model delta sigma weight residual 120.52 128.51 -7.99 9.90e-01 1.02e+00 6.51e+01 angle pdb=" N GLN A 226 " pdb=" CA GLN A 226 " pdb=" C GLN A 226 " ideal model delta sigma weight residual 111.82 121.15 -9.33 1.16e+00 7.43e-01 6.46e+01 ... (remaining 27552 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.53: 12190 21.53 - 43.06: 291 43.06 - 64.59: 66 64.59 - 86.12: 32 86.12 - 107.65: 20 Dihedral angle restraints: 12599 sinusoidal: 5515 harmonic: 7084 Sorted by residual: dihedral pdb=" CB CYS D 318 " pdb=" SG CYS D 318 " pdb=" SG CYS D 337 " pdb=" CB CYS D 337 " ideal model delta sinusoidal sigma weight residual 93.00 130.37 -37.37 1 1.00e+01 1.00e-02 1.97e+01 dihedral pdb=" CB CYS A 318 " pdb=" SG CYS A 318 " pdb=" SG CYS A 337 " pdb=" CB CYS A 337 " ideal model delta sinusoidal sigma weight residual 93.00 130.37 -37.37 1 1.00e+01 1.00e-02 1.97e+01 dihedral pdb=" CB CYS B 318 " pdb=" SG CYS B 318 " pdb=" SG CYS B 337 " pdb=" CB CYS B 337 " ideal model delta sinusoidal sigma weight residual 93.00 130.37 -37.37 1 1.00e+01 1.00e-02 1.97e+01 ... (remaining 12596 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.101: 2292 0.101 - 0.203: 648 0.203 - 0.304: 144 0.304 - 0.405: 15 0.405 - 0.507: 8 Chirality restraints: 3107 Sorted by residual: chirality pdb=" C1 BMA N 3 " pdb=" O4 NAG N 2 " pdb=" C2 BMA N 3 " pdb=" O5 BMA N 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 5.05e+01 chirality pdb=" C1 BMA S 3 " pdb=" O4 NAG S 2 " pdb=" C2 BMA S 3 " pdb=" O5 BMA S 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 5.05e+01 chirality pdb=" C1 BMA R 3 " pdb=" O4 NAG R 2 " pdb=" C2 BMA R 3 " pdb=" O5 BMA R 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.54 0.14 2.00e-02 2.50e+03 5.05e+01 ... (remaining 3104 not shown) Planarity restraints: 3498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG T 2 " -0.096 2.00e-02 2.50e+03 8.14e-02 8.28e+01 pdb=" C7 NAG T 2 " 0.023 2.00e-02 2.50e+03 pdb=" C8 NAG T 2 " 0.021 2.00e-02 2.50e+03 pdb=" N2 NAG T 2 " 0.130 2.00e-02 2.50e+03 pdb=" O7 NAG T 2 " -0.078 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 456 " 0.070 2.00e-02 2.50e+03 3.45e-02 2.98e+01 pdb=" CG TRP A 456 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP A 456 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 456 " -0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP A 456 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 456 " -0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP A 456 " -0.045 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 456 " 0.029 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 456 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 456 " 0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 456 " -0.070 2.00e-02 2.50e+03 3.45e-02 2.98e+01 pdb=" CG TRP B 456 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP B 456 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP B 456 " 0.039 2.00e-02 2.50e+03 pdb=" NE1 TRP B 456 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP B 456 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP B 456 " 0.045 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 456 " -0.029 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 456 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 456 " -0.041 2.00e-02 2.50e+03 ... (remaining 3495 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 8545 2.90 - 3.40: 17140 3.40 - 3.90: 35063 3.90 - 4.40: 42355 4.40 - 4.90: 69527 Nonbonded interactions: 172630 Sorted by model distance: nonbonded pdb=" OH TYR A 354 " pdb=" O CYS A 421 " model vdw 2.401 3.040 nonbonded pdb=" OH TYR B 354 " pdb=" O CYS B 421 " model vdw 2.401 3.040 nonbonded pdb=" OH TYR D 354 " pdb=" O CYS D 421 " model vdw 2.401 3.040 nonbonded pdb=" OH TYR C 354 " pdb=" O CYS C 421 " model vdw 2.401 3.040 nonbonded pdb=" N ASP C 416 " pdb=" OD1 ASP C 416 " model vdw 2.450 3.120 ... (remaining 172625 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' and resid 82 through 468) selection = (chain 'C' and resid 82 through 468) selection = (chain 'D' and resid 82 through 468) } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'L' } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'T' } ncs_group { reference = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 18.660 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: 0.010 Load rotamer database and sin/cos tables:8.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 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 : 0.021 0.210 20349 Z= 1.093 Angle : 1.748 11.208 27786 Z= 1.145 Chirality : 0.100 0.507 3107 Planarity : 0.009 0.081 3487 Dihedral : 11.602 107.652 7971 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 0.94 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.12 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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 (0.16), residues: 2448 helix: -2.49 (0.45), residues: 48 sheet: 1.24 (0.17), residues: 852 loop : 0.70 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 430 TYR 0.060 0.009 TYR B 155 PHE 0.036 0.008 PHE A 131 TRP 0.070 0.009 TRP B 456 HIS 0.010 0.002 HIS A 274 Details of bonding type rmsd covalent geometry : bond 0.02041 (20258) covalent geometry : angle 1.73099 (27557) SS BOND : bond 0.06341 ( 44) SS BOND : angle 3.42784 ( 88) hydrogen bonds : bond 0.16166 ( 640) hydrogen bonds : angle 8.59763 ( 1620) link_ALPHA1-2 : bond 0.04351 ( 8) link_ALPHA1-2 : angle 3.34232 ( 24) link_ALPHA1-3 : bond 0.03787 ( 8) link_ALPHA1-3 : angle 2.45233 ( 24) link_ALPHA1-6 : bond 0.03080 ( 8) link_ALPHA1-6 : angle 2.80400 ( 24) link_BETA1-4 : bond 0.03152 ( 12) link_BETA1-4 : angle 3.48197 ( 36) link_NAG-ASN : bond 0.02882 ( 11) link_NAG-ASN : angle 2.85053 ( 33) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 348 time to evaluate : 0.769 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 outliers start: 0 outliers final: 0 residues processed: 348 average time/residue: 0.5971 time to fit residues: 233.3422 Evaluate side-chains 144 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 216 optimal weight: 1.9990 chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 227 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN A 441 ASN I 53 ASN I 79 GLN K 30 ASN K 81 GLN K 105 GLN D 83 ASN D 441 ASN E 53 ASN E 79 GLN F 30 ASN F 81 GLN F 105 GLN G 53 ASN G 79 GLN J 30 ASN J 81 GLN J 105 GLN C 83 ASN C 441 ASN B 83 ASN L 53 ASN L 79 GLN H 30 ASN H 81 GLN H 105 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.097259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.082410 restraints weight = 27090.689| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.59 r_work: 0.2892 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 20349 Z= 0.152 Angle : 0.650 7.690 27786 Z= 0.340 Chirality : 0.045 0.157 3107 Planarity : 0.004 0.034 3487 Dihedral : 9.704 81.524 3651 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.33 % Allowed : 1.63 % Favored : 98.04 % Rotamer: Outliers : 1.13 % Allowed : 8.22 % Favored : 90.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.72 (0.17), residues: 2448 helix: -4.38 (0.15), residues: 24 sheet: 0.89 (0.17), residues: 876 loop : 0.42 (0.16), residues: 1548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 141 TYR 0.019 0.002 TYR B 121 PHE 0.010 0.002 PHE A 410 TRP 0.024 0.002 TRP D 206 HIS 0.005 0.001 HIS K 35 Details of bonding type rmsd covalent geometry : bond 0.00341 (20258) covalent geometry : angle 0.63210 (27557) SS BOND : bond 0.00175 ( 44) SS BOND : angle 1.31016 ( 88) hydrogen bonds : bond 0.04507 ( 640) hydrogen bonds : angle 6.82006 ( 1620) link_ALPHA1-2 : bond 0.01169 ( 8) link_ALPHA1-2 : angle 1.97136 ( 24) link_ALPHA1-3 : bond 0.01128 ( 8) link_ALPHA1-3 : angle 1.42485 ( 24) link_ALPHA1-6 : bond 0.01185 ( 8) link_ALPHA1-6 : angle 1.39746 ( 24) link_BETA1-4 : bond 0.00649 ( 12) link_BETA1-4 : angle 2.40695 ( 36) link_NAG-ASN : bond 0.00155 ( 11) link_NAG-ASN : angle 2.29500 ( 33) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 239 time to evaluate : 0.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8801 (tm-30) REVERT: I 79 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7339 (mm-40) REVERT: I 82 ASP cc_start: 0.8664 (m-30) cc_final: 0.8257 (m-30) REVERT: K 57 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8358 (mttm) REVERT: D 110 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8806 (tm-30) REVERT: E 79 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7335 (mm-40) REVERT: E 82 ASP cc_start: 0.8666 (m-30) cc_final: 0.8262 (m-30) REVERT: F 57 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8358 (mttm) REVERT: G 79 GLN cc_start: 0.7791 (mm-40) cc_final: 0.7336 (mm-40) REVERT: G 82 ASP cc_start: 0.8666 (m-30) cc_final: 0.8264 (m-30) REVERT: J 57 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8356 (mttm) REVERT: C 110 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8813 (tm-30) REVERT: B 110 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8805 (tm-30) REVERT: L 79 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7338 (mm-40) REVERT: L 82 ASP cc_start: 0.8657 (m-30) cc_final: 0.8253 (m-30) REVERT: H 57 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8357 (mttm) outliers start: 24 outliers final: 4 residues processed: 247 average time/residue: 0.4888 time to fit residues: 140.6217 Evaluate side-chains 180 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain H residue 57 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 54 optimal weight: 6.9990 chunk 140 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 chunk 135 optimal weight: 2.9990 chunk 198 optimal weight: 0.6980 chunk 183 optimal weight: 0.0170 chunk 226 optimal weight: 6.9990 chunk 225 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 39 optimal weight: 0.0020 chunk 103 optimal weight: 4.9990 overall best weight: 0.9228 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 30 ASN K 76 ASN K 105 GLN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 30 ASN F 76 ASN F 105 GLN J 30 ASN J 76 ASN J 105 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 441 ASN H 30 ASN H 76 ASN H 105 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.095778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.080797 restraints weight = 27240.115| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.59 r_work: 0.2840 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2729 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 20349 Z= 0.131 Angle : 0.581 7.007 27786 Z= 