Starting phenix.real_space_refine on Tue Sep 15 12:33:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9pvb_71888/09_2026/9pvb_71888.cif Found real_map, /net/cci-nas-00/data/ceres_data/9pvb_71888/09_2026/9pvb_71888.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.04 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9pvb_71888/09_2026/9pvb_71888.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9pvb_71888/09_2026/9pvb_71888.map" model { file = "/net/cci-nas-00/data/ceres_data/9pvb_71888/09_2026/9pvb_71888.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9pvb_71888/09_2026/9pvb_71888.cif" } resolution = 2.04 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= 0.003 sd= 0.066 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: 6 Type Number sf(0) Gaussians P 16 5.49 5 Mg 8 5.21 5 S 232 5.16 5 C 23927 2.51 5 N 6455 2.21 5 O 8695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 127 residue(s): 0.03s 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: 39333 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 3651 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 435} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 435} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3590 Chain: "C" Number of atoms: 3654 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 435} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 435} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3587 Chain: "D" Number of atoms: 3654 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 435} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 435} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3587 Chain: "B" Number of atoms: 3654 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 435} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 435} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3587 Chain: "E" Number of atoms: 3654 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 435} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 435} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3587 Chain: "G" Number of atoms: 3654 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 435} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 435} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3587 Chain: "H" Number of atoms: 3654 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 435} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 435} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3587 Chain: "F" Number of atoms: 3654 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 435} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 458, 3579 Classifications: {'peptide': 458} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 435} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3587 Chain: "M" Number of atoms: 1032 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 997 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 8, 'TRANS': 113} Conformer: "B" Number of residues, atoms: 122, 997 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 8, 'TRANS': 113} bond proxies already assigned to first conformer: 985 Chain: "K" Number of atoms: 1032 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 997 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 8, 'TRANS': 113} Conformer: "B" Number of residues, atoms: 122, 997 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 8, 'TRANS': 113} bond proxies already assigned to first conformer: 985 Chain: "O" Number of atoms: 1032 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 997 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 8, 'TRANS': 113} Conformer: "B" Number of residues, atoms: 122, 997 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 8, 'TRANS': 113} bond proxies already assigned to first conformer: 985 Chain: "P" Number of atoms: 1032 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 997 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 8, 'TRANS': 113} Conformer: "B" Number of residues, atoms: 122, 997 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 8, 'TRANS': 113} bond proxies already assigned to first conformer: 985 Chain: "N" Number of atoms: 1032 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 997 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 8, 'TRANS': 113} Conformer: "B" Number of residues, atoms: 122, 997 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 8, 'TRANS': 113} bond proxies already assigned to first conformer: 985 Chain: "I" Number of atoms: 1032 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 997 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 8, 'TRANS': 113} Conformer: "B" Number of residues, atoms: 122, 997 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 8, 'TRANS': 113} bond proxies already assigned to first conformer: 985 Chain: "J" Number of atoms: 1032 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 997 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 8, 'TRANS': 113} Conformer: "B" Number of residues, atoms: 122, 997 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 8, 'TRANS': 113} bond proxies already assigned to first conformer: 985 Chain: "L" Number of atoms: 1032 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 122, 997 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 8, 'TRANS': 113} Conformer: "B" Number of residues, atoms: 122, 997 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 8, 'TRANS': 113} bond proxies already assigned to first conformer: 985 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 167 Classifications: {'water': 167} Link IDs: {None: 166} Chain: "C" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 163 Classifications: {'water': 163} Link IDs: {None: 162} Chain: "D" Number of atoms: 174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 174 Classifications: {'water': 174} Link IDs: {None: 173} Chain: "B" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 161 Classifications: {'water': 161} Link IDs: {None: 160} Chain: "E" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 172 Classifications: {'water': 172} Link IDs: {None: 171} Chain: "G" Number of atoms: 165 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 165 Classifications: {'water': 165} Link IDs: {None: 164} Chain: "H" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 164 Classifications: {'water': 164} Link IDs: {None: 163} Chain: "F" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 163 Classifications: {'water': 163} Link IDs: {None: 162} Chain: "M" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 38 Classifications: {'water': 38} Link IDs: {None: 37} Chain: "K" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "O" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "P" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 45 Classifications: {'water': 45} Link IDs: {None: 44} Chain: "N" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Chain: "L" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 43 Classifications: {'water': 43} Link IDs: {None: 42} Residues with excluded nonbonded symmetry interactions: 111 residue: pdb=" N ASER A 76 " occ=0.61 ... (10 atoms not shown) pdb=" OG BSER A 76 " occ=0.39 residue: pdb=" N AARG A 83 " occ=0.54 ... (20 atoms not shown) pdb=" NH2BARG A 83 " occ=0.46 residue: pdb=" N AASP A 106 " occ=0.61 ... (14 atoms not shown) pdb=" OD2BASP A 106 " occ=0.39 residue: pdb=" N ALYS A 161 " occ=0.54 ... (16 atoms not shown) pdb=" NZ BLYS A 161 " occ=0.46 residue: pdb=" N ALYS A 252 " occ=0.42 ... (16 atoms not shown) pdb=" NZ BLYS A 252 " occ=0.58 residue: pdb=" N AGLN A 401 " occ=0.55 ... (16 atoms not shown) pdb=" NE2BGLN A 401 " occ=0.45 residue: pdb=" N ACYS A 459 " occ=0.46 ... (10 atoms not shown) pdb=" SG BCYS A 459 " occ=0.54 residue: pdb=" N AGLU A 460 " occ=0.46 ... (16 atoms not shown) pdb=" OE2BGLU A 460 " occ=0.54 residue: pdb=" N AILE C 36 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE C 36 " occ=0.48 residue: pdb=" N ASER C 76 " occ=0.59 ... (10 atoms not shown) pdb=" OG BSER C 76 " occ=0.41 residue: pdb=" N AARG C 83 " occ=0.57 ... (20 atoms not shown) pdb=" NH2BARG C 83 " occ=0.43 residue: pdb=" N AASP C 106 " occ=0.56 ... (14 atoms not shown) pdb=" OD2BASP C 106 " occ=0.44 ... (remaining 99 not shown) Time building chain proxies: 14.44, per 1000 atoms: 0.37 Number of scatterers: 39333 At special positions: 0 Unit cell: (131.472, 131.472, 129.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 232 16.00 P 16 15.00 Mg 8 11.99 O 8695 8.00 N 6455 7.00 C 23927 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 247 " - pdb=" SG CYS B 247 " distance=2.06 Simple disulfide: pdb=" SG CYS E 247 " - pdb=" SG CYS F 247 " distance=2.06 Simple disulfide: pdb=" SG CYS G 247 " - pdb=" SG CYS H 247 " distance=2.06 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 Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 2.8 seconds 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8688 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 32 sheets defined 47.2% alpha, 13.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 20 through 25 removed outlier: 3.805A pdb=" N TYR A 25 " --> pdb=" O LYS A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 60 Processing helix chain 'A' and resid 69 through 75 removed outlier: 3.584A pdb=" N ASP A 72 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 81 removed outlier: 3.875A pdb=" N TYR A 80 " --> pdb=" O ASER A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 112 through 122 Processing helix chain 'A' and resid 123 through 127 removed outlier: 3.559A pdb=" N PHE A 127 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 213 through 233 Processing helix chain 'A' and resid 246 through 261 Processing helix chain 'A' and resid 269 through 273 Processing helix chain 'A' and resid 273 through 288 Processing helix chain 'A' and resid 297 through 303 removed outlier: 4.047A pdb=" N ILE A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG A 303 " --> pdb=" O ALA A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 322 removed outlier: 3.803A pdb=" N LEU A 314 " --> pdb=" O HIS A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 357 through 361 Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 403 through 408 removed outlier: 3.693A pdb=" N LEU A 407 " --> pdb=" O GLY A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 433 Processing helix chain 'A' and resid 436 through 449 removed outlier: 6.637A pdb=" N ASN A 442 " --> pdb=" O ALA A 438 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N GLU A 443 " --> pdb=" O VAL A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 462 removed outlier: 3.630A pdb=" N AGLU A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL A 461 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N TRP A 462 " --> pdb=" O ALA A 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 25 removed outlier: 3.814A pdb=" N TYR C 25 " --> pdb=" O LYS C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 60 Processing helix chain 'C' and resid 69 through 75 removed outlier: 3.593A pdb=" N ASP C 72 " --> pdb=" O VAL C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.593A pdb=" N ARG C 79 " --> pdb=" O ASER C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 112 through 122 Processing helix chain 'C' and resid 123 through 127 removed outlier: 3.593A pdb=" N PHE C 127 " --> pdb=" O VAL C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 146 Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 213 through 233 Processing helix chain 'C' and resid 246 through 261 Processing helix chain 'C' and resid 269 through 273 Processing helix chain 'C' and resid 273 through 288 Processing helix chain 'C' and resid 297 through 303 removed outlier: 4.068A pdb=" N ILE C 301 " --> pdb=" O MET C 297 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG C 303 " --> pdb=" O ALA C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 322 removed outlier: 3.814A pdb=" N LEU C 314 " --> pdb=" O HIS C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 338 through 351 Processing helix chain 'C' and resid 357 through 361 Processing helix chain 'C' and resid 383 through 385 No H-bonds generated for 'chain 'C' and resid 383 through 385' Processing helix chain 'C' and resid 386 through 395 Processing helix chain 'C' and resid 403 through 408 removed outlier: 3.629A pdb=" N LEU C 407 " --> pdb=" O GLY C 403 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 433 Processing helix chain 'C' and resid 436 through 449 removed outlier: 6.679A pdb=" N ASN C 442 " --> pdb=" O ALA C 438 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N GLU C 443 " --> pdb=" O VAL C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 452 through 462 removed outlier: 3.625A pdb=" N AGLU C 460 " --> pdb=" O ALA C 456 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N VAL C 461 " --> pdb=" O ALA C 457 