Starting phenix.real_space_refine on Sun Sep 13 01:34:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6pzw_20538/09_2026/6pzw_20538.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pzw_20538/09_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_20538/09_2026/6pzw_20538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pzw_20538/09_2026/6pzw_20538.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6pzw_20538/09_2026/6pzw_20538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pzw_20538/09_2026/6pzw_20538.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6pzw_20538/09_2026/6pzw_20538.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6pzw_20538/09_2026/6pzw_20538.cif" } 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-2.2.1-6174/lib/python3.11/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 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 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 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 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 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 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 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 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 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 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 chiralities: 1 Time building chain proxies: 4.43, per 1000 atoms: 0.22 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: 2.07 Conformation dependent library (CDL) restraints added in 782.4 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: 0.83 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: 4.01 Time building geometry restraints manager: 2.65 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 - 17.37: 11225 17.37 - 34.73: 343 34.73 - 52.10: 60 52.10 - 69.46: 32 69.46 - 86.83: 8 Dihedral angle restraints: 11668 sinusoidal: 4584 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 11665 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 19.710 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 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 : 9.562 86.826 7040 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/Z covalent geometry : bond 0.02041 / 1.08 (20258) covalent geometry : angle 1.73099 / 1.14 (27557) SS BOND : bond 0.06341 / 4.47 ( 44) SS BOND : angle 3.42784 / 2.49 ( 88) hydrogen bonds : bond 0.16166 / 10.81 ( 640) hydrogen bonds : angle 8.59763 / 6.03 ( 1620) link_ALPHA1-2 : bond 0.04351 / 2.34 ( 8) link_ALPHA1-2 : angle 3.34232 / 2.11 ( 24) link_ALPHA1-3 : bond 0.03787 / 2.04 ( 8) link_ALPHA1-3 : angle 2.45233 / 1.57 ( 24) link_ALPHA1-6 : bond 0.03080 / 1.64 ( 8) link_ALPHA1-6 : angle 2.80400 / 1.79 ( 24) link_BETA1-4 : bond 0.03152 / 1.92 ( 12) link_BETA1-4 : angle 3.48197 / 2.31 ( 36) link_NAG-ASN : bond 0.02882 / 1.72 ( 11) link_NAG-ASN : angle 2.85053 / 2.04 ( 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 : 0.845 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: 0.6275 time to fit residues: 247.1792 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 : 0.820 ------------------------------------------------------------------------------- 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... 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 79 GLN J 30 ASN J 81 GLN J 105 GLN C 83 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: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.097072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.082213 restraints weight = 27110.400| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 1.59 r_work: 0.2891 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20349 Z= 0.153 Angle : 0.653 7.618 27786 Z= 0.344 Chirality : 0.044 0.160 3107 Planarity : 0.004 0.033 3487 Dihedral : 5.049 18.076 2720 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.33 % Allowed : 1.63 % Favored : 98.04 % Rotamer: Outliers : 1.13 % Allowed : 8.18 % Favored : 90.70 % 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: 0.74 (0.17), residues: 2448 helix: -4.38 (0.15), residues: 24 sheet: 0.90 (0.17), residues: 876 loop : 0.44 (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 A 121 PHE 0.011 0.002 PHE A 410 TRP 0.024 0.002 TRP D 206 HIS 0.005 0.001 HIS F 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (20258) covalent geometry : angle 0.63594 / 0.34 (27557) SS BOND : bond 0.00442 / 0.31 ( 44) SS BOND : angle 1.50511 / 1.09 ( 88) hydrogen bonds : bond 0.04608 / 3.14 ( 640) hydrogen bonds : angle 6.82970 / 4.83 ( 1620) link_ALPHA1-2 : bond 0.01115 / 0.62 ( 8) link_ALPHA1-2 : angle 1.66372 / 1.11 ( 24) link_ALPHA1-3 : bond 0.00683 / 0.37 ( 8) link_ALPHA1-3 : angle 1.28490 / 0.92 ( 24) link_ALPHA1-6 : bond 0.01099 / 0.59 ( 8) link_ALPHA1-6 : angle 1.58570 / 1.14 ( 24) link_BETA1-4 : bond 0.00611 / 0.41 ( 12) link_BETA1-4 : angle 2.17494 / 1.42 ( 36) link_NAG-ASN : bond 0.00113 / 0.07 ( 11) link_NAG-ASN : angle 2.13582 / 1.46 ( 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 262 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 238 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 110 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8804 (tm-30) REVERT: I 79 GLN cc_start: 0.7790 (mm-40) cc_final: 0.7346 (mm-40) REVERT: I 82 ASP cc_start: 0.8663 (m-30) cc_final: 0.8248 (m-30) REVERT: K 57 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8365 (mttm) REVERT: D 110 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8810 (tm-30) REVERT: E 79 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7342 (mm-40) REVERT: E 82 ASP cc_start: 0.8668 (m-30) cc_final: 0.8257 (m-30) REVERT: F 57 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8365 (mttm) REVERT: G 79 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7341 (mm-40) REVERT: G 82 ASP cc_start: 0.8672 (m-30) cc_final: 0.8263 (m-30) REVERT: J 57 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8365 (mttm) REVERT: C 110 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8817 (tm-30) REVERT: B 110 GLU cc_start: 0.9032 (tm-30) cc_final: 0.8811 (tm-30) REVERT: L 79 GLN cc_start: 0.7788 (mm-40) cc_final: 0.7343 (mm-40) REVERT: L 82 ASP cc_start: 0.8659 (m-30) cc_final: 0.8247 (m-30) REVERT: H 57 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8361 (mttm) outliers start: 24 outliers final: 4 residues processed: 246 average time/residue: 0.4738 time to fit residues: 136.5588 Evaluate side-chains 184 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 0.759 ------------------------------------------------------------------------------- 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: 7.9990 chunk 140 optimal weight: 5.9990 chunk 239 optimal weight: 4.9990 chunk 135 optimal weight: 0.6980 chunk 198 optimal weight: 0.0970 chunk 183 optimal weight: 6.9990 chunk 226 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 G 53 ASN J 30 ASN J 76 ASN J 105 GLN C 441 ASN B 441 ASN H 30 ASN H 76 ASN H 105 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.090401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.075099 restraints weight = 27958.233| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 1.63 r_work: 0.2788 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 20349 Z= 0.215 Angle : 0.659 9.728 27786 Z= 0.340 Chirality : 0.045 0.140 3107 Planarity : 0.005 0.041 3487 Dihedral : 5.017 17.888 2720 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.33 % Allowed : 3.27 % Favored : 96.41 % Rotamer: Outliers : 2.07 % Allowed : 11.18 % Favored : 86.75 % 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: -4.27 (0.13), residues: 24 sheet: 0.61 (0.17), residues: 904 loop : 0.30 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 141 TYR 0.027 0.002 TYR A 121 PHE 0.013 0.002 PHE C 410 TRP 0.014 0.002 TRP D 456 HIS 0.007 0.002 HIS B 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.22 (20258) covalent geometry : angle 0.63736 / 0.33 (27557) SS BOND : bond 0.00276 / 0.20 ( 44) SS BOND : angle 1.87698 / 1.30 ( 88) hydrogen bonds : bond 0.04186 / 2.86 ( 640) hydrogen bonds : angle 6.30894 / 4.44 ( 1620) link_ALPHA1-2 : bond 0.00696 / 0.38 ( 8) link_ALPHA1-2 : angle 2.52653 / 1.68 ( 24) link_ALPHA1-3 : bond 0.00634 / 0.35 ( 8) link_ALPHA1-3 : angle 1.32191 / 0.92 ( 24) link_ALPHA1-6 : bond 0.00894 / 0.47 ( 8) link_ALPHA1-6 : angle 1.69139 / 1.17 ( 24) link_BETA1-4 : bond 0.00476 / 0.32 ( 12) link_BETA1-4 : angle 2.09829 / 1.43 ( 36) link_NAG-ASN : bond 0.00214 / 0.13 ( 11) link_NAG-ASN : angle 1.98387 / 1.39 ( 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 268 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 224 time to evaluate : 0.765 Fit side-chains REVERT: A 292 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8547 (ttm170) REVERT: I 12 SER cc_start: 0.8647 (p) cc_final: 0.8421 (m) REVERT: I 79 GLN cc_start: 0.7913 (mm-40) cc_final: 0.7507 (mm110) REVERT: I 82 ASP cc_start: 0.8690 (m-30) cc_final: 0.8379 (m-30) REVERT: K 57 LYS cc_start: 0.8661 (mttm) cc_final: 0.8370 (mttm) REVERT: D 292 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8540 (ttm170) REVERT: E 12 SER cc_start: 0.8649 (p) cc_final: 0.8423 (m) REVERT: E 79 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7505 (mm110) REVERT: E 82 ASP cc_start: 0.8695 (m-30) cc_final: 0.8382 (m-30) REVERT: F 57 LYS cc_start: 0.8668 (mttm) cc_final: 0.8380 (mttm) REVERT: G 12 SER cc_start: 0.8644 (p) cc_final: 0.8419 (m) REVERT: G 79 GLN cc_start: 0.7917 (mm-40) cc_final: 0.7511 (mm110) REVERT: G 82 ASP cc_start: 0.8705 (m-30) cc_final: 0.8391 (m-30) REVERT: J 57 LYS cc_start: 0.8663 (mttm) cc_final: 0.8373 (mttm) REVERT: C 292 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8548 (ttm170) REVERT: B 292 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8547 (ttm170) REVERT: L 12 SER cc_start: 0.8652 (p) cc_final: 0.8426 (m) REVERT: L 79 GLN cc_start: 0.7919 (mm-40) cc_final: 0.7516 (mm110) REVERT: L 82 ASP cc_start: 0.8710 (m-30) cc_final: 0.8398 (m-30) REVERT: H 57 LYS cc_start: 0.8661 (mttm) cc_final: 0.8371 (mttm) outliers start: 44 outliers final: 24 residues processed: 244 average time/residue: 0.5418 time to fit residues: 152.1467 Evaluate side-chains 204 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 176 time to evaluate : 0.621 ------------------------------------------------------------------------------- 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 292 ARG Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain K residue 70 SER 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 148 THR Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 70 SER Chi-restraints excluded: chain F residue 105 GLN Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain J residue 70 SER 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 148 THR Chi-restraints excluded: chain C residue 292 ARG 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 292 ARG Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 70 SER 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: 2.9990 chunk 119 optimal weight: 4.9990 chunk 217 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 192 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 226 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 153 optimal weight: 0.9990 chunk 171 optimal weight: 4.9990 chunk 134 optimal weight: 0.5980 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 H 105 