0.303 Chirality : 0.043 0.170 3107 Planarity : 0.004 0.039 3487 Dihedral : 8.814 71.518 3651 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.78 % Favored : 96.90 % Rotamer: Outliers : 1.50 % Allowed : 11.09 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.68 (0.17), residues: 2448 helix: -4.26 (0.12), residues: 24 sheet: 1.05 (0.17), residues: 836 loop : 0.27 (0.16), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 19 TYR 0.019 0.002 TYR D 121 PHE 0.011 0.002 PHE B 410 TRP 0.016 0.001 TRP A 206 HIS 0.004 0.001 HIS K 35 Details of bonding type rmsd covalent geometry : bond 0.00296 (20258) covalent geometry : angle 0.55910 (27557) SS BOND : bond 0.00295 ( 44) SS BOND : angle 1.77294 ( 88) hydrogen bonds : bond 0.03751 ( 640) hydrogen bonds : angle 6.28990 ( 1620) link_ALPHA1-2 : bond 0.00781 ( 8) link_ALPHA1-2 : angle 2.47065 ( 24) link_ALPHA1-3 : bond 0.00977 ( 8) link_ALPHA1-3 : angle 1.26851 ( 24) link_ALPHA1-6 : bond 0.01028 ( 8) link_ALPHA1-6 : angle 1.50829 ( 24) link_BETA1-4 : bond 0.00586 ( 12) link_BETA1-4 : angle 2.04373 ( 36) link_NAG-ASN : bond 0.00089 ( 11) link_NAG-ASN : angle 1.82604 ( 33) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 229 time to evaluate : 0.757 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 12 SER cc_start: 0.8636 (p) cc_final: 0.8387 (m) REVERT: I 79 GLN cc_start: 0.7845 (mm-40) cc_final: 0.7420 (mm110) REVERT: I 82 ASP cc_start: 0.8700 (m-30) cc_final: 0.8336 (m-30) REVERT: K 53 ASP cc_start: 0.9021 (p0) cc_final: 0.8792 (p0) REVERT: K 57 LYS cc_start: 0.8656 (mttm) cc_final: 0.8340 (mttm) REVERT: E 12 SER cc_start: 0.8637 (p) cc_final: 0.8389 (m) REVERT: E 79 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7422 (mm110) REVERT: E 82 ASP cc_start: 0.8702 (m-30) cc_final: 0.8337 (m-30) REVERT: F 53 ASP cc_start: 0.9020 (p0) cc_final: 0.8789 (p0) REVERT: F 57 LYS cc_start: 0.8662 (mttm) cc_final: 0.8350 (mttm) REVERT: G 12 SER cc_start: 0.8633 (p) cc_final: 0.8384 (m) REVERT: G 79 GLN cc_start: 0.7848 (mm-40) cc_final: 0.7426 (mm110) REVERT: G 82 ASP cc_start: 0.8700 (m-30) cc_final: 0.8341 (m-30) REVERT: J 53 ASP cc_start: 0.9021 (p0) cc_final: 0.8785 (p0) REVERT: J 57 LYS cc_start: 0.8659 (mttm) cc_final: 0.8344 (mttm) REVERT: L 12 SER cc_start: 0.8640 (p) cc_final: 0.8392 (m) REVERT: L 79 GLN cc_start: 0.7842 (mm-40) cc_final: 0.7422 (mm110) REVERT: L 82 ASP cc_start: 0.8701 (m-30) cc_final: 0.8338 (m-30) REVERT: H 53 ASP cc_start: 0.9022 (p0) cc_final: 0.8790 (p0) REVERT: H 57 LYS cc_start: 0.8654 (mttm) cc_final: 0.8336 (mttm) outliers start: 32 outliers final: 16 residues processed: 245 average time/residue: 0.5711 time to fit residues: 159.3681 Evaluate side-chains 195 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 179 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain H residue 105 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 70 optimal weight: 3.9990 chunk 119 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 192 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 153 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN J 105 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.085748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.069929 restraints weight = 27368.448| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 1.80 r_work: 0.2656 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2536 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 20349 Z= 0.239 Angle : 0.669 7.089 27786 Z= 0.343 Chirality : 0.046 0.160 3107 Planarity : 0.005 0.044 3487 Dihedral : 8.833 69.997 3651 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.45 % Favored : 97.22 % Rotamer: Outliers : 3.20 % Allowed : 11.09 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.35 (0.17), residues: 2448 helix: -4.21 (0.12), residues: 24 sheet: 0.51 (0.17), residues: 932 loop : 0.23 (0.17), residues: 1492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 210 TYR 0.025 0.002 TYR B 121 PHE 0.011 0.002 PHE A 84 TRP 0.015 0.002 TRP D 456 HIS 0.008 0.002 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00564 (20258) covalent geometry : angle 0.64699 (27557) SS BOND : bond 0.00323 ( 44) SS BOND : angle 1.78704 ( 88) hydrogen bonds : bond 0.04032 ( 640) hydrogen bonds : angle 6.32255 ( 1620) link_ALPHA1-2 : bond 0.00634 ( 8) link_ALPHA1-2 : angle 2.72584 ( 24) link_ALPHA1-3 : bond 0.00745 ( 8) link_ALPHA1-3 : angle 1.71986 ( 24) link_ALPHA1-6 : bond 0.00874 ( 8) link_ALPHA1-6 : angle 1.76195 ( 24) link_BETA1-4 : bond 0.00522 ( 12) link_BETA1-4 : angle 2.29651 ( 36) link_NAG-ASN : bond 0.00260 ( 11) link_NAG-ASN : angle 1.92041 ( 33) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 192 time to evaluate : 0.697 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 12 SER cc_start: 0.8771 (p) cc_final: 0.8422 (m) REVERT: I 79 GLN cc_start: 0.7451 (mm-40) cc_final: 0.7153 (mm110) REVERT: I 82 ASP cc_start: 0.8580 (m-30) cc_final: 0.8167 (m-30) REVERT: K 57 LYS cc_start: 0.8590 (OUTLIER) cc_final: 0.8266 (mttm) REVERT: E 12 SER cc_start: 0.8773 (p) cc_final: 0.8423 (m) REVERT: E 79 GLN cc_start: 0.7452 (mm-40) cc_final: 0.7153 (mm110) REVERT: E 82 ASP cc_start: 0.8582 (m-30) cc_final: 0.8170 (m-30) REVERT: F 57 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8264 (mttm) REVERT: G 12 SER cc_start: 0.8769 (p) cc_final: 0.8418 (m) REVERT: G 79 GLN cc_start: 0.7446 (mm-40) cc_final: 0.7147 (mm110) REVERT: G 82 ASP cc_start: 0.8594 (m-30) cc_final: 0.8184 (m-30) REVERT: J 57 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8266 (mttm) REVERT: L 12 SER cc_start: 0.8775 (p) cc_final: 0.8423 (m) REVERT: L 79 GLN cc_start: 0.7455 (mm-40) cc_final: 0.7161 (mm110) REVERT: L 82 ASP cc_start: 0.8585 (m-30) cc_final: 0.8175 (m-30) REVERT: H 57 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8269 (mttm) outliers start: 68 outliers final: 48 residues processed: 224 average time/residue: 0.5420 time to fit residues: 139.4065 Evaluate side-chains 228 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 176 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 27 ASP Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 416 ASP Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 92 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 168 optimal weight: 0.9980 chunk 158 optimal weight: 1.9990 chunk 35 optimal weight: 0.0270 chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 162 optimal weight: 0.0270 chunk 61 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 124 optimal weight: 0.7980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 98 HIS A 441 ASN K 105 GLN D 98 HIS D 441 ASN F 105 GLN J 105 GLN C 98 HIS C 441 ASN B 98 HIS ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.089803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.073467 restraints weight = 26768.831| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 1.85 r_work: 0.2713 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 20349 Z= 0.102 Angle : 0.546 5.068 27786 Z= 0.281 Chirality : 0.042 0.159 3107 Planarity : 0.004 0.046 3487 Dihedral : 8.122 62.560 3651 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.12 % Favored : 97.71 % Rotamer: Outliers : 3.15 % Allowed : 11.61 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.55 (0.17), residues: 2448 helix: -4.15 (0.11), residues: 24 sheet: 0.91 (0.17), residues: 896 loop : 0.18 (0.17), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 156 TYR 0.015 0.001 TYR B 121 PHE 0.009 0.001 PHE F 98 TRP 0.013 0.001 TRP B 206 HIS 0.003 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00225 (20258) covalent geometry : angle 0.52846 (27557) SS BOND : bond 0.00136 ( 44) SS BOND : angle 1.18581 ( 88) hydrogen bonds : bond 0.03296 ( 640) hydrogen bonds : angle 6.02171 ( 1620) link_ALPHA1-2 : bond 0.00625 ( 8) link_ALPHA1-2 : angle 2.57686 ( 24) link_ALPHA1-3 : bond 0.00883 ( 8) link_ALPHA1-3 : angle 1.41063 ( 24) link_ALPHA1-6 : bond 0.00867 ( 8) link_ALPHA1-6 : angle 1.54892 ( 24) link_BETA1-4 : bond 0.00426 ( 12) link_BETA1-4 : angle 1.72248 ( 36) link_NAG-ASN : bond 0.00130 ( 11) link_NAG-ASN : angle 1.65004 ( 33) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 204 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LYS cc_start: 0.8093 (mttp) cc_final: 0.7433 (mmmt) REVERT: I 12 SER cc_start: 0.8635 (p) cc_final: 0.8229 (m) REVERT: I 79 GLN cc_start: 0.7392 (mm-40) cc_final: 0.6831 (mm-40) REVERT: I 82 ASP cc_start: 0.8537 (m-30) cc_final: 0.8012 (m-30) REVERT: K 57 LYS cc_start: 0.8517 (OUTLIER) cc_final: 0.8180 (mttm) REVERT: D 261 LYS cc_start: 0.8087 (mttp) cc_final: 0.7425 (mmmt) REVERT: E 12 SER cc_start: 0.8639 (p) cc_final: 0.8234 (m) REVERT: E 79 GLN cc_start: 0.7391 (mm-40) cc_final: 0.6831 (mm-40) REVERT: E 82 ASP cc_start: 0.8536 (m-30) cc_final: 0.8011 (m-30) REVERT: F 57 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.8182 (mttm) REVERT: G 12 SER cc_start: 0.8632 (p) cc_final: 0.8226 (m) REVERT: G 79 GLN cc_start: 0.7392 (mm-40) cc_final: 0.6831 (mm-40) REVERT: G 82 ASP cc_start: 0.8555 (m-30) cc_final: 0.8030 (m-30) REVERT: J 57 LYS cc_start: 0.8524 (OUTLIER) cc_final: 0.8188 (mttm) REVERT: C 261 LYS cc_start: 0.8084 (mttp) cc_final: 0.7418 (mmmt) REVERT: B 261 LYS cc_start: 0.8095 (mttp) cc_final: 0.7432 (mmmt) REVERT: L 12 SER cc_start: 0.8642 (p) cc_final: 0.8238 (m) REVERT: L 79 GLN cc_start: 0.7400 (mm-40) cc_final: 0.6842 (mm-40) REVERT: L 82 ASP cc_start: 0.8552 (m-30) cc_final: 0.8028 (m-30) REVERT: H 57 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8185 (mttm) outliers start: 67 outliers final: 48 residues processed: 235 average time/residue: 0.5273 time to fit residues: 142.3400 Evaluate side-chains 236 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 184 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 27 ASP Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 82 MET Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain K residue 105 GLN Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 MET Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 82 MET Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain J residue 105 GLN Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 105 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 19 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 180 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 229 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 209 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 222 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 