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TRP C 462 " --> pdb=" O ALA C 458 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 25 removed outlier: 3.804A pdb=" N TYR D 25 " --> pdb=" O LYS D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 60 Processing helix chain 'D' and resid 69 through 75 Processing helix chain 'D' and resid 76 through 81 removed outlier: 3.864A pdb=" N TYR D 80 " --> pdb=" O ASER D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 108 Processing helix chain 'D' and resid 112 through 122 Processing helix chain 'D' and resid 123 through 127 removed outlier: 3.506A pdb=" N PHE D 127 " --> pdb=" O VAL D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 146 Processing helix chain 'D' and resid 154 through 163 Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 213 through 233 Processing helix chain 'D' and resid 246 through 261 Processing helix chain 'D' and resid 269 through 273 Processing helix chain 'D' and resid 273 through 288 Processing helix chain 'D' and resid 297 through 303 removed outlier: 4.075A pdb=" N ILE D 301 " --> pdb=" O MET D 297 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG D 303 " --> pdb=" O ALA D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 322 removed outlier: 3.806A pdb=" N LEU D 314 " --> pdb=" O HIS D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 338 through 351 Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 383 through 385 No H-bonds generated for 'chain 'D' and resid 383 through 385' Processing helix chain 'D' and resid 386 through 395 Processing helix chain 'D' and resid 403 through 408 removed outlier: 3.640A pdb=" N LEU D 407 " --> pdb=" O GLY D 403 " (cutoff:3.500A) Processing helix chain 'D' and resid 412 through 433 Processing helix chain 'D' and resid 436 through 449 removed outlier: 6.691A pdb=" N ASN D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLU D 443 " --> pdb=" O VAL D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 452 through 462 removed outlier: 3.619A pdb=" N AGLU D 460 " --> pdb=" O ALA D 456 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL D 461 " --> pdb=" O ALA D 457 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N TRP D 462 " --> pdb=" O ALA D 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 25 removed outlier: 3.850A pdb=" N TYR B 25 " --> pdb=" O LYS B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 60 Processing helix chain 'B' and resid 69 through 75 removed outlier: 3.560A pdb=" N ASP B 72 " --> pdb=" O VAL B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 80 removed outlier: 3.584A pdb=" N ARG B 79 " --> pdb=" O ASER B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 108 Processing helix chain 'B' and resid 112 through 122 Processing helix chain 'B' and resid 123 through 127 removed outlier: 3.577A pdb=" N PHE B 127 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'B' and resid 154 through 163 Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 213 through 233 Processing helix chain 'B' and resid 246 through 261 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'B' and resid 273 through 288 Processing helix chain 'B' and resid 297 through 303 removed outlier: 4.051A pdb=" N ILE B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG B 303 " --> pdb=" O ALA B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 322 removed outlier: 3.803A pdb=" N LEU B 314 " --> pdb=" O HIS B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 351 Processing helix chain 'B' and resid 357 through 361 Processing helix chain 'B' and resid 383 through 385 No H-bonds generated for 'chain 'B' and resid 383 through 385' Processing helix chain 'B' and resid 386 through 395 Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.644A pdb=" N LEU B 407 " --> pdb=" O GLY B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 433 Processing helix chain 'B' and resid 436 through 449 removed outlier: 6.621A pdb=" N ASN B 442 " --> pdb=" O ALA B 438 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLU B 443 " --> pdb=" O VAL B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 462 removed outlier: 3.578A pdb=" N AGLU B 460 " --> pdb=" O ALA B 456 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL B 461 " --> pdb=" O ALA B 457 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N TRP B 462 " --> pdb=" O ALA B 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 25 removed outlier: 3.871A pdb=" N TYR E 25 " --> pdb=" O LYS E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 60 Processing helix chain 'E' and resid 69 through 75 removed outlier: 3.561A pdb=" N ASP E 72 " --> pdb=" O VAL E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 81 removed outlier: 3.891A pdb=" N TYR E 80 " --> pdb=" O ASER E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'E' and resid 112 through 122 Processing helix chain 'E' and resid 123 through 127 removed outlier: 3.515A pdb=" N PHE E 127 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 146 Processing helix chain 'E' and resid 154 through 163 Processing helix chain 'E' and resid 181 through 194 Processing helix chain 'E' and resid 213 through 233 Processing helix chain 'E' and resid 246 through 261 Processing helix chain 'E' and resid 269 through 273 Processing helix chain 'E' and resid 273 through 288 Processing helix chain 'E' and resid 297 through 303 removed outlier: 4.040A pdb=" N ILE E 301 " --> pdb=" O MET E 297 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG E 303 " --> pdb=" O ALA E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 322 removed outlier: 3.805A pdb=" N LEU E 314 " --> pdb=" O HIS E 310 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 351 Processing helix chain 'E' and resid 357 through 361 Processing helix chain 'E' and resid 383 through 385 No H-bonds generated for 'chain 'E' and resid 383 through 385' Processing helix chain 'E' and resid 386 through 395 Processing helix chain 'E' and resid 403 through 408 removed outlier: 3.662A pdb=" N LEU E 407 " --> pdb=" O GLY E 403 " (cutoff:3.500A) Processing helix chain 'E' and resid 412 through 433 Processing helix chain 'E' and resid 436 through 449 removed outlier: 7.000A pdb=" N ASN E 442 " --> pdb=" O ALA E 438 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N GLU E 443 " --> pdb=" O VAL E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 462 removed outlier: 3.612A pdb=" N AGLU E 460 " --> pdb=" O ALA E 456 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL E 461 " --> pdb=" O ALA E 457 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TRP E 462 " --> pdb=" O ALA E 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 25 removed outlier: 3.835A pdb=" N TYR G 25 " --> pdb=" O LYS G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 60 Processing helix chain 'G' and resid 69 through 75 Processing helix chain 'G' and resid 76 through 80 removed outlier: 3.531A pdb=" N ARG G 79 " --> pdb=" O ASER G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 108 Processing helix chain 'G' and resid 112 through 122 Processing helix chain 'G' and resid 123 through 127 removed outlier: 3.566A pdb=" N PHE G 127 " --> pdb=" O VAL G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 146 Processing helix chain 'G' and resid 154 through 163 Processing helix chain 'G' and resid 181 through 194 Processing helix chain 'G' and resid 213 through 233 Processing helix chain 'G' and resid 246 through 261 Processing helix chain 'G' and resid 269 through 273 Processing helix chain 'G' and resid 273 through 288 Processing helix chain 'G' and resid 297 through 303 removed outlier: 4.046A pdb=" N ILE G 301 " --> pdb=" O MET G 297 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG G 303 " --> pdb=" O ALA G 299 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 322 removed outlier: 3.816A pdb=" N LEU G 314 " --> pdb=" O HIS G 310 " (cutoff:3.500A) Processing helix chain 'G' and resid 338 through 351 Processing helix chain 'G' and resid 357 through 361 Processing helix chain 'G' and resid 383 through 385 No H-bonds generated for 'chain 'G' and resid 383 through 385' Processing helix chain 'G' and resid 386 through 395 Processing helix chain 'G' and resid 403 through 408 removed outlier: 3.693A pdb=" N LEU G 407 " --> pdb=" O GLY G 403 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 433 Processing helix chain 'G' and resid 436 through 449 removed outlier: 6.647A pdb=" N ASN G 442 " --> pdb=" O ALA G 438 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLU G 443 " --> pdb=" O VAL G 439 " (cutoff:3.500A) Processing helix chain 'G' and resid 452 through 462 removed outlier: 3.657A pdb=" N AGLU G 460 " --> pdb=" O ALA G 456 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL G 461 " --> pdb=" O ALA G 457 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TRP G 462 " --> pdb=" O ALA G 458 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 25 removed outlier: 3.828A pdb=" N TYR H 25 " --> pdb=" O LYS H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 60 Processing helix chain 'H' and resid 69 through 75 removed outlier: 3.597A pdb=" N ASP H 72 " --> pdb=" O VAL H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 81 removed outlier: 3.912A pdb=" N TYR H 80 " --> pdb=" O ASER H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 108 Processing helix chain 'H' and resid 112 through 121 Processing helix chain 'H' and resid 123 through 127 removed outlier: 3.645A pdb=" N PHE H 127 " --> pdb=" O VAL H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 146 Processing helix chain 'H' and resid 154 through 163 Processing helix chain 'H' and resid 181 through 194 Processing helix chain 'H' and resid 213 through 233 Processing helix chain 'H' and resid 246 through 261 Processing helix chain 'H' and resid 269 through 273 Processing helix chain 'H' and resid 273 through 288 Processing helix chain 'H' and resid 297 through 303 removed outlier: 4.022A pdb=" N ILE H 301 " --> pdb=" O MET H 297 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG H 303 " --> pdb=" O ALA H 299 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 322 removed outlier: 3.783A pdb=" N LEU H 314 " --> pdb=" O HIS H 310 " (cutoff:3.500A) Processing helix chain 'H' and resid 338 through 351 Processing helix chain 'H' and resid 357 through 361 Processing helix chain 'H' and resid 383 through 385 No H-bonds generated for 'chain 'H' and resid 383 through 385' Processing helix chain 'H' and resid 386 through 395 Processing helix chain 'H' and resid 403 through 408 removed outlier: 3.669A pdb=" N LEU H 407 " --> pdb=" O GLY H 403 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 433 Processing helix chain 'H' and resid 436 through 449 removed outlier: 6.919A pdb=" N ASN H 442 " --> pdb=" O ALA H 438 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N GLU H 443 " --> pdb=" O VAL H 439 " (cutoff:3.500A) Processing helix chain 'H' and resid 452 through 462 removed outlier: 3.563A pdb=" N AGLU H 460 " --> pdb=" O ALA H 456 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL H 461 " --> pdb=" O ALA H 457 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TRP H 462 " --> pdb=" O ALA H 458 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 25 removed outlier: 3.872A pdb=" N TYR F 25 " --> pdb=" O LYS F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 60 Processing helix chain 'F' and resid 69 through 75 removed outlier: 3.618A pdb=" N ASP F 72 " --> pdb=" O VAL F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 81 removed outlier: 3.898A pdb=" N TYR F 80 " --> pdb=" O ASER F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 112 through 122 Processing helix chain 'F' and resid 123 through 127 removed outlier: 3.597A pdb=" N PHE F 127 " --> pdb=" O VAL F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 146 Processing helix chain 'F' and resid 154 through 163 Processing helix chain 'F' and resid 181 through 195 removed outlier: 3.811A pdb=" N GLY F 195 " --> pdb=" O GLU F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 233 Processing helix chain 'F' and resid 246 through 261 Processing helix chain 'F' and resid 269 through 273 Processing helix chain 'F' and resid 273 through 288 Processing helix chain 'F' and resid 297 through 303 removed outlier: 4.059A pdb=" N ILE F 301 " --> pdb=" O MET F 297 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG F 303 " --> pdb=" O ALA F 299 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 322 removed outlier: 3.804A pdb=" N LEU F 314 " --> pdb=" O HIS F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 338 through 351 Processing helix chain 'F' and resid 357 through 361 Processing helix chain 'F' and resid 383 through 385 No H-bonds generated for 'chain 'F' and resid 383 through 385' Processing helix chain 'F' and resid 386 through 395 Processing helix chain 'F' and resid 403 through 408 removed outlier: 3.696A pdb=" N LEU F 407 " --> pdb=" O GLY F 403 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 433 Processing helix chain 'F' and resid 436 through 449 removed outlier: 6.765A pdb=" N ASN F 442 " --> pdb=" O ALA F 438 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N GLU F 443 " --> pdb=" O VAL F 439 " (cutoff:3.500A) Processing helix chain 'F' and resid 452 through 462 removed outlier: 3.612A pdb=" N AGLU F 460 " --> pdb=" O ALA F 456 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL F 461 " --> pdb=" O ALA F 457 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TRP F 462 " --> pdb=" O ALA F 458 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 36 Processing helix chain 'M' and resid 79 through 92 Processing helix chain 'K' and resid 22 through 36 Processing helix chain 'K' and resid 79 through 92 Processing helix chain 'O' and resid 22 through 36 Processing helix chain 'O' and resid 79 through 92 Processing helix chain 'P' and resid 22 through 36 Processing helix chain 'P' and resid 79 through 92 Processing helix chain 'N' and resid 22 through 36 Processing helix chain 'N' and resid 79 through 92 Processing helix chain 'I' and resid 22 through 36 Processing helix chain 'I' and resid 79 through 92 Processing helix chain 'J' and resid 22 through 36 Processing helix chain 'J' and resid 79 through 92 Processing helix chain 'L' and resid 22 through 36 Processing helix chain 'L' and resid 79 through 92 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 89 removed outlier: 5.805A pdb=" N CYS A 84 " --> pdb=" O ALA A 102 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ALA A 102 " --> pdb=" O CYS A 84 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N HIS A 86 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N LEU A 37 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU A 138 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ALA A 39 " --> pdb=" O GLU A 136 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 169 through 171 removed outlier: 6.485A pdb=" N LEU A 169 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N AGLN A 401 " --> pdb=" O PRO A 376 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ALA A 378 " --> pdb=" O AGLN A 401 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS A 327 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL A 265 " --> pdb=" O HIS A 292 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N HIS A 294 " --> pdb=" O VAL A 265 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N HIS A 267 " --> pdb=" O HIS A 294 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N HIS A 238 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N MET A 266 " --> pdb=" O HIS A 238 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU A 240 " --> pdb=" O MET A 266 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N ASP A 268 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR A 200 " --> pdb=" O TYR A 239 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ASN A 241 " --> pdb=" O THR A 200 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 354 Processing sheet with id=AA4, first strand: chain 'C' and resid 83 through 89 removed outlier: 5.808A pdb=" N CYS C 84 " --> pdb=" O ALA C 102 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA C 102 " --> pdb=" O CYS C 84 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N HIS C 86 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU C 37 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU C 138 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA C 39 " --> pdb=" O GLU C 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 169 through 171 removed outlier: 6.468A pdb=" N LEU C 169 " --> pdb=" O LEU C 400 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS C 327 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL C 265 " --> pdb=" O HIS C 292 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N HIS C 294 " --> pdb=" O VAL C 265 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N HIS C 267 " --> pdb=" O HIS C 294 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N HIS C 238 " --> pdb=" O ILE C 264 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N MET C 266 " --> pdb=" O HIS C 238 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LEU C 240 " --> pdb=" O MET C 266 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ASP C 268 " --> pdb=" O LEU C 240 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N THR C 200 " --> pdb=" O TYR C 239 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ASN C 241 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 353 through 354 Processing sheet with id=AA7, first strand: chain 'D' and resid 83 through 89 removed outlier: 5.826A pdb=" N CYS D 84 " --> pdb=" O ALA D 102 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA D 102 " --> pdb=" O CYS D 84 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N HIS D 86 " --> pdb=" O TYR D 100 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU D 37 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU D 138 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ALA D 39 " --> pdb=" O GLU D 136 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 169 through 171 removed outlier: 6.468A pdb=" N LEU D 169 " --> pdb=" O LEU D 400 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N HIS D 327 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL D 265 " --> pdb=" O HIS D 292 " (cutoff:3.500A) removed outlier: 8.017A pdb=" N HIS D 294 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N HIS D 267 " --> pdb=" O HIS D 294 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N HIS D 238 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N MET D 266 " --> pdb=" O HIS D 238 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU D 240 " --> pdb=" O MET D 266 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N ASP D 268 " --> pdb=" O LEU D 240 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N THR D 200 " --> pdb=" O TYR D 239 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N ASN D 241 " --> pdb=" O THR D 200 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 353 through 354 Processing sheet with id=AB1, first strand: chain 'B' and resid 83 through 89 removed outlier: 5.854A pdb=" N CYS B 84 " --> pdb=" O ALA B 102 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N ALA B 102 " --> pdb=" O CYS B 84 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N HIS B 86 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU B 37 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LEU B 138 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ALA B 39 " --> pdb=" O GLU B 136 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 169 through 171 removed outlier: 6.467A pdb=" N LEU B 169 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N AGLN B 401 " --> pdb=" O PRO B 376 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ALA B 378 " --> pdb=" O AGLN B 401 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS B 327 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL B 265 " --> pdb=" O HIS B 292 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N HIS B 294 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N HIS B 267 " --> pdb=" O HIS B 294 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N HIS B 238 " --> pdb=" O ILE B 264 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N MET B 266 " --> pdb=" O HIS B 238 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU B 240 " --> pdb=" O MET B 266 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N ASP B 268 " --> pdb=" O LEU B 240 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N THR B 200 " --> pdb=" O TYR B 239 " (cutoff:3.500A) removed outlier: 8.394A pdb=" N ASN B 241 " --> pdb=" O THR B 200 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 353 through 354 Processing sheet with id=AB4, first strand: chain 'E' and resid 83 through 89 removed outlier: 5.787A pdb=" N CYS E 84 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ALA E 102 " --> pdb=" O CYS E 84 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N HIS E 86 " --> pdb=" O TYR E 100 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LEU E 37 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU E 138 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA E 39 " --> pdb=" O GLU E 136 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 169 through 171 removed outlier: 6.483A pdb=" N LEU E 169 " --> pdb=" O LEU E 400 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS E 327 " --> pdb=" O ILE E 293 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL E 265 " --> pdb=" O HIS E 292 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N HIS E 294 " --> pdb=" O VAL E 265 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N HIS E 267 " --> pdb=" O HIS E 294 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N HIS E 238 " --> pdb=" O ILE E 264 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N MET E 266 " --> pdb=" O HIS E 238 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU E 240 " --> pdb=" O MET E 266 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ASP E 268 " --> pdb=" O LEU E 240 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N THR E 200 " --> pdb=" O TYR E 239 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ASN E 241 " --> pdb=" O THR E 200 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 353 through 354 Processing sheet with id=AB7, first strand: chain 'G' and resid 83 through 89 removed outlier: 5.794A pdb=" N CYS G 84 " --> pdb=" O ALA G 102 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N ALA G 102 " --> pdb=" O CYS G 84 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N HIS G 86 " --> pdb=" O TYR G 100 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N LEU G 37 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU G 138 " --> pdb=" O LEU G 37 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA G 39 " --> pdb=" O GLU G 136 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 169 through 171 removed outlier: 6.476A pdb=" N LEU G 169 " --> pdb=" O LEU G 400 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS G 327 " --> pdb=" O ILE G 293 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL G 265 " --> pdb=" O HIS G 292 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N HIS G 294 " --> pdb=" O VAL G 265 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N HIS G 267 " --> pdb=" O HIS G 294 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N HIS G 238 " --> pdb=" O ILE G 264 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET G 266 " --> pdb=" O HIS G 238 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU G 240 " --> pdb=" O MET G 266 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N ASP G 268 " --> pdb=" O LEU G 240 " (cutoff:3.500A) removed outlier: 7.309A pdb=" N THR G 200 " --> pdb=" O TYR G 239 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ASN G 241 " --> pdb=" O THR G 200 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 353 through 354 Processing sheet with id=AC1, first strand: chain 'H' and resid 83 through 89 removed outlier: 5.821A pdb=" N CYS H 84 " --> pdb=" O ALA H 102 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ALA H 102 " --> pdb=" O CYS H 84 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS H 86 " --> pdb=" O TYR H 100 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N LEU H 37 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU H 138 " --> pdb=" O LEU H 37 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ALA H 39 " --> pdb=" O GLU H 136 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 169 through 171 removed outlier: 6.482A pdb=" N LEU H 169 " --> pdb=" O LEU H 400 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N AGLN H 401 " --> pdb=" O PRO H 376 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA H 378 " --> pdb=" O AGLN H 401 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS H 327 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL H 265 " --> pdb=" O HIS H 292 " (cutoff:3.500A) removed outlier: 8.026A pdb=" N HIS H 294 " --> pdb=" O VAL H 265 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N HIS H 267 " --> pdb=" O HIS H 294 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N HIS H 238 " --> pdb=" O ILE H 264 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N MET H 266 " --> pdb=" O HIS H 238 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N LEU H 240 " --> pdb=" O MET H 266 " (cutoff:3.500A) removed outlier: 8.442A pdb=" N ASP H 268 " --> pdb=" O LEU H 240 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N THR H 200 " --> pdb=" O TYR H 239 " (cutoff:3.500A) removed outlier: 8.412A pdb=" N ASN H 241 " --> pdb=" O THR H 200 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'H' and resid 353 through 354 Processing sheet with id=AC4, first strand: chain 'F' and resid 83 through 89 removed outlier: 5.788A