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.089752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.074471 restraints weight = 27704.805| |-----------------------------------------------------------------------------| r_work (start): 0.2845 rms_B_bonded: 1.63 r_work: 0.2756 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 20349 Z= 0.203 Angle : 0.637 7.828 27786 Z= 0.328 Chirality : 0.044 0.139 3107 Planarity : 0.004 0.047 3487 Dihedral : 4.965 23.357 2720 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.94 % Favored : 96.73 % Rotamer: Outliers : 3.20 % Allowed : 11.37 % Favored : 85.43 % 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: 0.34 (0.17), residues: 2448 helix: -4.20 (0.11), residues: 24 sheet: 0.69 (0.17), residues: 896 loop : 0.09 (0.17), residues: 1528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 210 TYR 0.022 0.002 TYR D 121 PHE 0.012 0.002 PHE A 410 TRP 0.012 0.002 TRP C 206 HIS 0.006 0.002 HIS K 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (20258) covalent geometry : angle 0.61810 / 0.32 (27557) SS BOND : bond 0.00235 / 0.17 ( 44) SS BOND : angle 1.72540 / 1.26 ( 88) hydrogen bonds : bond 0.03877 / 2.66 ( 640) hydrogen bonds : angle 6.25007 / 4.41 ( 1620) link_ALPHA1-2 : bond 0.00600 / 0.33 ( 8) link_ALPHA1-2 : angle 2.43805 / 1.63 ( 24) link_ALPHA1-3 : bond 0.00464 / 0.25 ( 8) link_ALPHA1-3 : angle 1.30698 / 0.93 ( 24) link_ALPHA1-6 : bond 0.00799 / 0.42 ( 8) link_ALPHA1-6 : angle 1.58176 / 1.11 ( 24) link_BETA1-4 : bond 0.00390 / 0.26 ( 12) link_BETA1-4 : angle 1.87615 / 1.26 ( 36) link_NAG-ASN : bond 0.00136 / 0.09 ( 11) link_NAG-ASN : angle 1.87364 / 1.30 ( 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 264 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 196 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 292 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8623 (ttm170) REVERT: I 79 GLN cc_start: 0.7934 (mm-40) cc_final: 0.7659 (mm110) REVERT: I 82 ASP cc_start: 0.8730 (m-30) cc_final: 0.8361 (m-30) REVERT: K 57 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8459 (mttm) REVERT: D 292 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8624 (ttm170) REVERT: E 79 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7653 (mm110) REVERT: E 82 ASP cc_start: 0.8734 (m-30) cc_final: 0.8362 (m-30) REVERT: F 57 LYS cc_start: 0.8720 (OUTLIER) cc_final: 0.8461 (mttm) REVERT: G 79 GLN cc_start: 0.7930 (mm-40) cc_final: 0.7655 (mm110) REVERT: G 82 ASP cc_start: 0.8738 (m-30) cc_final: 0.8370 (m-30) REVERT: J 57 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8462 (mttm) REVERT: C 292 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8631 (ttm170) REVERT: B 292 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8627 (ttm170) REVERT: L 79 GLN cc_start: 0.7928 (mm-40) cc_final: 0.7654 (mm110) REVERT: L 82 ASP cc_start: 0.8747 (m-30) cc_final: 0.8378 (m-30) REVERT: H 57 LYS cc_start: 0.8717 (OUTLIER) cc_final: 0.8459 (mttm) outliers start: 68 outliers final: 44 residues processed: 232 average time/residue: 0.5347 time to fit residues: 143.0827 Evaluate side-chains 224 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 172 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 230 CYS Chi-restraints excluded: chain A residue 292 ARG 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 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 82 SER Chi-restraints excluded: chain K residue 92 CYS Chi-restraints excluded: chain D residue 96 SER Chi-restraints excluded: chain D residue 148 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 292 ARG 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 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 82 SER Chi-restraints excluded: chain F residue 92 CYS Chi-restraints excluded: chain G residue 18 SER 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 82 SER Chi-restraints excluded: chain J residue 92 CYS Chi-restraints excluded: chain C residue 96 SER Chi-restraints excluded: chain C residue 148 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 292 ARG 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 148 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 292 ARG 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 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 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: 5.9990 chunk 158 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 162 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 155 optimal weight: 4.9990 chunk 124 optimal weight: 4.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.089476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.074111 restraints weight = 27818.801| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 1.64 r_work: 0.2750 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2638 rms_B_bonded: 2.96 restraints_weight: 0.2500 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20349 Z= 0.188 Angle : 0.609 5.721 27786 Z= 0.312 Chirality : 0.044 0.141 3107 Planarity : 0.004 0.048 3487 Dihedral : 4.837 21.839 2720 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.33 % Allowed : 2.45 % Favored : 97.22 % Rotamer: Outliers : 3.05 % Allowed : 12.36 % 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: 0.27 (0.17), residues: 2448 helix: -4.13 (0.12), residues: 24 sheet: 0.67 (0.17), residues: 904 loop : 0.02 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 419 TYR 0.020 0.002 TYR D 121 PHE 0.013 0.002 PHE D 410 TRP 0.011 0.002 TRP F 47 HIS 0.006 0.002 HIS D 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (20258) covalent geometry : angle 0.59230 / 0.31 (27557) SS BOND : bond 0.00112 / 0.08 ( 44) SS BOND : angle 1.43453 / 1.06 ( 88) hydrogen bonds : bond 0.03707 / 2.54 ( 640) hydrogen bonds : angle 