215 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN J 105 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.089746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.073447 restraints weight = 27479.276| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 1.73 r_work: 0.2748 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 20349 Z= 0.203 Angle : 0.609 5.357 27786 Z= 0.311 Chirality : 0.045 0.163 3107 Planarity : 0.004 0.048 3487 Dihedral : 8.368 64.848 3651 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.78 % Favored : 97.06 % Rotamer: Outliers : 3.38 % Allowed : 11.47 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.37 (0.17), residues: 2448 helix: -4.13 (0.12), residues: 24 sheet: 0.71 (0.17), residues: 904 loop : 0.12 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 419 TYR 0.023 0.002 TYR A 121 PHE 0.010 0.002 PHE B 410 TRP 0.011 0.002 TRP H 47 HIS 0.006 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00482 (20258) covalent geometry : angle 0.58912 (27557) SS BOND : bond 0.00103 ( 44) SS BOND : angle 1.34309 ( 88) hydrogen bonds : bond 0.03729 ( 640) hydrogen bonds : angle 6.02930 ( 1620) link_ALPHA1-2 : bond 0.00457 ( 8) link_ALPHA1-2 : angle 2.77184 ( 24) link_ALPHA1-3 : bond 0.00753 ( 8) link_ALPHA1-3 : angle 1.62360 ( 24) link_ALPHA1-6 : bond 0.00821 ( 8) link_ALPHA1-6 : angle 1.71812 ( 24) link_BETA1-4 : bond 0.00499 ( 12) link_BETA1-4 : angle 2.08127 ( 36) link_NAG-ASN : bond 0.00148 ( 11) link_NAG-ASN : angle 1.75284 ( 33) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 176 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LYS cc_start: 0.8325 (mttp) cc_final: 0.7765 (mmmt) REVERT: I 12 SER cc_start: 0.8517 (p) cc_final: 0.8190 (m) REVERT: I 79 GLN cc_start: 0.7770 (mm-40) cc_final: 0.7304 (mm110) REVERT: I 82 ASP cc_start: 0.8753 (m-30) cc_final: 0.8396 (m-30) REVERT: K 57 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8385 (mttm) REVERT: D 261 LYS cc_start: 0.8328 (mttp) cc_final: 0.7768 (mmmt) REVERT: E 12 SER cc_start: 0.8511 (p) cc_final: 0.8183 (m) REVERT: E 79 GLN cc_start: 0.7767 (mm-40) cc_final: 0.7304 (mm110) REVERT: E 82 ASP cc_start: 0.8748 (m-30) cc_final: 0.8393 (m-30) REVERT: F 57 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8390 (mttm) REVERT: G 12 SER cc_start: 0.8509 (p) cc_final: 0.8180 (m) REVERT: G 79 GLN cc_start: 0.7760 (mm-40) cc_final: 0.7296 (mm110) REVERT: G 82 ASP cc_start: 0.8755 (m-30) cc_final: 0.8400 (m-30) REVERT: J 57 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8392 (mttm) REVERT: C 261 LYS cc_start: 0.8325 (mttp) cc_final: 0.7764 (mmmt) REVERT: B 261 LYS cc_start: 0.8319 (mttp) cc_final: 0.7759 (mmmt) REVERT: L 12 SER cc_start: 0.8507 (p) cc_final: 0.8178 (m) REVERT: L 79 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7286 (mm110) REVERT: L 82 ASP cc_start: 0.8749 (m-30) cc_final: 0.8390 (m-30) REVERT: H 57 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8390 (mttm) outliers start: 72 outliers final: 52 residues processed: 212 average time/residue: 0.5524 time to fit residues: 133.7622 Evaluate side-chains 220 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 164 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 27 ASP Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain K residue 21 SER Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 82 SER Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 82 SER Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain J residue 21 SER Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 82 SER Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 21 SER Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 82 SER Chi-restraints excluded: chain H residue 92 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 59 optimal weight: 0.8980 chunk 174 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 132 optimal weight: 0.0770 chunk 214 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN J 105 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.091547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.075354 restraints weight = 27358.111| |-----------------------------------------------------------------------------| r_work (start): 0.2879 rms_B_bonded: 1.73 r_work: 0.2774 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.3158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20349 Z= 0.132 Angle : 0.553 4.868 27786 Z= 0.283 Chirality : 0.043 0.165 3107 Planarity : 0.004 0.047 3487 Dihedral : 8.036 60.904 3651 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.45 % Favored : 97.39 % Rotamer: Outliers : 3.01 % Allowed : 12.22 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.46 (0.17), residues: 2448 helix: -4.15 (0.11), residues: 24 sheet: 0.84 (0.17), residues: 904 loop : 0.12 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 419 TYR 0.017 0.001 TYR A 121 PHE 0.014 0.001 PHE A 410 TRP 0.011 0.001 TRP C 161 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00304 (20258) covalent geometry : angle 0.53604 (27557) SS BOND : bond 0.00112 ( 44) SS BOND : angle 1.02800 ( 88) hydrogen bonds : bond 0.03361 ( 640) hydrogen bonds : angle 5.97473 ( 1620) link_ALPHA1-2 : bond 0.00570 ( 8) link_ALPHA1-2 : angle 2.66452 ( 24) link_ALPHA1-3 : bond 0.00814 ( 