pdb=" N CYS F 84 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ALA F 102 " --> pdb=" O CYS F 84 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N HIS F 86 " --> pdb=" O TYR F 100 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LEU F 37 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU F 138 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N ALA F 39 " --> pdb=" O GLU F 136 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 169 through 171 removed outlier: 6.472A pdb=" N LEU F 169 " --> pdb=" O LEU F 400 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N AGLN F 401 " --> pdb=" O PRO F 376 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA F 378 " --> pdb=" O AGLN F 401 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N HIS F 327 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N VAL F 265 " --> pdb=" O HIS F 292 " (cutoff:3.500A) removed outlier: 8.022A pdb=" N HIS F 294 " --> pdb=" O VAL F 265 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N HIS F 267 " --> pdb=" O HIS F 294 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N HIS F 238 " --> pdb=" O ILE F 264 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N MET F 266 " --> pdb=" O HIS F 238 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N LEU F 240 " --> pdb=" O MET F 266 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N ASP F 268 " --> pdb=" O LEU F 240 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N THR F 200 " --> pdb=" O TYR F 239 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N ASN F 241 " --> pdb=" O THR F 200 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 353 through 354 Processing sheet with id=AC7, first strand: chain 'M' and resid 67 through 68 removed outlier: 6.379A pdb=" N ILE M 98 " --> pdb=" O ILE M 116 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET M 112 " --> pdb=" O ALA M 102 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ASP M 104 " --> pdb=" O GLN M 110 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N GLN M 110 " --> pdb=" O ASP M 104 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 67 through 68 removed outlier: 6.390A pdb=" N ILE K 98 " --> pdb=" O ILE K 116 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N MET K 112 " --> pdb=" O ALA K 102 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ASP K 104 " --> pdb=" O GLN K 110 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N GLN K 110 " --> pdb=" O ASP K 104 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'O' and resid 67 through 68 removed outlier: 6.360A pdb=" N ILE O 98 " --> pdb=" O ILE O 116 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N MET O 112 " --> pdb=" O ALA O 102 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP O 104 " --> pdb=" O GLN O 110 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N GLN O 110 " --> pdb=" O ASP O 104 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 67 through 68 removed outlier: 6.307A pdb=" N ILE P 98 " --> pdb=" O ILE P 116 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N MET P 112 " --> pdb=" O ALA P 102 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP P 104 " --> pdb=" O GLN P 110 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N GLN P 110 " --> pdb=" O ASP P 104 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 67 through 68 removed outlier: 6.362A pdb=" N ILE N 98 " --> pdb=" O ILE N 116 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N MET N 112 " --> pdb=" O ALA N 102 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ASP N 104 " --> pdb=" O GLN N 110 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N GLN N 110 " --> pdb=" O ASP N 104 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 67 through 68 removed outlier: 6.322A pdb=" N ILE I 98 " --> pdb=" O ILE I 116 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N MET I 112 " --> pdb=" O ALA I 102 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ASP I 104 " --> pdb=" O GLN I 110 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N GLN I 110 " --> pdb=" O ASP I 104 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J' and resid 67 through 68 removed outlier: 6.325A pdb=" N ILE J 98 " --> pdb=" O ILE J 116 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N MET J 112 " --> pdb=" O ALA J 102 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ASP J 104 " --> pdb=" O GLN J 110 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N GLN J 110 " --> pdb=" O ASP J 104 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'L' and resid 67 through 68 removed outlier: 6.323A pdb=" N ILE L 98 " --> pdb=" O ILE L 116 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N MET L 112 " --> pdb=" O ALA L 102 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP L 104 " --> pdb=" O GLN L 110 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N GLN L 110 " --> pdb=" O ASP L 104 " (cutoff:3.500A) 1695 hydrogen bonds defined for protein. 4693 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: 10.10 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 12429 1.35 - 1.48: 9798 1.48 - 1.60: 16130 1.60 - 1.73: 16 1.73 - 1.86: 328 Bond restraints: 38701 Sorted by residual: bond pdb=" O1 CAP B 501 " pdb=" P1 CAP B 501 " ideal model delta sigma weight residual 1.708 1.610 0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" O1 CAP F 501 " pdb=" P1 CAP F 501 " ideal model delta sigma weight residual 1.708 1.610 0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" O1 CAP C 501 " pdb=" P1 CAP C 501 " ideal model delta sigma weight residual 1.708 1.610 0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" O1 CAP D 501 " pdb=" P1 CAP D 501 " ideal model delta sigma weight residual 1.708 1.610 0.098 2.00e-02 2.50e+03 2.38e+01 bond pdb=" O1 CAP H 501 " pdb=" P1 CAP H 501 " ideal model delta sigma weight residual 1.708 1.610 0.098 2.00e-02 2.50e+03 2.38e+01 ... (remaining 38696 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 51135 1.79 - 3.58: 1180 3.58 - 5.38: 255 5.38 - 7.17: 43 7.17 - 8.96: 31 Bond angle restraints: 52644 Sorted by residual: angle pdb=" O1 CAP F 501 " pdb=" P1 CAP F 501 " pdb=" O3P CAP F 501 " ideal model delta sigma weight residual 100.92 109.88 -8.96 3.00e+00 1.11e-01 8.92e+00 angle pdb=" O1 CAP E 501 " pdb=" P1 CAP E 501 " pdb=" O3P CAP E 501 " ideal model delta sigma weight residual 100.92 109.79 -8.87 3.00e+00 1.11e-01 8.74e+00 angle pdb=" C GLY G 344 " pdb=" N PHE G 345 " pdb=" CA PHE G 345 " ideal model delta sigma weight residual 121.14 115.97 5.17 1.75e+00 3.27e-01 8.73e+00 angle pdb=" O1 CAP A 501 " pdb=" P1 CAP A 501 " pdb=" O3P CAP A 501 " ideal model delta sigma weight residual 100.92 109.76 -8.84 3.00e+00 1.11e-01 8.69e+00 angle pdb=" O5 CAP B 501 " pdb=" P2 CAP B 501 " pdb=" O5P CAP B 501 " ideal model delta sigma weight residual 101.98 110.81 -8.83 3.00e+00 1.11e-01 8.66e+00 ... (remaining 52639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.02: 20241 18.02 - 36.03: 2020 36.03 - 54.05: 599 54.05 - 72.07: 131 72.07 - 90.09: 90 Dihedral angle restraints: 23081 sinusoidal: 9361 harmonic: 13720 Sorted by residual: dihedral pdb=" CA LYS H 81 " pdb=" C LYS H 81 " pdb=" N GLY H 82 " pdb=" CA GLY H 82 " ideal model delta harmonic sigma weight residual 180.00 161.96 18.04 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA LYS G 81 " pdb=" C LYS G 81 " pdb=" N GLY G 82 " pdb=" CA GLY G 82 " ideal model delta harmonic sigma weight residual 180.00 162.08 17.92 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA THR D 63 " pdb=" C THR D 63 " pdb=" N GLY D 64 " pdb=" CA GLY D 64 " ideal model delta harmonic sigma weight residual -180.00 -162.48 -17.52 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 23078 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4600 0.060 - 0.120: 861 0.120 - 0.180: 84 0.180 - 0.240: 10 0.240 - 0.301: 5 Chirality restraints: 5560 Sorted by residual: chirality pdb=" CB ILE I 86 " pdb=" CA ILE I 86 " pdb=" CG1 ILE I 86 " pdb=" CG2 ILE I 86 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CB ILE M 86 " pdb=" CA ILE M 86 " pdb=" CG1 ILE M 86 " pdb=" CG2 ILE M 86 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB ILE K 86 " pdb=" CA ILE K 86 " pdb=" CG1 ILE K 86 " pdb=" CG2 ILE K 86 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 5557 not shown) Planarity restraints: 6887 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 262 " -0.039 5.00e-02 4.00e+02 5.97e-02 5.71e+00 pdb=" N PRO G 263 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO G 263 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 263 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 262 " -0.037 5.00e-02 4.00e+02 5.60e-02 5.02e+00 pdb=" N PRO D 263 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO D 263 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 263 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 262 " -0.036 5.00e-02 4.00e+02 5.41e-02 4.68e+00 pdb=" N PRO B 263 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO B 263 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 263 " -0.030 5.00e-02 4.00e+02 ... (remaining 6884 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 81 2.62 - 3.19: 34982 3.19 - 3.76: 65531 3.76 - 4.33: 98275 4.33 - 4.90: 153892 Nonbonded interactions: 352761 Sorted by model distance: nonbonded pdb=" OE1 GLU G 204 " pdb="MG MG G 502 " model vdw 2.046 2.170 nonbonded pdb=" OE1 GLU D 204 " pdb="MG MG D 502 " model vdw 2.082 2.170 nonbonded pdb=" OE1 GLU F 204 " pdb="MG MG F 502 " model vdw 2.117 2.170 nonbonded pdb=" OE1 GLU C 204 " pdb="MG MG C 502 " model vdw 2.118 2.170 nonbonded pdb=" OE1 GLU A 204 " pdb="MG MG A 502 " model vdw 2.123 2.170 ... (remaining 352756 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' and (resid 12 through 35 or resid 37 through 75 or resid 77 through 8 \ 2 or resid 84 through 105 or resid 107 through 160 or resid 162 through 251 or r \ esid 253 through 400 or resid 402 through 458 or resid 461 through 502)) selection = (chain 'B' and (resid 12 through 35 or resid 37 through 75 or resid 77 through 8 \ 2 or resid 84 through 105 or resid 107 through 160 or resid 162 through 251 or r \ esid 253 through 400 or resid 402 through 458 or resid 461 through 502)) selection = (chain 'C' and (resid 12 through 35 or resid 37 through 75 or resid 77 through 8 \ 2 or resid 84 through 105 or resid 107 through 160 or resid 162 through 251 or r \ esid 253 through 400 or resid 402 through 458 or resid 461 through 502)) selection = (chain 'D' and (resid 12 through 35 or resid 37 through 75 or resid 77 through 8 \ 2 or resid 84 through 105 or resid 107 through 160 or resid 162 through 251 or r \ esid 253 through 400 or resid 402 through 458 or resid 461 through 502)) selection = (chain 'E' and (resid 12 through 35 or resid 37 through 75 or resid 77 through 8 \ 2 or resid 84 through 105 or resid 107 through 160 or resid 162 through 251 or r \ esid 253 through 400 or resid 402 through 458 or resid 461 through 502)) selection = (chain 'F' and (resid 12 through 35 or resid 37 through 75 or resid 77 through 8 \ 2 or resid 84 through 105 or resid 107 through 160 or resid 162 through 251 or r \ esid 253 through 400 or resid 402 through 458 or resid 461 through 502)) selection = (chain 'G' and (resid 12 through 35 or resid 37 through 75 or resid 77 through 8 \ 2 or resid 84 through 105 or resid 107 through 160 or resid 162 through 251 or r \ esid 253 through 400 or resid 402 through 458 or resid 461 through 502)) selection = (chain 'H' and (resid 12 through 35 or resid 37 through 75 or resid 77 through 8 \ 2 or resid 84 through 105 or resid 107 through 160 or resid 162 through 251 or r \ esid 253 through 400 or resid 402 through 458 or resid 461 through 502)) } ncs_group { reference = (chain 'I' and (resid 1 through 33 or resid 35 through 55 or resid 57 through 89 \ or resid 91 through 99 or resid 101 through 110 or resid 112 through 122)) selection = (chain 'J' and (resid 1 through 33 or resid 35 through 55 or resid 57 through 89 \ or resid 91 through 99 or resid 101 through 110 or resid 112 through 122)) selection = (chain 'K' and (resid 1 through 33 or resid 35 through 55 or resid 57 through 89 \ or resid 91 through 99 or resid 101 through 110 or resid 112 through 122)) selection = (chain 'L' and (resid 1 through 33 or resid 35 through 55 or resid 57 through 89 \ or resid 91 through 99 or resid 101 through 110 or resid 112 through 122)) selection = (chain 'M' and (resid 1 through 33 or resid 35 through 55 or resid 57 through 89 \ or resid 91 through 99 or resid 101 through 110 or resid 112 through 122)) selection = (chain 'N' and (resid 1 through 33 or resid 35 through 55 or resid 57 through 89 \ or resid 91 through 99 or resid 101 through 110 or resid 112 through 122)) selection = (chain 'O' and (resid 1 through 33 or resid 35 through 55 or resid 57 through 89 \ or resid 91 through 99 or resid 101 through 110 or resid 112 through 122)) selection = (chain 'P' and (resid 1 through 33 or resid 35 through 55 or resid 57 through 89 \ or resid 91 through 99 or resid 101 through 110 or resid 112 through 122)) } 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=0.36 max=1.00 mean=0.98 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: 2.