6.16398 / 4.35 ( 1620) link_ALPHA1-2 : bond 0.00661 / 0.36 ( 8) link_ALPHA1-2 : angle 2.49737 / 1.68 ( 24) link_ALPHA1-3 : bond 0.00504 / 0.28 ( 8) link_ALPHA1-3 : angle 1.36669 / 0.97 ( 24) link_ALPHA1-6 : bond 0.00764 / 0.40 ( 8) link_ALPHA1-6 : angle 1.55844 / 1.10 ( 24) link_BETA1-4 : bond 0.00373 / 0.25 ( 12) link_BETA1-4 : angle 1.76505 / 1.19 ( 36) link_NAG-ASN : bond 0.00092 / 0.05 ( 11) link_NAG-ASN : angle 1.76261 / 1.21 ( 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 257 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 192 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: 0.8296 (mttp) cc_final: 0.7849 (mmmt) REVERT: A 292 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8576 (ttm170) REVERT: I 79 GLN cc_start: 0.7929 (mm-40) cc_final: 0.7465 (mm-40) REVERT: I 82 ASP cc_start: 0.8742 (m-30) cc_final: 0.8388 (m-30) REVERT: K 57 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8446 (mttm) REVERT: D 261 LYS cc_start: 0.8303 (mttp) cc_final: 0.7852 (mmmt) REVERT: D 292 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8581 (ttm170) REVERT: E 79 GLN cc_start: 0.7920 (mm-40) cc_final: 0.7456 (mm-40) REVERT: E 82 ASP cc_start: 0.8756 (m-30) cc_final: 0.8401 (m-30) REVERT: F 57 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8452 (mttm) REVERT: G 79 GLN cc_start: 0.7915 (mm-40) cc_final: 0.7456 (mm-40) REVERT: G 82 ASP cc_start: 0.8766 (m-30) cc_final: 0.8411 (m-30) REVERT: J 57 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8447 (mttm) REVERT: C 261 LYS cc_start: 0.8300 (mttp) cc_final: 0.7843 (mmmt) REVERT: C 292 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8583 (ttm170) REVERT: B 261 LYS cc_start: 0.8290 (mttp) cc_final: 0.7845 (mmmt) REVERT: B 292 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8576 (ttm170) REVERT: L 79 GLN cc_start: 0.7918 (mm-40) cc_final: 0.7460 (mm-40) REVERT: L 82 ASP cc_start: 0.8762 (m-30) cc_final: 0.8407 (m-30) REVERT: H 57 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8451 (mttm) outliers start: 65 outliers final: 57 residues processed: 233 average time/residue: 0.5809 time to fit residues: 155.6134 Evaluate side-chains 237 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 172 time to evaluate : 0.797 ------------------------------------------------------------------------------- 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 292 ARG Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 416 ASP Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 19 ILE 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 230 CYS Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 318 CYS Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 416 ASP Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 12 SER Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 19 ILE 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 12 SER Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 19 ILE 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 230 CYS Chi-restraints excluded: chain C residue 292 ARG Chi-restraints excluded: chain C residue 318 CYS Chi-restraints excluded: chain C residue 339 ASP Chi-restraints excluded: chain C residue 416 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 148 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 318 CYS Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 416 ASP Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 19 optimal weight: 0.4980 chunk 181 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 229 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 209 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 222 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 215 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.087233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.071201 restraints weight = 27216.736| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 1.81 r_work: 0.2677 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20349 Z= 0.149 Angle : 0.570 5.453 27786 Z= 0.293 Chirality : 0.043 0.145 3107 Planarity : 0.004 0.048 3487 Dihedral : 4.681 19.517 2720 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.02 % Favored : 96.81 % Rotamer: Outliers : 3.76 % Allowed : 11.56 % Favored : 84.68 % 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: 0.32 (0.17), residues: 2448 helix: -4.13 (0.12), residues: 24 sheet: 0.72 (0.17), residues: 904 loop : 0.04 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 19 TYR 0.017 0.001 TYR B 121 PHE 0.011 0.001 PHE D 410 TRP 0.011 0.001 TRP C 161 HIS 0.005 0.001 HIS D 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (20258) covalent geometry : angle 0.55503 / 0.29 (27557) SS BOND : bond 0.00137 / 0.10 ( 44) SS BOND : angle 1.15644 / 0.84 ( 88) hydrogen bonds : bond 0.03486 / 2.40 ( 640) hydrogen bonds : angle 6.06911 / 4.29 ( 1620) link_ALPHA1-2 : bond 0.00589 / 0.32 ( 8) link_ALPHA1-2 : angle 2.42967 / 1.64 ( 24) link_ALPHA1-3 : bond 0.00423 / 0.23 ( 8) link_ALPHA1-3 : angle 1.31981 / 0.95 ( 24) link_ALPHA1-6 : bond 0.00729 / 0.39 ( 8) link_ALPHA1-6 : angle 1.50316 / 1.06 ( 24) link_BETA1-4 : bond 0.00371 / 0.25 ( 12) link_BETA1-4 : angle 1.64486 / 1.09 ( 36) link_NAG-ASN : bond 0.00032 / 0.02 ( 11) link_NAG-ASN : angle 1.69502 / 1.17 ( 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 264 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 184 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LYS cc_start: 0.8122 (mttp) cc_final: 0.7513 (mmmt) REVERT: A 292 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8486 (ttm170) REVERT: I 79 GLN cc_start: 0.7450 (mm-40) cc_final: 0.6960 (mm-40) REVERT: I 82 ASP cc_start: 0.8577 (m-30) cc_final: 0.8121 (m-30) REVERT: K 57 