8) link_ALPHA1-3 : angle 1.45731 ( 24) link_ALPHA1-6 : bond 0.00844 ( 8) link_ALPHA1-6 : angle 1.61532 ( 24) link_BETA1-4 : bond 0.00417 ( 12) link_BETA1-4 : angle 1.76332 ( 36) link_NAG-ASN : bond 0.00048 ( 11) link_NAG-ASN : angle 1.63790 ( 33) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 188 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LYS cc_start: 0.8315 (mttp) cc_final: 0.7794 (mmmt) REVERT: I 12 SER cc_start: 0.8437 (p) cc_final: 0.8156 (m) REVERT: I 79 GLN cc_start: 0.7757 (mm-40) cc_final: 0.7260 (mm110) REVERT: I 82 ASP cc_start: 0.8677 (m-30) cc_final: 0.8231 (m-30) REVERT: K 57 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8348 (mttm) REVERT: D 261 LYS cc_start: 0.8317 (mttp) cc_final: 0.7800 (mmmt) REVERT: E 12 SER cc_start: 0.8442 (p) cc_final: 0.8159 (m) REVERT: E 79 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7256 (mm110) REVERT: E 82 ASP cc_start: 0.8673 (m-30) cc_final: 0.8229 (m-30) REVERT: F 57 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8351 (mttm) REVERT: G 12 SER cc_start: 0.8433 (p) cc_final: 0.8152 (m) REVERT: G 79 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7248 (mm110) REVERT: G 82 ASP cc_start: 0.8678 (m-30) cc_final: 0.8237 (m-30) REVERT: J 57 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8350 (mttm) REVERT: C 261 LYS cc_start: 0.8315 (mttp) cc_final: 0.7798 (mmmt) REVERT: B 261 LYS cc_start: 0.8308 (mttp) cc_final: 0.7791 (mmmt) REVERT: L 12 SER cc_start: 0.8435 (p) cc_final: 0.8154 (m) REVERT: L 79 GLN cc_start: 0.7748 (mm-40) cc_final: 0.7250 (mm110) REVERT: L 82 ASP cc_start: 0.8669 (m-30) cc_final: 0.8223 (m-30) REVERT: H 57 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8351 (mttm) outliers start: 64 outliers final: 40 residues processed: 228 average time/residue: 0.5281 time to fit residues: 138.2564 Evaluate side-chains 220 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 176 time to evaluate : 0.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 27 ASP Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 70 SER Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 70 SER Chi-restraints excluded: chain H residue 92 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 172 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 83 optimal weight: 1.9990 chunk 152 optimal weight: 0.6980 chunk 130 optimal weight: 5.9990 chunk 135 optimal weight: 0.4980 chunk 140 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 chunk 109 optimal weight: 0.4980 chunk 16 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN K 105 GLN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN F 105 GLN J 76 ASN J 105 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 105 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.092481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.076421 restraints weight = 27298.479| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.73 r_work: 0.2792 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2675 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 20349 Z= 0.108 Angle : 0.543 6.688 27786 Z= 0.278 Chirality : 0.043 0.169 3107 Planarity : 0.004 0.046 3487 Dihedral : 7.736 59.290 3651 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.45 % Favored : 97.39 % Rotamer: Outliers : 3.20 % Allowed : 12.22 % Favored : 84.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.17), residues: 2448 helix: -4.17 (0.11), residues: 24 sheet: 0.96 (0.17), residues: 904 loop : 0.17 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 19 TYR 0.016 0.001 TYR H 79 PHE 0.009 0.001 PHE A 410 TRP 0.012 0.001 TRP B 161 HIS 0.003 0.001 HIS J 35 Details of bonding type rmsd covalent geometry : bond 0.00244 (20258) covalent geometry : angle 0.52060 (27557) SS BOND : bond 0.00426 ( 44) SS BOND : angle 1.70692 ( 88) hydrogen bonds : bond 0.03201 ( 640) hydrogen bonds : angle 5.89214 ( 1620) link_ALPHA1-2 : bond 0.00607 ( 8) link_ALPHA1-2 : angle 2.62500 ( 24) link_ALPHA1-3 : bond 0.00841 ( 8) link_ALPHA1-3 : angle 1.43562 ( 24) link_ALPHA1-6 : bond 0.00868 ( 8) link_ALPHA1-6 : angle 1.59156 ( 24) link_BETA1-4 : bond 0.00440 ( 12) link_BETA1-4 : angle 1.65180 ( 36) link_NAG-ASN : bond 0.00069 ( 11) link_NAG-ASN : angle 1.54819 ( 33) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 188 time to evaluate : 0.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LYS cc_start: 0.8255 (mttp) cc_final: 0.7759 (mmmt) REVERT: I 79 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7274 (mm110) REVERT: I 82 ASP cc_start: 0.8675 (m-30) cc_final: 0.8275 (m-30) REVERT: K 57 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8301 (mttm) REVERT: D 261 LYS cc_start: 0.8263 (mttp) cc_final: 0.7768 (mmmt) REVERT: E 79 GLN cc_start: 0.7750 (mm-40) cc_final: 0.7272 (mm110) REVERT: E 82 ASP cc_start: 0.8668 (m-30) cc_final: 0.8268 (m-30) REVERT: F 57 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8302 (mttm) REVERT: G 79 GLN cc_start: 0.7738 (mm-40) cc_final: 0.7259 (mm110) REVERT: G 82 ASP cc_start: 0.8675 (m-30) cc_final: 0.8276 (m-30) REVERT: J 57 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8301 (mttm) REVERT: C 261 LYS cc_start: 0.8263 (mttp) cc_final: 0.7779 (mmmt) REVERT: B 261 LYS cc_start: 0.8254 (mttp) cc_final: 0.7775 (mmmt) REVERT: L 79 GLN cc_start: 0.7743 (mm-40) cc_final: 0.7263 (mm110) REVERT: L 82 ASP cc_start: 0.8666 (m-30) cc_final: 0.8266 (m-30) REVERT: H 57 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8304 (mttm) outliers start: 68 outliers final: 32 residues processed: 228 average time/residue: 0.5525 time to fit residues: 144.6729 Evaluate side-chains 208 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 27 ASP Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 92 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 221 optimal weight: 30.0000 chunk 113 optimal weight: 2.9990 chunk 219 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 232 optimal weight: 0.0770 chunk 91 optimal weight: 4.9990 chunk 115 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 133 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN J 105 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.091223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.075007 restraints weight = 27345.462| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 1.73 r_work: 0.2766 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20349 Z= 0.159 Angle : 0.583 10.211 27786 Z= 0.296 Chirality : 0.044 0.212 3107 Planarity : 0.004 0.046 3487 Dihedral : 7.947 59.982 3651 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.43 % Favored : 96.41 % Rotamer: Outliers : 2.63 % Allowed : 12.83 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.50 (0.17), residues: 2448 helix: -4.19 (0.10), residues: 24 sheet: 0.92 (0.17), residues: 904 loop : 0.11 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 419 TYR 0.018 0.001 TYR C 121 PHE 0.010 0.002 PHE A 410 TRP 0.010 0.001 TRP J 47 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00376 (20258) covalent geometry : angle 0.56496 (27557) SS BOND : bond 0.00513 ( 44) SS BOND : angle 1.29329 ( 88) hydrogen bonds : bond 0.03416 ( 640) hydrogen bonds : angle 5.98477 ( 1620) link_ALPHA1-2 : bond 0.00531 ( 8) link_ALPHA1-2 : angle 2.72591 ( 24) link_ALPHA1-3 : bond 0.00772 ( 8) link_ALPHA1-3 : angle 1.50352 ( 24) link_ALPHA1-6 : bond 0.00837 ( 8) link_ALPHA1-6 : angle 1.67374 ( 24) link_BETA1-4 : bond 0.00429 ( 12) link_BETA1-4 : angle 1.84211 ( 36) link_NAG-ASN : bond 0.00109 ( 11) link_NAG-ASN : angle 1.63656 ( 33) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 204 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LYS cc_start: 0.8258 (mttp) cc_final: 0.7776 (mmmt) REVERT: I 79 GLN cc_start: 0.7792 (mm-40) cc_final: 0.7325 (mm110) REVERT: I 82 ASP cc_start: 0.8704 (m-30) cc_final: 0.8301 (m-30) REVERT: I 103 LYS cc_start: 0.8299 (ttmm) cc_final: 0.8011 (ttmt) REVERT: K 57 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8344 (mttm) REVERT: D 261 LYS cc_start: 0.8271 (mttp) cc_final: 0.7795 (mmmt) REVERT: E 79 GLN cc_start: 0.7786 (mm-40) cc_final: 0.7320 (mm110) REVERT: E 82 ASP cc_start: 0.8697 (m-30) cc_final: 0.8293 (m-30) REVERT: E 103 LYS cc_start: 0.8289 (ttmm) cc_final: 0.8001 (ttmt) REVERT: F 57 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8347 (mttm) REVERT: G 79 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7309 (mm110) REVERT: G 82 ASP cc_start: 0.8701 (m-30) cc_final: 0.8302 (m-30) REVERT: G 103 LYS cc_start: 0.8290 (ttmm) cc_final: 0.8002 (ttmt) REVERT: J 57 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8350 (mttm) REVERT: C 261 LYS cc_start: 0.8272 (mttp) cc_final: 0.7793 (mmmt) REVERT: B 261 LYS cc_start: 0.8262 (mttp) cc_final: 0.7785 (mmmt) REVERT: L 79 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7308 (mm110) REVERT: L 82 ASP cc_start: 0.8694 (m-30) cc_final: 0.8290 (m-30) REVERT: L 103 LYS cc_start: 0.8290 (ttmm) cc_final: 0.8004 (ttmt) REVERT: H 57 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8351 (mttm) outliers start: 56 outliers final: 36 residues processed: 236 average time/residue: 0.5395 time to fit residues: 145.2927 Evaluate side-chains 228 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 27 ASP Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 92 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 52 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 197 optimal weight: 0.5980 chunk 204 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 144 optimal weight: 1.9990 chunk 232 optimal weight: 6.9990 chunk 176 optimal weight: 0.9990 overall best weight: 1.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN J 105 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.091703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.075549 restraints weight = 27357.336| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 1.73 r_work: 0.2777 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20349 Z= 0.143 Angle : 0.573 9.617 27786 Z= 0.292 Chirality : 0.044 0.196 3107 Planarity : 0.004 0.048 3487 Dihedral : 7.866 59.799 3651 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.45 % Favored : 97.39 % Rotamer: Outliers : 2.44 % Allowed : 13.72 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.47 (0.17), residues: 2448 helix: -4.20 (0.10), residues: 24 sheet: 0.89 (0.17), residues: 904 loop : 0.09 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 209 TYR 0.017 0.001 TYR D 121 PHE 0.010 0.001 PHE B 410 TRP 0.010 0.001 TRP B 161 HIS 0.004 0.001 HIS F 35 Details of bonding type rmsd covalent geometry : bond 0.00335 (20258) covalent geometry : angle 0.55621 (27557) SS BOND : bond 0.00454 ( 44) SS BOND : angle 1.18875 ( 88) hydrogen bonds : bond 0.03337 ( 640) hydrogen bonds : angle 5.97116 ( 1620) link_ALPHA1-2 : bond 0.00558 ( 8) link_ALPHA1-2 : angle 2.68048 ( 24) link_ALPHA1-3 : bond 0.00787 ( 8) link_ALPHA1-3 : angle 1.46115 ( 24) link_ALPHA1-6 : bond 0.00840 ( 8) link_ALPHA1-6 : angle 1.63310 ( 24) link_BETA1-4 : bond 0.00414 ( 12) link_BETA1-4 : angle 1.75340 ( 36) link_NAG-ASN : bond 0.00053 ( 11) link_NAG-ASN : angle 1.60545 ( 33) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4896 Ramachandran restraints generated. 