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.770 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 45.920 Find NCS groups from input model: 1.140 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8795 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 : 0.004 0.098 38704 Z= 0.201 Angle : 0.720 8.959 52650 Z= 0.386 Chirality : 0.047 0.301 5560 Planarity : 0.005 0.060 6887 Dihedral : 16.856 90.087 14384 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.18 % Favored : 96.77 % Rotamer: Outliers : 2.24 % Allowed : 13.82 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.62 (0.12), residues: 4902 helix: 1.61 (0.12), residues: 1856 sheet: -0.04 (0.18), residues: 678 loop : -0.38 (0.12), residues: 2368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 79 TYR 0.017 0.002 TYR C 239 PHE 0.031 0.002 PHE D 345 TRP 0.025 0.001 TRP G 411 HIS 0.007 0.001 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.20 (38701) covalent geometry : angle 0.71854 / 0.39 (52644) SS BOND : bond 0.02631 / 1.48 ( 3) SS BOND : angle 4.82934 / 2.66 ( 6) hydrogen bonds : bond 0.14653 / 9.90 ( 1695) hydrogen bonds : angle 6.34780 / 4.50 ( 4693) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 577 time to evaluate : 1.425 Fit side-chains REVERT: A 18 LYS cc_start: 0.6960 (OUTLIER) cc_final: 0.6266 (mmpt) REVERT: A 30 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7182 (mp0) REVERT: A 443 GLU cc_start: 0.7156 (tp30) cc_final: 0.6758 (mm-30) REVERT: C 18 LYS cc_start: 0.6906 (OUTLIER) cc_final: 0.6044 (mptt) REVERT: C 21 LYS cc_start: 0.7448 (ptmm) cc_final: 0.7237 (pttm) REVERT: D 30 GLU cc_start: 0.7651 (mt-10) cc_final: 0.7165 (mp0) REVERT: D 77 LEU cc_start: 0.8348 (mt) cc_final: 0.8132 (mt) REVERT: D 443 GLU cc_start: 0.6865 (mp0) cc_final: 0.6367 (mm-30) REVERT: B 30 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7397 (mt-10) REVERT: B 336 GLU cc_start: 0.6748 (tt0) cc_final: 0.5888 (tp30) REVERT: B 443 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6637 (tp30) REVERT: E 21 LYS cc_start: 0.7380 (ptmm) cc_final: 0.7067 (pttm) REVERT: E 355 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8091 (mm-30) REVERT: E 443 GLU cc_start: 0.7159 (tp30) cc_final: 0.6919 (mp0) REVERT: G 21 LYS cc_start: 0.7505 (ptmm) cc_final: 0.7304 (pttm) REVERT: G 30 GLU cc_start: 0.7387 (mt-10) cc_final: 0.6914 (mp0) REVERT: H 21 LYS cc_start: 0.7430 (ptmm) cc_final: 0.7191 (pttm) REVERT: H 336 GLU cc_start: 0.7026 (tt0) cc_final: 0.6146 (tp30) REVERT: H 443 GLU cc_start: 0.7117 (mp0) cc_final: 0.6780 (tp30) REVERT: F 18 LYS cc_start: 0.6593 (OUTLIER) cc_final: 0.6137 (mtpt) REVERT: F 443 GLU cc_start: 0.7095 (tp30) cc_final: 0.6647 (mm-30) REVERT: K 117 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7679 (tt0) REVERT: O 117 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8098 (tt0) REVERT: P 81 GLN cc_start: 0.7484 (mm110) cc_final: 0.7170 (mt0) REVERT: P 91 LYS cc_start: 0.7718 (tttm) cc_final: 0.7164 (ttpp) REVERT: N 21 LEU cc_start: 0.7759 (mp) cc_final: 0.7360 (mt) REVERT: N 117 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: N 118 LYS cc_start: 0.8189 (mtmm) cc_final: 0.7787 (mtmt) REVERT: I 81 GLN cc_start: 0.7570 (mp-120) cc_final: 0.7356 (mt0) outliers start: 32 outliers final: 14 residues processed: 597 average time/residue: 0.7659 time to fit residues: 548.7000 Evaluate side-chains 559 residues out of total 3712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 539 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 392 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain G residue 392 GLU Chi-restraints excluded: chain F residue 18 LYS Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 439 VAL Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain O residue 117 GLN Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain N residue 117 GLN Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain L residue 101 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 0.6980 chunk 388 optimal weight: 10.0000 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 30.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 7.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 401 GLN B D 123 ASN E 401 GLN B H 123 ASN F 123 ASN K 87 GLN K 108 GLN O 87 GLN P 87 GLN P 108 GLN P 110 GLN P 117 GLN I 87 GLN J 110 GLN J 117 GLN L 108 GLN L 117 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.138373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.113009 restraints weight = 228635.618| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 3.16 r_work: 0.2863 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2751 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2751 r_free = 0.2751 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.2751 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 38704 Z= 0.232 Angle : 0.757 8.279 52650 Z= 0.417 Chirality : 0.051 0.210 5560 Planarity : 0.006 0.060 6887 Dihedral : 7.052 64.680 5603 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.36 % Favored : 96.60 % Rotamer: Outliers : 2.64 % Allowed : 13.52 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.56 (0.12), residues: 4902 helix: 1.60 (0.12), residues: 1864 sheet: -0.20 (0.17), residues: 774 loop : -0.41 (0.13), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 213 TYR 0.024 0.003 TYR F 269 PHE 0.031 0.003 PHE B 345 TRP 0.021 0.001 TRP G 411 HIS 0.010 0.002 HIS H 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.23 (38701) covalent geometry : angle 0.75403 / 0.42 (52644) SS BOND : bond 0.03692 / 2.07 ( 3) SS BOND : angle 5.95925 / 3.32 ( 6) hydrogen bonds : bond 0.08140 / 5.38 ( 1695) hydrogen bonds : angle 5.37095 / 3.82 ( 4693) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 3712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 541 time to evaluate : 1.575 Fit side-chains REVERT: A 18 LYS cc_start: 0.6741 (OUTLIER) cc_final: 0.6040 (mmpt) REVERT: C 18 LYS cc_start: 0.6707 (OUTLIER) cc_final: 0.5778 (mptt) REVERT: C 21 LYS cc_start: 0.7577 (ptmm) cc_final: 0.7345 (pttm) REVERT: D 443 GLU cc_start: 0.7287 (mp0) cc_final: 0.6849 (tp30) REVERT: B 30 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7400 (mt-10) REVERT: E 21 LYS cc_start: 0.7509 (ptmm) cc_final: 0.7143 (pttm) REVERT: E 355 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8359 (mm-30) REVERT: E 443 GLU cc_start: 0.7453 (tp30) cc_final: 0.6892 (mm-30) REVERT: G 21 LYS cc_start: 0.7544 (ptmm) cc_final: 0.7272 (pttm) REVERT: G 94 GLU cc_start: 0.6343 (OUTLIER) cc_final: 0.6097 (mm-30) REVERT: H 21 LYS cc_start: 0.7513 (ptmm) cc_final: 0.7206 (pttm) REVERT: H 79 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7440 (ptp90) REVERT: H 443 GLU cc_start: 0.7291 (mp0) cc_final: 0.6877 (tp30) REVERT: F 336 GLU cc_start: 0.7132 (tt0) cc_final: 0.6338 (tp30) REVERT: F 443 GLU cc_start: 0.7397 (tp30) cc_final: 0.6887 (mm-30) REVERT: M 81 GLN cc_start: 0.7443 (OUTLIER) cc_final: 0.6854 (mp10) REVERT: K 81 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.6814 (mp10) REVERT: K 117 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.8748 (tt0) REVERT: O 117 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8622 (tt0) REVERT: N 117 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8739 (tt0) REVERT: N 118 LYS cc_start: 0.8554 (mtmm) cc_final: 0.8101 (mtmt) REVERT: I 81 GLN cc_start: 0.7507 (OUTLIER) cc_final: 0.6897 (mp10) REVERT: L 81 GLN cc_start: 0.7445 (OUTLIER) cc_final: 0.6827 (mp10) outliers start: 47 outliers final: 22 residues processed: 570 average time/residue: 0.7700 time to fit residues: 523.0787 Evaluate side-chains 547 residues out of total 3712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 514 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain D residue 392 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain B residue 439 VAL Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 392 GLU Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain F residue 392 GLU Chi-restraints excluded: chain M residue 81 GLN Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain O residue 117 GLN Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain N residue 117 GLN Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 101 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 187 optimal weight: 3.9990 chunk 45 optimal weight: 40.0000 chunk 87 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 270 optimal weight: 9.9990 chunk 354 optimal weight: 8.9990 chunk 290 optimal weight: 0.6980 chunk 216 optimal weight: 30.0000 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 108 GLN K 87 GLN O 87 GLN P 87 GLN P 117 GLN N 87 GLN I 87 GLN J 87 GLN J 117 GLN L 87 GLN L 117 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.138075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.112866 restraints weight = 224358.467| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 3.17 r_work: 0.2859 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2746 r_free = 0.2746 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 38704 Z= 0.234 Angle : 0.758 8.652 52650 Z= 0.417 Chirality : 0.051 0.233 5560 Planarity : 0.005 0.059 6887 Dihedral : 7.024 59.709 5595 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.38 % Favored : 96.58 % Rotamer: Outliers : 2.90 % Allowed : 13.82 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.56 (0.12), residues: 4902 helix: 1.64 (0.11), residues: 1864 sheet: -0.21 (0.17), residues: 774 loop : -0.44 (0.13), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 215 TYR 0.024 0.003 TYR F 269 PHE 0.031 0.003 PHE B 345 TRP 0.017 0.001 TRP G 411 HIS 0.009 0.002 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.23 (38701) covalent geometry : angle 0.75537 / 0.42 (52644) SS BOND : bond 0.03786 / 2.13 ( 3) SS BOND : angle 6.21444 / 3.44 ( 6) hydrogen bonds : bond 0.08031 / 5.31 ( 1695) hydrogen bonds : angle 5.28727 / 3.76 ( 4693) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 524 time to evaluate : 1.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.6691 (OUTLIER) cc_final: 0.6037 (mmpt) REVERT: A 79 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.7632 (ptp90) REVERT: C 18 LYS cc_start: 0.6689 (OUTLIER) cc_final: 0.5755 (mptt) REVERT: C 21 LYS cc_start: 0.7619 (ptmm) cc_final: 0.7384 (pttm) REVERT: D 79 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7495 (ptp90) REVERT: B 30 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7341 (mt-10) REVERT: B 52 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.6270 (tm-30) REVERT: B 94 GLU cc_start: 0.6229 (OUTLIER) cc_final: 0.6017 (mm-30) REVERT: E 21 LYS cc_start: 0.7563 (ptmm) cc_final: 0.7223 (pttm) REVERT: E 355 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8373 (mm-30) REVERT: E 443 GLU cc_start: 0.7408 (tp30) cc_final: 0.6888 (mm-30) REVERT: G 21 LYS cc_start: 0.7595 (ptmm) cc_final: 0.7333 (pttm) REVERT: G 79 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.7546 (ptp90) REVERT: G 94 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.6140 (mm-30) REVERT: G 355 GLU cc_start: 0.8621 (mm-30) cc_final: 0.8372 (mm-30) REVERT: G 439 VAL cc_start: 0.6808 (OUTLIER) cc_final: 0.6459 (p) REVERT: H 21 LYS cc_start: 0.7575 (ptmm) cc_final: 0.7277 (pttm) REVERT: H 79 ARG cc_start: 0.8305 (OUTLIER) cc_final: 0.7529 (ptp90) REVERT: H 94 GLU cc_start: 0.5970 (OUTLIER) cc_final: 0.5743 (mp0) REVERT: H 443 GLU cc_start: 0.7341 (mp0) cc_final: 0.6929 (tp30) REVERT: F 30 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7370 (mt-10) REVERT: F 336 GLU cc_start: 0.7252 (tt0) cc_final: 0.6458 (tp30) REVERT: F 443 GLU cc_start: 0.7423 (tp30) cc_final: 0.6928 (mm-30) REVERT: K 81 GLN cc_start: 0.7544 (OUTLIER) cc_final: 0.6921 (mp10) REVERT: K 117 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8778 (tt0) REVERT: O 117 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8646 (tt0) REVERT: P 81 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.6899 (mp10) REVERT: N 107 LYS cc_start: 0.7737 (mtmt) cc_final: 0.7488 (mtpt) REVERT: N 117 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8666 (tt0) REVERT: N 118 LYS cc_start: 0.8564 (mtmm) cc_final: 0.8114 (mtmt) REVERT: I 81 GLN cc_start: 0.7487 (OUTLIER) cc_final: 0.6867 (mp10) outliers start: 57 outliers final: 22 residues processed: 558 average time/residue: 0.8196 time to fit residues: 544.4860 Evaluate side-chains 544 residues out of total 3712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 505 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 392 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 392 GLU Chi-restraints excluded: chain G residue 439 VAL Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain M residue 81 GLN Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain O residue 117 GLN Chi-restraints excluded: chain P residue 81 GLN Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain N residue 81 GLN Chi-restraints excluded: chain N residue 117 GLN Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain L residue 101 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 200 optimal weight: 5.9990 chunk 381 optimal weight: 8.9990 chunk 250 optimal weight: 10.0000 chunk 398 optimal weight: 8.9990 chunk 328 optimal weight: 5.9990 chunk 399 optimal weight: 5.9990 chunk 226 optimal weight: 6.9990 chunk 142 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 351 optimal weight: 5.9990 chunk 81 optimal weight: 30.