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8271 (mttm) REVERT: D 261 LYS cc_start: 0.8122 (mttp) cc_final: 0.7512 (mmmt) REVERT: D 292 ARG cc_start: 0.8810 (OUTLIER) cc_final: 0.8486 (ttm170) REVERT: E 79 GLN cc_start: 0.7455 (mm-40) cc_final: 0.6965 (mm-40) REVERT: E 82 ASP cc_start: 0.8582 (m-30) cc_final: 0.8128 (m-30) REVERT: F 57 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8264 (mttm) REVERT: G 79 GLN cc_start: 0.7456 (mm-40) cc_final: 0.6967 (mm-40) REVERT: G 82 ASP cc_start: 0.8592 (m-30) cc_final: 0.8138 (m-30) REVERT: J 57 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8280 (mttm) REVERT: C 261 LYS cc_start: 0.8119 (mttp) cc_final: 0.7506 (mmmt) REVERT: C 292 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8489 (ttm170) REVERT: B 261 LYS cc_start: 0.8116 (mttp) cc_final: 0.7505 (mmmt) REVERT: B 292 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8483 (ttm170) REVERT: L 79 GLN cc_start: 0.7470 (mm-40) cc_final: 0.6982 (mm-40) REVERT: L 82 ASP cc_start: 0.8587 (m-30) cc_final: 0.8133 (m-30) REVERT: H 57 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8272 (mttm) outliers start: 80 outliers final: 48 residues processed: 228 average time/residue: 0.5516 time to fit residues: 144.7080 Evaluate side-chains 232 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 176 time to evaluate : 0.744 ------------------------------------------------------------------------------- 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 292 ARG 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 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 292 ARG 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 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 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 292 ARG 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 292 ARG 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 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: 6.9990 chunk 174 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 128 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 214 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN J 76 ASN H 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.085179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.069232 restraints weight = 27726.148| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 1.81 r_work: 0.2631 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2510 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 20349 Z= 0.248 Angle : 0.644 6.306 27786 Z= 0.328 Chirality : 0.046 0.178 3107 Planarity : 0.005 0.049 3487 Dihedral : 4.779 17.411 2720 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.76 % Favored : 96.08 % Rotamer: Outliers : 4.14 % Allowed : 11.00 % Favored : 84.87 % 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: 0.22 (0.17), residues: 2448 helix: -4.15 (0.12), residues: 24 sheet: 0.63 (0.17), residues: 904 loop : -0.01 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 419 TYR 0.020 0.002 TYR D 121 PHE 0.010 0.002 PHE A 257 TRP 0.012 0.002 TRP J 47 HIS 0.007 0.002 HIS K 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.25 (20258) covalent geometry : angle 0.62320 / 0.32 (27557) SS BOND : bond 0.00406 / 0.29 ( 44) SS BOND : angle 1.84295 / 1.29 ( 88) hydrogen bonds : bond 0.03893 / 2.66 ( 640) hydrogen bonds : angle 6.18548 / 4.37 ( 1620) link_ALPHA1-2 : bond 0.00615 / 0.33 ( 8) link_ALPHA1-2 : angle 2.62523 / 1.77 ( 24) link_ALPHA1-3 : bond 0.00411 / 0.22 ( 8) link_ALPHA1-3 : angle 1.40358 / 0.98 ( 24) link_ALPHA1-6 : bond 0.00702 / 0.37 ( 8) link_ALPHA1-6 : angle 1.61969 / 1.13 ( 24) link_BETA1-4 : bond 0.00395 / 0.27 ( 12) link_BETA1-4 : angle 1.88678 / 1.27 ( 36) link_NAG-ASN : bond 0.00191 / 0.11 ( 11) link_NAG-ASN : angle 1.79464 / 1.24 ( 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 260 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 172 time to evaluate : 0.716 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LYS cc_start: 0.8147 (mttp) cc_final: 0.7544 (mmmt) REVERT: A 292 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8453 (ttm170) REVERT: I 79 GLN cc_start: 0.7537 (mm-40) cc_final: 0.7072 (mm110) REVERT: I 82 ASP cc_start: 0.8657 (m-30) cc_final: 0.8267 (m-30) REVERT: K 11 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8703 (t) REVERT: K 34 MET cc_start: 0.9076 (mmt) cc_final: 0.8857 (mmm) REVERT: K 57 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8331 (mttm) REVERT: D 261 LYS cc_start: 0.8145 (mttp) cc_final: 0.7543 (mmmt) REVERT: D 292 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8452 (ttm170) REVERT: E 79 GLN cc_start: 0.7534 (mm-40) cc_final: 0.7071 (mm110) REVERT: E 82 ASP cc_start: 0.8663 (m-30) cc_final: 0.8275 (m-30) REVERT: F 11 VAL cc_start: 0.8953 (OUTLIER) cc_final: 0.8706 (t) REVERT: F 34 MET cc_start: 0.9076 (mmt) cc_final: 0.8859 (mmm) REVERT: F 57 LYS cc_start: 0.8619 (OUTLIER) cc_final: 0.8333 (mttm) REVERT: G 79 GLN cc_start: 0.7526 (mm-40) cc_final: 0.7061 (mm110) REVERT: G 82 ASP cc_start: 0.8666 (m-30) cc_final: 0.8277 (m-30) REVERT: J 11 VAL cc_start: 0.8949 (OUTLIER) cc_final: 0.8701 (t) REVERT: J 34 MET cc_start: 0.9076 (mmt) cc_final: 0.8863 (mmm) REVERT: J 57 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8341 (mttm) REVERT: C 261 LYS cc_start: 0.8145 (mttp) cc_final: 0.7542 (mmmt) REVERT: C 292 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8460 (ttm170) REVERT: B 261 LYS cc_start: 0.8141 (mttp) cc_final: 0.7540 (mmmt) REVERT: B 292 ARG cc_start: 0.8841 (OUTLIER) cc_final: 0.8455 (ttm170) REVERT: L 79 GLN cc_start: 0.7544 (mm-40) cc_final: 0.7081 (mm110) REVERT: L 82 ASP cc_start: 0.8671 (m-30) cc_final: 0.8283 (m-30) REVERT: H 11 VAL cc_start: 0.8950 (OUTLIER) cc_final: 