2448 Oldfield, 0 Emsley, 2448 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 180 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LYS cc_start: 0.8287 (mttp) cc_final: 0.7790 (mmmt) REVERT: I 79 GLN cc_start: 0.7789 (mm-40) cc_final: 0.7315 (mm110) REVERT: I 82 ASP cc_start: 0.8684 (m-30) cc_final: 0.8267 (m-30) REVERT: I 103 LYS cc_start: 0.8297 (ttmm) cc_final: 0.8001 (ttmt) REVERT: K 57 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8324 (mttm) REVERT: D 261 LYS cc_start: 0.8288 (mttp) cc_final: 0.7794 (mmmt) REVERT: E 79 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7302 (mm110) REVERT: E 82 ASP cc_start: 0.8678 (m-30) cc_final: 0.8261 (m-30) REVERT: E 103 LYS cc_start: 0.8291 (ttmm) cc_final: 0.7994 (ttmt) REVERT: F 57 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8326 (mttm) REVERT: G 79 GLN cc_start: 0.7777 (mm-40) cc_final: 0.7302 (mm110) REVERT: G 82 ASP cc_start: 0.8684 (m-30) cc_final: 0.8273 (m-30) REVERT: G 103 LYS cc_start: 0.8285 (ttmm) cc_final: 0.7987 (ttmt) REVERT: J 57 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8325 (mttm) REVERT: C 261 LYS cc_start: 0.8292 (mttp) cc_final: 0.7797 (mmmt) REVERT: B 261 LYS cc_start: 0.8288 (mttp) cc_final: 0.7794 (mmmt) REVERT: L 79 GLN cc_start: 0.7771 (mm-40) cc_final: 0.7296 (mm110) REVERT: L 82 ASP cc_start: 0.8675 (m-30) cc_final: 0.8260 (m-30) REVERT: L 103 LYS cc_start: 0.8290 (ttmm) cc_final: 0.7993 (ttmt) REVERT: H 57 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8326 (mttm) outliers start: 52 outliers final: 40 residues processed: 216 average time/residue: 0.5605 time to fit residues: 138.0511 Evaluate side-chains 224 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 180 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 127 ASP Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 27 ASP Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain K residue 57 LYS Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 127 ASP Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 57 LYS Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 27 ASP Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain J residue 57 LYS Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 127 ASP Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 464 ILE Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 127 ASP Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 27 ASP Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 57 LYS Chi-restraints excluded: chain H residue 92 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 25 optimal weight: 9.9990 chunk 238 optimal weight: 0.9990 chunk 191 optimal weight: 4.9990 chunk 159 optimal weight: 1.9990 chunk 227 optimal weight: 0.9980 chunk 224 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 143 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 105 GLN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN J 105 GLN ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.091394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.075218 restraints weight = 27373.415| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 1.73 r_work: 0.2774 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20349 Z= 0.148 Angle : 0.576 8.596 27786 Z= 0.293 Chirality : 0.044 0.186 3107 Planarity : 0.004 0.048 3487 Dihedral : 7.871 59.668 3651 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.23 % Favored : 96.61 % Rotamer: Outliers : 2.63 % Allowed : 13.53 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.34 % 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: 0.43 (0.17), residues: 2448 helix: -4.19 (0.10), residues: 24 sheet: 0.87 (0.17), residues: 908 loop : 0.05 (0.16), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 209 TYR 0.018 0.001 TYR A 121 PHE 0.010 0.001 PHE A 410 TRP 0.010 0.001 TRP H 47 HIS 0.005 0.001 HIS K 35 Details of bonding type rmsd covalent geometry : bond 0.00348 (20258) covalent geometry : angle 0.55848 (27557) SS BOND : bond 0.00410 ( 44) SS BOND : angle 1.13750 ( 88) hydrogen bonds : bond 0.03392 ( 640) hydrogen bonds : angle 5.98916 ( 1620) link_ALPHA1-2 : bond 0.00548 ( 8) link_ALPHA1-2 : angle 2.68721 ( 24) link_ALPHA1-3 : bond 0.00772 ( 8) link_ALPHA1-3 : angle 1.46930 ( 24) link_ALPHA1-6 : bond 0.00839 ( 8) link_ALPHA1-6 : angle 1.65637 ( 24) link_BETA1-4 : bond 0.00426 ( 12) link_BETA1-4 : angle 1.80589 ( 36) link_NAG-ASN : bond 0.00085 ( 11) link_NAG-ASN : angle 1.62350 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5871.55 seconds wall clock time: 101 minutes 6.31 seconds (6066.31 seconds total)