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 87 GLN O 87 GLN P 87 GLN P 117 GLN N 87 GLN I 87 GLN I 108 GLN J 87 GLN J 117 GLN L 87 GLN L 117 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.137826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.112869 restraints weight = 224130.630| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.05 r_work: 0.2849 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2743 r_free = 0.2743 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 38704 Z= 0.241 Angle : 0.767 8.767 52650 Z= 0.423 Chirality : 0.051 0.256 5560 Planarity : 0.006 0.058 6887 Dihedral : 7.037 59.774 5594 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 2.90 % Allowed : 13.92 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.56 (0.12), residues: 4902 helix: 1.64 (0.11), residues: 1864 sheet: -0.20 (0.17), residues: 774 loop : -0.44 (0.13), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 213 TYR 0.024 0.003 TYR F 269 PHE 0.030 0.003 PHE B 345 TRP 0.013 0.001 TRP G 411 HIS 0.009 0.002 HIS C 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.24 (38701) covalent geometry : angle 0.76423 / 0.42 (52644) SS BOND : bond 0.03811 / 2.14 ( 3) SS BOND : angle 6.21320 / 3.44 ( 6) hydrogen bonds : bond 0.08117 / 5.37 ( 1695) hydrogen bonds : angle 5.28810 / 3.77 ( 4693) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 3712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 513 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 18 LYS cc_start: 0.6688 (OUTLIER) cc_final: 0.6013 (mmpt) REVERT: A 79 ARG cc_start: 0.8391 (OUTLIER) cc_final: 0.7620 (ptp90) REVERT: C 18 LYS cc_start: 0.6660 (OUTLIER) cc_final: 0.5733 (mptt) REVERT: C 21 LYS cc_start: 0.7596 (ptmm) cc_final: 0.7340 (pttm) REVERT: D 79 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.7484 (ptp90) REVERT: B 30 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7321 (mt-10) REVERT: B 52 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.6240 (tm-30) REVERT: B 94 GLU cc_start: 0.6196 (OUTLIER) cc_final: 0.5929 (mm-30) REVERT: E 21 LYS cc_start: 0.7577 (ptmm) cc_final: 0.7232 (pttm) REVERT: E 79 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7501 (ptp90) REVERT: E 355 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8399 (mm-30) REVERT: E 443 GLU cc_start: 0.7391 (tp30) cc_final: 0.6894 (mm-30) REVERT: G 21 LYS cc_start: 0.7581 (ptmm) cc_final: 0.7300 (pttm) REVERT: G 79 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.7574 (ptp90) REVERT: G 94 GLU cc_start: 0.6305 (OUTLIER) cc_final: 0.6075 (mm-30) REVERT: H 21 LYS cc_start: 0.7570 (ptmm) cc_final: 0.7254 (pttm) REVERT: H 79 ARG cc_start: 0.8312 (OUTLIER) cc_final: 0.7519 (ptp90) REVERT: H 94 GLU cc_start: 0.6104 (OUTLIER) cc_final: 0.5856 (mp0) REVERT: H 443 GLU cc_start: 0.7295 (mp0) cc_final: 0.6907 (tp30) REVERT: F 30 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7354 (mt-10) REVERT: F 336 GLU cc_start: 0.7386 (tt0) cc_final: 0.6561 (tp30) REVERT: K 117 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8786 (tt0) REVERT: O 117 GLN cc_start: 0.8944 (OUTLIER) cc_final: 0.8664 (tt0) REVERT: N 10 LYS cc_start: 0.8991 (OUTLIER) cc_final: 0.8375 (mmmt) REVERT: N 107 LYS cc_start: 0.7734 (mtmt) cc_final: 0.7499 (mtpt) REVERT: N 117 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8664 (tt0) REVERT: N 118 LYS cc_start: 0.8589 (mtmm) cc_final: 0.8135 (mtmt) REVERT: L 10 LYS cc_start: 0.8994 (OUTLIER) cc_final: 0.8218 (mmmt) outliers start: 58 outliers final: 27 residues processed: 547 average time/residue: 0.8185 time to fit residues: 533.2192 Evaluate side-chains 533 residues out of total 3712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 490 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 392 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain G residue 79 ARG Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 392 GLU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 392 GLU Chi-restraints excluded: chain M residue 81 GLN Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain O residue 117 GLN Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain N residue 10 LYS Chi-restraints excluded: chain N residue 117 GLN Chi-restraints excluded: chain J residue 76 CYS Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain L residue 76 CYS Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 101 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 2 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 429 optimal weight: 5.9990 chunk 392 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 331 optimal weight: 20.0000 chunk 96 optimal weight: 8.9990 chunk 421 optimal weight: 10.0000 chunk 380 optimal weight: 7.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 87 GLN O 87 GLN P 87 GLN P 117 GLN N 87 GLN I 87 GLN J 87 GLN J 110 GLN J 117 GLN L 87 GLN L 117 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.139340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.114034 restraints weight = 235470.264| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 3.19 r_work: 0.2894 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 38704 Z= 0.192 Angle : 0.686 6.796 52650 Z= 0.378 Chirality : 0.049 0.249 5560 Planarity : 0.005 0.058 6887 Dihedral : 6.804 59.677 5593 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.67 % Allowed : 14.33 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.66 (0.12), residues: 4902 helix: 1.77 (0.12), residues: 1872 sheet: -0.21 (0.17), residues: 790 loop : -0.41 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 215 TYR 0.021 0.002 TYR F 269 PHE 0.029 0.002 PHE B 345 TRP 0.012 0.001 TRP G 411 HIS 0.008 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.19 (38701) covalent geometry : angle 0.68318 / 0.38 (52644) SS BOND : bond 0.03369 / 1.89 ( 3) SS BOND : angle 5.79497 / 3.22 ( 6) hydrogen bonds : bond 0.07027 / 4.65 ( 1695) hydrogen bonds : angle 5.09024 / 3.63 ( 4693) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 3712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 518 time to evaluate : 1.444 Fit side-chains revert: symmetry clash REVERT: A 18 LYS cc_start: 0.6612 (OUTLIER) cc_final: 0.5658 (mptt) REVERT: A 79 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7540 (ptp90) REVERT: C 18 LYS cc_start: 0.6600 (OUTLIER) cc_final: 0.5665 (mptt) REVERT: C 21 LYS cc_start: 0.7543 (ptmm) cc_final: 0.7288 (pttm) REVERT: D 79 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7415 (ptp90) REVERT: D 392 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7918 (tm-30) REVERT: B 30 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7274 (mt-10) REVERT: B 79 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7491 (ptp90) REVERT: E 21 LYS cc_start: 0.7554 (ptmm) cc_final: 0.7212 (pttm) REVERT: E 79 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7386 (ptp90) REVERT: E 355 GLU cc_start: 0.8557 (mm-30) cc_final: 0.8298 (mm-30) REVERT: E 443 GLU cc_start: 0.7326 (tp30) cc_final: 0.6980 (mp0) REVERT: G 21 LYS cc_start: 0.7551 (ptmm) cc_final: 0.7257 (pttm) REVERT: G 94 GLU cc_start: 0.6313 (OUTLIER) cc_final: 0.6074 (mm-30) REVERT: G 355 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8325 (mm-30) REVERT: G 392 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7925 (tm-30) REVERT: H 21 LYS cc_start: 0.7540 (ptmm) cc_final: 0.7243 (pttm) REVERT: H 79 ARG cc_start: 0.8241 (OUTLIER) cc_final: 0.7439 (ptp90) REVERT: H 94 GLU cc_start: 0.6070 (OUTLIER) cc_final: 0.5869 (mp0) REVERT: H 443 GLU cc_start: 0.7252 (mp0) cc_final: 0.6855 (tp30) REVERT: F 30 GLU cc_start: 0.7639 (mm-30) cc_final: 0.7286 (mt-10) REVERT: F 336 GLU cc_start: 0.7340 (tt0) cc_final: 0.6506 (tp30) REVERT: K 81 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.6827 (mp10) REVERT: K 117 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8721 (tt0) REVERT: O 81 GLN cc_start: 0.7428 (OUTLIER) cc_final: 0.6831 (mp10) REVERT: O 117 GLN cc_start: 0.8925 (OUTLIER) cc_final: 0.8602 (tt0) REVERT: N 107 LYS cc_start: 0.7672 (mtmt) cc_final: 0.7449 (mtpt) REVERT: N 117 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.8600 (tt0) REVERT: N 118 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8094 (mtmt) REVERT: L 10 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8233 (mmmt) REVERT: L 81 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.6777 (mp-120) outliers start: 49 outliers final: 23 residues processed: 551 average time/residue: 0.8269 time to fit residues: 543.5153 Evaluate side-chains 539 residues out of total 3712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 498 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 119 SER Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 392 GLU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 392 GLU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 94 GLU Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain M residue 81 GLN Chi-restraints excluded: chain K residue 76 CYS Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain O residue 117 GLN Chi-restraints excluded: chain P residue 76 CYS Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain N residue 117 GLN Chi-restraints excluded: chain I residue 76 CYS Chi-restraints excluded: chain J residue 76 CYS Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 101 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 351 optimal weight: 8.9990 chunk 336 optimal weight: 20.0000 chunk 152 optimal weight: 20.0000 chunk 269 optimal weight: 0.3980 chunk 119 optimal weight: 10.0000 chunk 9 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 chunk 97 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 444 optimal weight: 0.0570 chunk 105 optimal weight: 2.9990 overall best weight: 2.4904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 87 GLN K 110 GLN O 87 GLN P 87 GLN P 110 GLN P 117 GLN N 87 GLN I 87 GLN J 87 GLN J 108 GLN L 87 GLN L 117 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.116746 restraints weight = 223016.321| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 3.08 r_work: 0.2926 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2815 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.10 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2815 r_free = 0.2815 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2815 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 38704 Z= 0.153 Angle : 0.613 5.724 52650 Z= 0.338 Chirality : 0.046 0.249 5560 Planarity : 0.004 0.056 6887 Dihedral : 6.494 59.329 5593 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.59 % Allowed : 14.33 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.81 (0.12), residues: 4902 helix: 1.95 (0.12), residues: 1872 sheet: -0.11 (0.17), residues: 790 loop : -0.39 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 79 TYR 0.018 0.002 TYR F 269 PHE 0.030 0.002 PHE B 345 TRP 0.011 0.001 TRP G 411 HIS 0.007 0.001 HIS F 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.15 (38701) covalent geometry : angle 0.61025 / 0.34 (52644) SS BOND : bond 0.02763 / 1.55 ( 3) SS BOND : angle 5.07629 / 2.81 ( 6) hydrogen bonds : bond 0.05894 / 3.90 ( 1695) hydrogen bonds : angle 4.86428 / 3.47 ( 4693) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 3712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 533 time to evaluate : 1.518 Fit side-chains REVERT: A 18 LYS cc_start: 0.6566 (OUTLIER) cc_final: 0.5589 (mptt) REVERT: C 18 LYS cc_start: 0.6547 (OUTLIER) cc_final: 0.5595 (mptt) REVERT: C 21 LYS cc_start: 0.7560 (ptmm) cc_final: 0.7301 (pttm) REVERT: D 392 GLU cc_start: 0.8277 (OUTLIER) cc_final: 0.7899 (tm-30) REVERT: D 443 GLU cc_start: 0.7255 (mp0) cc_final: 0.6849 (tp30) REVERT: B 30 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7255 (mt-10) REVERT: B 52 GLU cc_start: 0.7463 (OUTLIER) cc_final: 0.6200 (tm-30) REVERT: B 94 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.5888 (mm-30) REVERT: E 21 LYS cc_start: 0.7545 (ptmm) cc_final: 0.7197 (pttm) REVERT: E 79 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7312 (ptp90) REVERT: E 355 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8322 (mm-30) REVERT: E 443 GLU cc_start: 0.7330 (tp30) cc_final: 0.6817 (mm-30) REVERT: G 21 LYS cc_start: 0.7539 (ptmm) cc_final: 0.7263 (pttm) REVERT: G 355 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8343 (mm-30) REVERT: G 392 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7904 (tm-30) REVERT: H 21 LYS cc_start: 0.7533 (ptmm) cc_final: 0.7226 (pttm) REVERT: H 79 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7368 (ptp90) REVERT: H 443 GLU cc_start: 0.7293 (mp0) cc_final: 0.6877 (tp30) REVERT: F 336 GLU cc_start: 0.7311 (tt0) cc_final: 0.6418 (tp30) REVERT: M 81 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6842 (mp10) REVERT: K 81 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.6850 (mp10) REVERT: K 117 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.8689 (tt0) REVERT: O 117 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8571 (tt0) REVERT: N 10 LYS cc_start: 0.8934 (OUTLIER) cc_final: 0.8340 (mmmt) REVERT: N 81 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.6784 (mp-120) REVERT: N 107 LYS cc_start: 0.7620 (mtmt) cc_final: 0.7396 (mtpt) REVERT: N 117 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8601 (tt0) REVERT: N 118 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8099 (mtmt) REVERT: L 10 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8240 (mmmt) REVERT: L 81 GLN cc_start: 0.7356 (OUTLIER) cc_final: 0.6772 (mp-120) outliers start: 46 outliers final: 17 residues processed: 561 average time/residue: 0.8360 time to fit residues: 557.4531 Evaluate side-chains 541 residues out of total 3712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 507 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain A residue 439 VAL Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain C residue 439 VAL Chi-restraints excluded: chain D residue 392 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 392 GLU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain M residue 81 GLN Chi-restraints excluded: chain K residue 81 GLN Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain O residue 117 GLN Chi-restraints excluded: chain P residue 76 CYS Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain N residue 10 LYS Chi-restraints excluded: chain N residue 81 GLN Chi-restraints excluded: chain N residue 117 GLN Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain L residue 81 GLN Chi-restraints excluded: chain L residue 101 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 344 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 164 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 407 optimal weight: 7.9990 chunk 374 optimal weight: 20.0000 chunk 421 optimal weight: 4.9990 chunk 202 optimal weight: 6.9990 chunk 284 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 chunk 280 optimal weight: 10.0000 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... M 108 GLN K 87 GLN K 108 GLN O 87 GLN P 87 GLN P 108 GLN P 117 GLN I 87 GLN I 108 GLN I 117 GLN J 87 GLN J 108 GLN L 87 GLN L 108 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.140273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.115394 restraints weight = 227391.438| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 3.07 r_work: 0.2901 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2791 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.07 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2791 r_free = 0.2791 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 38704 Z= 0.175 Angle : 0.652 6.329 52650 Z= 0.358 Chirality : 0.048 0.273 5560 Planarity : 0.005 0.057 6887 Dihedral : 6.585 59.922 5591 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.62 % Allowed : 14.28 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.79 (0.12), residues: 4902 helix: 1.91 (0.12), residues: 1872 sheet: -0.13 (0.17), residues: 790 loop : -0.37 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 79 TYR 0.020 0.002 TYR F 269 PHE 0.030 0.002 PHE B 345 TRP 0.011 0.001 TRP G 411 HIS 0.008 0.001 HIS G 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.17 (38701) covalent geometry : angle 0.64938 / 0.36 (52644) SS BOND : bond 0.03169 / 1.78 ( 3) SS BOND : angle 5.37529 / 2.99 ( 6) hydrogen bonds : bond 0.06602 / 4.37 ( 1695) hydrogen bonds : angle 4.95755 / 3.54 ( 4693) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 3712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 513 time to evaluate : 1.597 Fit side-chains REVERT: A 18 LYS cc_start: 0.6580 (OUTLIER) cc_final: 0.5615 (mptt) REVERT: A 52 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6283 (tm-30) REVERT: A 79 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7518 (ptp90) REVERT: C 18 LYS cc_start: 0.6575 (OUTLIER) cc_final: 0.5606 (mptt) REVERT: C 21 LYS cc_start: 0.7561 (ptmm) cc_final: 0.7305 (pttm) REVERT: D 392 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7890 (tm-30) REVERT: D 443 GLU cc_start: 0.7286 (mp0) cc_final: 0.6885 (tp30) REVERT: B 30 GLU cc_start: 0.7580 (mm-30) cc_final: 0.7266 (mt-10) REVERT: B 52 GLU cc_start: 0.7470 (OUTLIER) cc_final: 0.6214 (tm-30) REVERT: B 79 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7475 (ptp90) REVERT: B 94 GLU cc_start: 0.6154 (OUTLIER) cc_final: 0.5902 (mm-30) REVERT: E 21 LYS cc_start: 0.7548 (ptmm) cc_final: 0.7188 (pttm) REVERT: E 79 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7354 (ptp90) REVERT: E 355 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8318 (mm-30) REVERT: E 443 GLU cc_start: 0.7327 (tp30) cc_final: 0.6820 (mm-30) REVERT: G 21 LYS cc_start: 0.7545 (ptmm) cc_final: 0.7268 (pttm) REVERT: G 52 GLU cc_start: 0.7561 (OUTLIER) cc_final: 0.6261 (tm-30) REVERT: G 355 GLU cc_start: 0.8606 (mm-30) cc_final: 0.8355 (mm-30) REVERT: G 392 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7913 (tm-30) REVERT: H 21 LYS cc_start: 0.7524 (ptmm) cc_final: 0.7219 (pttm) REVERT: H 79 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7394 (ptp90) REVERT: H 443 GLU cc_start: 0.7289 (mp0) cc_final: 0.6884 (tp30) REVERT: F 30 GLU cc_start: 0.7616 (mm-30) cc_final: 0.7269 (mt-10) REVERT: F 336 GLU cc_start: 0.7388 (tt0) cc_final: 0.6504 (tp30) REVERT: K 117 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8698 (tt0) REVERT: O 81 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.6806 (mp-120) REVERT: O 117 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8605 (tt0) REVERT: N 10 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8369 (mmmt) REVERT: N 107 LYS cc_start: 0.7638 (mtmt) cc_final: 0.7274 (mtpp) REVERT: N 117 GLN cc_start: 0.8933 (OUTLIER) cc_final: 0.8586 (tt0) REVERT: N 118 LYS cc_start: 0.8544 (mtmm) cc_final: 0.8096 (mtmt) REVERT: L 10 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8224 (mmmt) outliers start: 47 outliers final: 21 residues processed: 544 average time/residue: 0.8926 time to fit residues: 577.2258 Evaluate side-chains 540 residues out of total 3712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 501 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 392 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 392 GLU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain M residue 76 CYS Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain O residue 81 GLN Chi-restraints excluded: chain O residue 117 GLN Chi-restraints excluded: chain P residue 76 CYS Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain N residue 10 LYS Chi-restraints excluded: chain N residue 117 GLN Chi-restraints excluded: chain J residue 76 CYS Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain L residue 101 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 240 optimal weight: 5.9990 chunk 265 optimal weight: 9.9990 chunk 201 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 200 optimal weight: 0.6980 chunk 37 optimal weight: 8.9990 chunk 83 optimal weight: 7.9990 chunk 377 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 169 optimal weight: 8.9990 chunk 60 optimal weight: 8.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 401 GLN B F 401 GLN B M 108 GLN K 87 GLN K 108 GLN K 110 GLN O 87 GLN P 87 GLN P 108 GLN I 87 GLN I 108 GLN J 87 GLN L 87 GLN L 108 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.139393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.114391 restraints weight = 229441.300| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.10 r_work: 0.2889 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2776 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2776 r_free = 0.2776 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 38704 Z= 0.194 Angle : 0.685 7.144 52650 Z= 0.376 Chirality : 0.049 0.294 5560 Planarity : 0.005 0.057 6887 Dihedral : 6.708 59.864 5591 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.52 % Allowed : 14.48 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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 (0.12), residues: 4902 helix: 1.85 (0.12), residues: 1872 sheet: -0.17 (0.17), residues: 790 loop : -0.37 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 213 TYR 0.021 0.002 TYR F 269 PHE 0.030 0.002 PHE B 345 TRP 0.010 0.001 TRP G 411 HIS 0.008 0.002 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.19 (38701) covalent geometry : angle 0.68224 / 0.38 (52644) SS BOND : bond 0.03439 / 1.93 ( 3) SS BOND : angle 5.62293 / 3.13 ( 6) hydrogen bonds : bond 0.07114 / 4.71 ( 1695) hydrogen bonds : angle 5.04689 / 3.60 ( 4693) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 3712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 501 time to evaluate : 1.629 Fit side-chains REVERT: A 18 LYS cc_start: 0.6610 (OUTLIER) cc_final: 0.5650 (mptt) REVERT: A 52 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6304 (tm-30) REVERT: A 79 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.7537 (ptp90) REVERT: C 18 LYS cc_start: 0.6581 (OUTLIER) cc_final: 0.5615 (mptt) REVERT: C 21 LYS cc_start: 0.7546 (ptmm) cc_final: 0.7290 (pttm) REVERT: D 392 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7945 (tm-30) REVERT: D 443 GLU cc_start: 0.7275 (mp0) cc_final: 0.6886 (tp30) REVERT: B 30 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7245 (mt-10) REVERT: B 52 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6223 (tm-30) REVERT: B 79 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7480 (ptp90) REVERT: B 94 GLU cc_start: 0.6193 (OUTLIER) cc_final: 0.5929 (mm-30) REVERT: E 21 LYS cc_start: 0.7536 (ptmm) cc_final: 0.7171 (pttm) REVERT: E 79 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7372 (ptp90) REVERT: E 355 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8314 (mm-30) REVERT: E 443 GLU cc_start: 0.7318 (tp30) cc_final: 0.6809 (mm-30) REVERT: G 21 LYS cc_start: 0.7533 (ptmm) cc_final: 0.7256 (pttm) REVERT: G 52 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.6244 (tm-30) REVERT: G 355 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8347 (mm-30) REVERT: G 392 GLU cc_start: 0.8307 (OUTLIER) cc_final: 0.7908 (tm-30) REVERT: H 21 LYS cc_start: 0.7526 (ptmm) cc_final: 0.7228 (pttm) REVERT: H 79 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.7415 (ptp90) REVERT: H 443 GLU cc_start: 0.7253 (mp0) cc_final: 0.6859 (tp30) REVERT: F 30 GLU cc_start: 0.7631 (mm-30) cc_final: 0.7281 (mt-10) REVERT: F 336 GLU cc_start: 0.7418 (tt0) cc_final: 0.6555 (tp30) REVERT: K 117 GLN cc_start: 0.8952 (OUTLIER) cc_final: 0.8733 (tt0) REVERT: O 117 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8630 (tt0) REVERT: N 10 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8329 (mmmt) REVERT: N 107 LYS cc_start: 0.7662 (mtmt) cc_final: 0.7440 (mtpt) REVERT: N 117 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.8589 (tt0) REVERT: N 118 LYS cc_start: 0.8534 (mtmm) cc_final: 0.8085 (mtmt) REVERT: L 10 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8217 (mmmt) outliers start: 43 outliers final: 21 residues processed: 531 average time/residue: 0.8908 time to fit residues: 562.1858 Evaluate side-chains 529 residues out of total 3712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 491 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 392 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 392 GLU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain M residue 76 CYS Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain O residue 117 GLN Chi-restraints excluded: chain P residue 76 CYS Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain N residue 10 LYS Chi-restraints excluded: chain N residue 117 GLN Chi-restraints excluded: chain J residue 76 CYS Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain L residue 101 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 399 optimal weight: 6.9990 chunk 297 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 368 optimal weight: 10.0000 chunk 377 optimal weight: 2.9990 chunk 380 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 45 optimal weight: 