0.8702 (t) REVERT: H 34 MET cc_start: 0.9077 (mmt) cc_final: 0.8860 (mmm) REVERT: H 57 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8336 (mttm) outliers start: 88 outliers final: 56 residues processed: 220 average time/residue: 0.5556 time to fit residues: 140.7646 Evaluate side-chains 236 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 168 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 292 ARG Chi-restraints excluded: chain A residue 339 ASP Chi-restraints excluded: chain A residue 464 ILE Chi-restraints excluded: chain I residue 3 VAL Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 19 ILE Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain K residue 11 VAL 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 148 THR Chi-restraints excluded: chain D residue 230 CYS Chi-restraints excluded: chain D residue 292 ARG Chi-restraints excluded: chain D residue 339 ASP Chi-restraints excluded: chain D residue 464 ILE Chi-restraints excluded: chain E residue 3 VAL Chi-restraints excluded: chain E residue 18 SER Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 11 VAL 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 3 VAL Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain J residue 11 VAL 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 148 THR Chi-restraints excluded: chain C residue 230 CYS Chi-restraints excluded: chain C residue 292 ARG 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 148 THR Chi-restraints excluded: chain B residue 230 CYS Chi-restraints excluded: chain B residue 292 ARG Chi-restraints excluded: chain B residue 339 ASP Chi-restraints excluded: chain B residue 464 ILE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 19 ILE Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 11 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 172 optimal weight: 5.9990 chunk 100 optimal weight: 0.0470 chunk 5 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 152 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 140 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 overall best weight: 1.0882 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 441 ASN ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.090546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.074477 restraints weight = 27319.854| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 1.73 r_work: 0.2765 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20349 Z= 0.128 Angle : 0.565 9.970 27786 Z= 0.289 Chirality : 0.043 0.209 3107 Planarity : 0.004 0.049 3487 Dihedral : 4.651 24.672 2720 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.78 % Favored : 97.06 % Rotamer: Outliers : 3.24 % Allowed : 12.69 % Favored : 84.07 % 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: 0.32 (0.17), residues: 2448 helix: -4.18 (0.11), residues: 24 sheet: 0.78 (0.17), residues: 904 loop : -0.01 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 156 TYR 0.016 0.001 TYR B 121 PHE 0.010 0.001 PHE D 410 TRP 0.012 0.001 TRP B 161 HIS 0.003 0.001 HIS K 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (20258) covalent geometry : angle 0.54980 / 0.29 (27557) SS BOND : bond 0.00482 / 0.35 ( 44) SS BOND : angle 1.25924 / 0.93 ( 88) hydrogen bonds : bond 0.03375 / 2.32 ( 640) hydrogen bonds : angle 6.06721 / 4.29 ( 1620) link_ALPHA1-2 : bond 0.00594 / 0.33 ( 8) link_ALPHA1-2 : angle 2.40812 / 1.63 ( 24) link_ALPHA1-3 : bond 0.00419 / 0.23 ( 8) link_ALPHA1-3 : angle 1.30964 / 0.95 ( 24) link_ALPHA1-6 : bond 0.00692 / 0.37 ( 8) link_ALPHA1-6 : angle 1.47854 / 1.05 ( 24) link_BETA1-4 : bond 0.00350 / 0.23 ( 12) link_BETA1-4 : angle 1.58404 / 1.05 ( 36) link_NAG-ASN : bond 0.00052 / 0.03 ( 11) link_NAG-ASN : angle 1.66670 / 1.15 ( 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 261 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 192 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LYS cc_start: 0.8262 (mttp) cc_final: 0.7746 (mmmt) REVERT: I 79 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7344 (mm110) REVERT: I 82 ASP cc_start: 0.8673 (m-30) cc_final: 0.8296 (m-30) REVERT: K 11 VAL cc_start: 0.8975 (OUTLIER) cc_final: 0.8758 (t) REVERT: K 57 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8337 (mttm) REVERT: D 261 LYS cc_start: 0.8271 (mttp) cc_final: 0.7755 (mmmt) REVERT: E 79 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7330 (mm110) REVERT: E 82 ASP cc_start: 0.8663 (m-30) cc_final: 0.8286 (m-30) REVERT: F 11 VAL cc_start: 0.8972 (OUTLIER) cc_final: 0.8757 (t) REVERT: F 57 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8336 (mttm) REVERT: G 79 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7337 (mm110) REVERT: G 82 ASP cc_start: 0.8673 (m-30) cc_final: 0.8296 (m-30) REVERT: J 11 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8758 (t) REVERT: J 57 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8338 (mttm) REVERT: C 261 LYS cc_start: 0.8268 (mttp) cc_final: 0.7753 (mmmt) REVERT: B 261 LYS cc_start: 0.8261 (mttp) cc_final: 0.7748 (mmmt) REVERT: L 79 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7339 (mm110) REVERT: L 82 ASP cc_start: 0.8672 (m-30) cc_final: 0.8294 (m-30) REVERT: H 11 VAL cc_start: 0.8973 (OUTLIER) cc_final: 0.8755 (t) REVERT: H 57 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8342 (mttm) outliers start: 69 outliers final: 40 residues processed: 234 average time/residue: 0.5471 time to fit residues: 147.4341 Evaluate side-chains 232 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 184 time to evaluate : 0.743 ------------------------------------------------------------------------------- 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 19 ILE Chi-restraints excluded: chain I residue 95 THR Chi-restraints excluded: chain K residue 11 VAL 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 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 19 ILE Chi-restraints excluded: chain E residue 95 THR Chi-restraints excluded: chain F residue 11 VAL 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 92 CYS Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 95 THR Chi-restraints excluded: chain J residue 11 VAL 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 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 19 ILE Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain H residue 11 VAL 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 92 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 240 random chunks: chunk 221 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 chunk 219 optimal weight: 7.9990 chunk 88 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 232 optimal weight: 7.9990 chunk 91 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 133 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 441 ASN ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.090503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.074435 restraints weight = 27370.843| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 1.73 r_work: 0.2761 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2644 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 20349 Z= 0.140 Angle : 0.568 8.986 27786 Z= 0.290 Chirality : 0.043 0.196 3107 Planarity : 0.004 0.049 3487 Dihedral : 4.592 22.437 2720 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.10 % Favored : 96.73 % Rotamer: Outliers : 3.29 % Allowed : 12.41 % Favored : 84.30 % 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: 0.40 (0.17), residues: 2448 helix: -4.18 (0.11), residues: 24 sheet: 0.87 (0.17), residues: 904 loop : 0.02 (0.17), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 209 TYR 0.017 0.001 TYR B 121 PHE 0.011 0.001 PHE D 410 TRP 0.012 0.001 TRP C 161 HIS 0.004 0.001 HIS K 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.14 (20258) covalent geometry : angle 0.55343 / 0.29 (27557) SS BOND : bond 0.00469 / 0.34 ( 44) SS BOND : angle 1.15382 / 0.84 ( 88) hydrogen bonds : bond 0.03392 / 2.33 ( 640) hydrogen bonds : angle 6.03290 / 4.26 ( 1620) link_ALPHA1-2 : bond 0.00582 / 0.32 ( 8) link_ALPHA1-2 : angle 2.43376 / 1.65 ( 24) link_ALPHA1-3 : bond 0.00427 / 0.23 ( 8) link_ALPHA1-3 : angle 1.33944 / 0.96 ( 24) link_ALPHA1-6 : bond 0.00699 / 0.37 ( 8) link_ALPHA1-6 : angle 1.49479 / 1.06 ( 24) link_BETA1-4 : bond 0.00386 / 0.26 ( 12) link_BETA1-4 : angle 1.60714 / 1.07 ( 36) link_NAG-ASN : bond 0.00023 / 0.01 ( 11) link_NAG-ASN : angle 1.64603 / 1.13 ( 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 266 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 196 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LYS cc_start: 0.8294 (mttp) cc_final: 0.7796 (mmmt) REVERT: I 79 GLN cc_start: 0.7787 (mm-40) cc_final: 0.7367 (mm110) REVERT: I 82 ASP cc_start: 0.8688 (m-30) cc_final: 0.8279 (m-30) REVERT: K 11 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8752 (t) REVERT: K 57 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.8350 (mttm) REVERT: D 261 LYS cc_start: 0.8305 (mttp) cc_final: 0.7810 (mmmt) REVERT: E 79 GLN cc_start: 0.7779 (mm-40) cc_final: 0.7360 (mm110) REVERT: E 82 ASP cc_start: 0.8674 (m-30) cc_final: 0.8264 (m-30) REVERT: F 11 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8754 (t) REVERT: F 57 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8354 (mttm) REVERT: G 79 GLN cc_start: 0.7785 (mm-40) cc_final: 0.7368 (mm110) REVERT: G 82 ASP cc_start: 0.8693 (m-30) cc_final: 0.8287 (m-30) REVERT: J 11 VAL cc_start: 0.8981 (OUTLIER) cc_final: 0.8749 (t) REVERT: J 57 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8354 (mttm) REVERT: C 261 LYS cc_start: 0.8296 (mttp) cc_final: 0.7800 (mmmt) REVERT: B 261 LYS cc_start: 0.8291 (mttp) cc_final: 0.7797 (mmmt) REVERT: L 79 GLN cc_start: 0.7783 (mm-40) cc_final: 0.7366 (mm110) REVERT: L 82 ASP cc_start: 0.8680 (m-30) cc_final: 0.8275 (m-30) REVERT: H 11 VAL cc_start: 0.8986 (OUTLIER) cc_final: 0.8750 (t) REVERT: H 57 LYS cc_start: 0.8655 (OUTLIER) cc_final: 0.8351 (mttm) outliers start: 70 outliers final: 48 residues processed: 230 average time/residue: 0.5182 time to fit residues: 137.6319 Evaluate side-chains 240 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 184 time to evaluate : 0.733 ------------------------------------------------------------------------------- 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 95 THR Chi-restraints excluded: chain K residue 11 VAL 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 MET 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 95 THR Chi-restraints excluded: chain F residue 11 VAL 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 MET 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 95 THR Chi-restraints excluded: chain J residue 11 VAL 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 MET 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 95 THR Chi-restraints excluded: chain H residue 11 VAL 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 MET 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: 4.9990 chunk 204 optimal weight: 0.7980 chunk 151 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 132 optimal weight: 0.7980 chunk 144 optimal weight: 4.9990 chunk 232 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.088514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.072489 restraints weight = 27766.009| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.72 r_work: 0.2727 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 