40.0000 chunk 54 optimal weight: 2.9990 chunk 454 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 87 GLN O 87 GLN P 87 GLN I 87 GLN J 87 GLN L 87 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.139367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.113978 restraints weight = 238318.119| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 3.26 r_work: 0.2889 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2777 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2777 r_free = 0.2777 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2777 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 38704 Z= 0.196 Angle : 0.688 7.115 52650 Z= 0.378 Chirality : 0.049 0.313 5560 Planarity : 0.005 0.057 6887 Dihedral : 6.716 59.691 5591 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.59 % Allowed : 14.35 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.73 (0.12), residues: 4902 helix: 1.83 (0.12), residues: 1872 sheet: -0.20 (0.17), residues: 790 loop : -0.37 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 213 TYR 0.020 0.002 TYR F 269 PHE 0.030 0.002 PHE B 345 TRP 0.010 0.001 TRP G 411 HIS 0.009 0.002 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.20 (38701) covalent geometry : angle 0.68497 / 0.38 (52644) SS BOND : bond 0.03442 / 1.94 ( 3) SS BOND : angle 5.66055 / 3.14 ( 6) hydrogen bonds : bond 0.07103 / 4.70 ( 1695) hydrogen bonds : angle 5.05811 / 3.61 ( 4693) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 3712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 493 time to evaluate : 1.551 Fit side-chains REVERT: A 18 LYS cc_start: 0.6641 (OUTLIER) cc_final: 0.5683 (mptt) REVERT: A 52 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6319 (tm-30) REVERT: A 79 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7534 (ptp90) REVERT: C 18 LYS cc_start: 0.6618 (OUTLIER) cc_final: 0.5653 (mptt) REVERT: C 21 LYS cc_start: 0.7561 (ptmm) cc_final: 0.7311 (pttm) REVERT: C 79 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7417 (ptp90) REVERT: D 392 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7948 (tm-30) REVERT: D 443 GLU cc_start: 0.7295 (mp0) cc_final: 0.6910 (tp30) REVERT: B 30 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7267 (mt-10) REVERT: B 52 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.6252 (tm-30) REVERT: B 79 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7480 (ptp90) REVERT: B 94 GLU cc_start: 0.6191 (OUTLIER) cc_final: 0.5946 (mm-30) REVERT: E 21 LYS cc_start: 0.7545 (ptmm) cc_final: 0.7261 (pttm) REVERT: E 79 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7378 (ptp90) REVERT: E 355 GLU cc_start: 0.8549 (mm-30) cc_final: 0.8290 (mm-30) REVERT: E 443 GLU cc_start: 0.7313 (tp30) cc_final: 0.6808 (mm-30) REVERT: G 21 LYS cc_start: 0.7554 (ptmm) cc_final: 0.7283 (pttm) REVERT: G 52 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6278 (tm-30) REVERT: G 94 GLU cc_start: 0.6329 (OUTLIER) cc_final: 0.6075 (mm-30) REVERT: G 355 GLU cc_start: 0.8594 (mm-30) cc_final: 0.8339 (mm-30) REVERT: G 392 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7959 (tm-30) REVERT: G 443 GLU cc_start: 0.7292 (mp0) cc_final: 0.6901 (tp30) REVERT: H 21 LYS cc_start: 0.7537 (ptmm) cc_final: 0.7244 (pttm) REVERT: H 79 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7429 (ptp90) REVERT: H 443 GLU cc_start: 0.7261 (mp0) cc_final: 0.6873 (tp30) REVERT: F 30 GLU cc_start: 0.7629 (mm-30) cc_final: 0.7284 (mt-10) REVERT: F 336 GLU cc_start: 0.7427 (tt0) cc_final: 0.6567 (tp30) REVERT: K 117 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8739 (tt0) REVERT: O 117 GLN cc_start: 0.8941 (OUTLIER) cc_final: 0.8636 (tt0) REVERT: P 10 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8311 (mmmt) REVERT: N 10 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8330 (mmmt) REVERT: N 107 LYS cc_start: 0.7656 (mtmt) cc_final: 0.7443 (mtpt) REVERT: N 117 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8585 (tt0) REVERT: N 118 LYS cc_start: 0.8533 (mtmm) cc_final: 0.8084 (mtmt) REVERT: L 10 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8221 (mmmt) outliers start: 46 outliers final: 21 residues processed: 525 average time/residue: 0.8989 time to fit residues: 560.4524 Evaluate side-chains 530 residues out of total 3712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 489 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 392 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 392 GLU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain M residue 76 CYS Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain O residue 117 GLN Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 76 CYS Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain N residue 10 LYS Chi-restraints excluded: chain N residue 117 GLN Chi-restraints excluded: chain J residue 76 CYS Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain L residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 159 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 203 optimal weight: 20.0000 chunk 14 optimal weight: 6.9990 chunk 332 optimal weight: 9.9990 chunk 353 optimal weight: 8.9990 chunk 360 optimal weight: 10.0000 chunk 308 optimal weight: 9.9990 chunk 150 optimal weight: 8.9990 chunk 257 optimal weight: 0.0010 chunk 400 optimal weight: 6.9990 overall best weight: 4.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 87 GLN O 87 GLN P 87 GLN I 87 GLN J 87 GLN L 87 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.138929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.113589 restraints weight = 232871.766| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 3.23 r_work: 0.2882 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2769 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2769 r_free = 0.2769 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2769 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 38704 Z= 0.207 Angle : 0.708 7.725 52650 Z= 0.389 Chirality : 0.050 0.325 5560 Planarity : 0.005 0.057 6887 Dihedral : 6.763 59.412 5591 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 2.49 % Allowed : 14.56 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.70 (0.12), residues: 4902 helix: 1.80 (0.12), residues: 1872 sheet: -0.24 (0.17), residues: 806 loop : -0.36 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 213 TYR 0.021 0.002 TYR F 269 PHE 0.030 0.002 PHE B 345 TRP 0.010 0.001 TRP G 411 HIS 0.009 0.002 HIS B 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.21 (38701) covalent geometry : angle 0.70568 / 0.39 (52644) SS BOND : bond 0.03592 / 2.02 ( 3) SS BOND : angle 5.80731 / 3.23 ( 6) hydrogen bonds : bond 0.07393 / 4.89 ( 1695) hydrogen bonds : angle 5.10986 / 3.65 ( 4693) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9804 Ramachandran restraints generated. 4902 Oldfield, 0 Emsley, 4902 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 3712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 487 time to evaluate : 1.465 Fit side-chains REVERT: A 18 LYS cc_start: 0.6637 (OUTLIER) cc_final: 0.5685 (mptt) REVERT: A 52 GLU cc_start: 0.7582 (OUTLIER) cc_final: 0.6320 (tm-30) REVERT: A 79 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.7544 (ptp90) REVERT: C 18 LYS cc_start: 0.6606 (OUTLIER) cc_final: 0.5656 (mptt) REVERT: C 21 LYS cc_start: 0.7564 (ptmm) cc_final: 0.7312 (pttm) REVERT: C 79 ARG cc_start: 0.8304 (OUTLIER) cc_final: 0.7428 (ptp90) REVERT: D 392 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7946 (tm-30) REVERT: D 443 GLU cc_start: 0.7290 (mp0) cc_final: 0.6910 (tp30) REVERT: B 30 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7245 (mt-10) REVERT: B 52 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.6264 (tm-30) REVERT: B 79 ARG cc_start: 0.8292 (OUTLIER) cc_final: 0.7489 (ptp90) REVERT: B 94 GLU cc_start: 0.6190 (OUTLIER) cc_final: 0.5948 (mm-30) REVERT: E 21 LYS cc_start: 0.7545 (ptmm) cc_final: 0.7262 (pttm) REVERT: E 79 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7387 (ptp90) REVERT: E 355 GLU cc_start: 0.8566 (mm-30) cc_final: 0.8309 (mm-30) REVERT: E 443 GLU cc_start: 0.7328 (tp30) cc_final: 0.6983 (mp0) REVERT: G 21 LYS cc_start: 0.7555 (ptmm) cc_final: 0.7286 (pttm) REVERT: G 52 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6281 (tm-30) REVERT: G 94 GLU cc_start: 0.6331 (OUTLIER) cc_final: 0.6077 (mm-30) REVERT: G 355 GLU cc_start: 0.8605 (mm-30) cc_final: 0.8349 (mm-30) REVERT: G 392 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7950 (tm-30) REVERT: H 21 LYS cc_start: 0.7543 (ptmm) cc_final: 0.7251 (pttm) REVERT: H 79 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7466 (ptp90) REVERT: H 443 GLU cc_start: 0.7275 (mp0) cc_final: 0.6896 (tp30) REVERT: F 30 GLU cc_start: 0.7637 (mm-30) cc_final: 0.7288 (mt-10) REVERT: F 336 GLU cc_start: 0.7464 (tt0) cc_final: 0.6594 (tp30) REVERT: K 117 GLN cc_start: 0.8948 (OUTLIER) cc_final: 0.8747 (tt0) REVERT: O 117 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.8623 (tt0) REVERT: P 10 LYS cc_start: 0.8980 (OUTLIER) cc_final: 0.8301 (mmmt) REVERT: N 10 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8331 (mmmt) REVERT: N 107 LYS cc_start: 0.7677 (mtmt) cc_final: 0.7459 (mtpt) REVERT: N 117 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8580 (tt0) REVERT: L 10 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8151 (mmmt) outliers start: 42 outliers final: 21 residues processed: 517 average time/residue: 0.8896 time to fit residues: 547.5981 Evaluate side-chains 525 residues out of total 3712 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 484 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 LYS Chi-restraints excluded: chain A residue 52 GLU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 172 CYS Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 392 GLU Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 79 ARG Chi-restraints excluded: chain C residue 172 CYS Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 392 GLU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 392 GLU Chi-restraints excluded: chain B residue 52 GLU Chi-restraints excluded: chain B residue 79 ARG Chi-restraints excluded: chain B residue 94 GLU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 392 GLU Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 94 GLU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 392 GLU Chi-restraints excluded: chain H residue 79 ARG Chi-restraints excluded: chain H residue 119 SER Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain M residue 76 CYS Chi-restraints excluded: chain K residue 101 LEU Chi-restraints excluded: chain K residue 117 GLN Chi-restraints excluded: chain O residue 117 GLN Chi-restraints excluded: chain P residue 10 LYS Chi-restraints excluded: chain P residue 76 CYS Chi-restraints excluded: chain P residue 101 LEU Chi-restraints excluded: chain N residue 10 LYS Chi-restraints excluded: chain N residue 117 GLN Chi-restraints excluded: chain J residue 76 CYS Chi-restraints excluded: chain J residue 101 LEU Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain L residue 101 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 207 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 271 optimal weight: 0.7980 chunk 307 optimal weight: 1.9990 chunk 242 optimal weight: 5.9990 chunk 258 optimal weight: 10.0000 chunk 121 optimal weight: 20.0000 chunk 104 optimal weight: 5.9990 chunk 341 optimal weight: 10.0000 chunk 327 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 87 GLN O 87 GLN P 87 GLN I 87 GLN J 87 GLN L 87 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.140522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.114924 restraints weight = 244904.890| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 3.31 r_work: 0.2909 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2800 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2800 r_free = 0.2800 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 38704 Z= 0.170 Angle : 0.644 5.954 52650 Z= 0.354 Chirality : 0.048 0.319 5560 Planarity : 0.005 0.056 6887 Dihedral : 6.587 59.976 5591 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.52 % Allowed : 14.56 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.79 (0.12), residues: 4902 helix: 1.91 (0.12), residues: 1872 sheet: -0.14 (0.17), residues: 790 loop : -0.37 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 79 TYR 0.019 0.002 TYR F 269 PHE 0.030 0.002 PHE B 345 TRP 0.010 0.001 TRP G 411 HIS 0.008 0.001 HIS B 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.17 (38701) covalent geometry : angle 0.64154 / 0.35 (52644) SS BOND : bond 0.03065 / 1.72 ( 3) SS BOND : angle 5.35204 / 2.97 ( 6) hydrogen bonds : bond 0.06418 / 4.25 ( 1695) hydrogen bonds : angle 4.94417 / 3.53 ( 4693) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19533.85 seconds wall clock time: 332 minutes 26.46 seconds (19946.46 seconds total)