20349 Z= 0.232 Angle : 0.639 8.683 27786 Z= 0.325 Chirality : 0.045 0.199 3107 Planarity : 0.005 0.049 3487 Dihedral : 4.844 22.972 2720 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.72 % Favored : 96.12 % Rotamer: Outliers : 3.01 % Allowed : 12.97 % Favored : 84.02 % 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: 0.20 (0.17), residues: 2448 helix: -4.18 (0.11), residues: 24 sheet: 0.69 (0.17), residues: 908 loop : -0.09 (0.17), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 419 TYR 0.021 0.002 TYR C 121 PHE 0.010 0.002 PHE A 410 TRP 0.013 0.002 TRP D 456 HIS 0.007 0.002 HIS F 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.23 (20258) covalent geometry : angle 0.62189 / 0.32 (27557) SS BOND : bond 0.00402 / 0.29 ( 44) SS BOND : angle 1.38599 / 1.01 ( 88) hydrogen bonds : bond 0.03789 / 2.59 ( 640) hydrogen bonds : angle 6.15921 / 4.35 ( 1620) link_ALPHA1-2 : bond 0.00567 / 0.31 ( 8) link_ALPHA1-2 : angle 2.64550 / 1.79 ( 24) link_ALPHA1-3 : bond 0.00383 / 0.21 ( 8) link_ALPHA1-3 : angle 1.39072 / 0.97 ( 24) link_ALPHA1-6 : bond 0.00672 / 0.36 ( 8) link_ALPHA1-6 : angle 1.59660 / 1.11 ( 24) link_BETA1-4 : bond 0.00382 / 0.26 ( 12) link_BETA1-4 : angle 1.83468 / 1.23 ( 36) link_NAG-ASN : bond 0.00188 / 0.11 ( 11) link_NAG-ASN : angle 1.78708 / 1.23 ( 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 238 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 174 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 261 LYS cc_start: 0.8323 (mttp) cc_final: 0.7806 (mmmt) REVERT: I 79 GLN cc_start: 0.7812 (mm-40) cc_final: 0.7413 (mm110) REVERT: I 82 ASP cc_start: 0.8737 (m-30) cc_final: 0.8430 (m-30) REVERT: K 57 LYS cc_start: 0.8678 (OUTLIER) cc_final: 0.8405 (mttm) REVERT: D 261 LYS cc_start: 0.8325 (mttp) cc_final: 0.7813 (mmmt) REVERT: E 79 GLN cc_start: 0.7807 (mm-40) cc_final: 0.7410 (mm110) REVERT: E 82 ASP cc_start: 0.8730 (m-30) cc_final: 0.8426 (m-30) REVERT: F 57 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8404 (mttm) REVERT: G 79 GLN cc_start: 0.7810 (mm-40) cc_final: 0.7414 (mm110) REVERT: G 82 ASP cc_start: 0.8746 (m-30) cc_final: 0.8443 (m-30) REVERT: J 57 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8409 (mttm) REVERT: C 261 LYS cc_start: 0.8317 (mttp) cc_final: 0.7804 (mmmt) REVERT: B 261 LYS cc_start: 0.8314 (mttp) cc_final: 0.7799 (mmmt) REVERT: L 79 GLN cc_start: 0.7803 (mm-40) cc_final: 0.7405 (mm110) REVERT: L 82 ASP cc_start: 0.8733 (m-30) cc_final: 0.8429 (m-30) REVERT: H 57 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8411 (mttm) outliers start: 64 outliers final: 56 residues processed: 206 average time/residue: 0.5212 time to fit residues: 124.4440 Evaluate side-chains 230 residues out of total 2128 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 170 time to evaluate : 0.713 ------------------------------------------------------------------------------- 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 95 THR Chi-restraints excluded: chain K residue 11 VAL 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 MET 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 95 THR Chi-restraints excluded: chain F residue 11 VAL 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 MET 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 95 THR Chi-restraints excluded: chain J residue 11 VAL 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 MET 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 95 THR Chi-restraints excluded: chain H residue 11 VAL 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 MET Chi-restraints excluded: chain H residue 82 SER 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: 0.0980 chunk 238 optimal weight: 0.9980 chunk 191 optimal weight: 0.9990 chunk 159 optimal weight: 0.9980 chunk 227 optimal weight: 0.7980 chunk 224 optimal weight: 9.9990 chunk 192 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 155 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 143 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.091955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.075950 restraints weight = 27365.773| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.73 r_work: 0.2781 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2664 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 20349 Z= 0.109 Angle : 0.544 7.528 27786 Z= 0.281 Chirality : 0.043 0.179 3107 Planarity : 0.004 0.048 3487 Dihedral : 4.570 22.868 2720 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.78 % Favored : 97.06 % Rotamer: Outliers : 3.01 % Allowed : 12.97 % Favored : 84.02 % 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: -4.19 (0.10), residues: 24 sheet: 0.88 (0.17), residues: 908 loop : -0.01 (0.17), residues: 1516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 209 TYR 0.015 0.001 TYR B 121 PHE 0.011 0.001 PHE B 410 TRP 0.015 0.001 TRP D 161 HIS 0.003 0.001 HIS K 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (20258) covalent geometry : angle 0.53045 / 0.28 (27557) SS BOND : bond 0.00416 / 0.30 ( 44) SS BOND : angle 0.94701 / 0.69 ( 88) hydrogen bonds : bond 0.03165 / 2.18 ( 640) hydrogen bonds : angle 5.94188 / 4.20 ( 1620) link_ALPHA1-2 : bond 0.00654 / 0.36 ( 8) link_ALPHA1-2 : angle 2.29927 / 1.56 ( 24) link_ALPHA1-3 : bond 0.00424 / 0.23 ( 8) link_ALPHA1-3 : angle 1.32880 / 0.97 ( 24) link_ALPHA1-6 : bond 0.00683 / 0.36 ( 8) link_ALPHA1-6 : angle 1.41946 / 1.02 ( 24) link_BETA1-4 : bond 0.00367 / 0.24 ( 12) link_BETA1-4 : angle 1.48831 / 0.97 ( 36) link_NAG-ASN : bond 0.00108 / 0.07 ( 11) link_NAG-ASN : angle 1.55689 / 1.07 ( 33) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5734.24 seconds wall clock time: 98 minutes 54.00 seconds (5934.00 seconds total)