Starting phenix.real_space_refine on Tue Aug 26 22:02:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b16_44069/08_2025/9b16_44069_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b16_44069/08_2025/9b16_44069.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b16_44069/08_2025/9b16_44069.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b16_44069/08_2025/9b16_44069.map" model { file = "/net/cci-nas-00/data/ceres_data/9b16_44069/08_2025/9b16_44069_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b16_44069/08_2025/9b16_44069_trim.cif" } resolution = 2.89 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.023 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 S 120 5.16 5 C 13792 2.51 5 N 4016 2.21 5 O 4096 1.98 5 H 20392 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 42432 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 358, 5236 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 340} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 Conformer: "B" Number of residues, atoms: 358, 5236 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 340} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 bond proxies already assigned to first conformer: 5265 Chain: "B" Number of atoms: 5261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 358, 5236 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 340} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 Conformer: "B" Number of residues, atoms: 358, 5236 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 340} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 bond proxies already assigned to first conformer: 5265 Chain: "C" Number of atoms: 5261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 358, 5236 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 340} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 Conformer: "B" Number of residues, atoms: 358, 5236 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 340} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 bond proxies already assigned to first conformer: 5265 Chain: "D" Number of atoms: 5261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 358, 5236 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 340} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 Conformer: "B" Number of residues, atoms: 358, 5236 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 340} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 bond proxies already assigned to first conformer: 5265 Chain: "E" Number of atoms: 5261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 358, 5236 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 340} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 Conformer: "B" Number of residues, atoms: 358, 5236 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 340} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 bond proxies already assigned to first conformer: 5265 Chain: "F" Number of atoms: 5261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 358, 5236 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 340} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 Conformer: "B" Number of residues, atoms: 358, 5236 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 340} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 bond proxies already assigned to first conformer: 5265 Chain: "G" Number of atoms: 5261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 358, 5236 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 340} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 Conformer: "B" Number of residues, atoms: 358, 5236 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 340} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 bond proxies already assigned to first conformer: 5265 Chain: "H" Number of atoms: 5261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 358, 5236 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 340} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 Conformer: "B" Number of residues, atoms: 358, 5236 Classifications: {'peptide': 358} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 340} Chain breaks: 2 Unresolved non-hydrogen bonds: 195 Unresolved non-hydrogen angles: 233 Unresolved non-hydrogen dihedrals: 164 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 8, 'HIS:plan': 1, 'PHE:plan': 1, 'TYR:plan': 1, 'ASP:plan': 5, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 129 bond proxies already assigned to first conformer: 5265 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'ADP': 1, 'KLU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'ADP': 1, 'KLU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 2 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'ADP': 1, 'KLU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 2 Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'ADP': 1, 'KLU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 2 Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'ADP': 1, 'KLU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 2 Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'ADP': 1, 'KLU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 2 Chain: "G" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'ADP': 1, 'KLU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 2 Chain: "H" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'ADP': 1, 'KLU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 2 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N AARG A 151 " occ=0.39 ... (46 atoms not shown) pdb="HH22BARG A 151 " occ=0.61 residue: pdb=" N AARG B 151 " occ=0.43 ... (46 atoms not shown) pdb="HH22BARG B 151 " occ=0.57 residue: pdb=" N AARG C 151 " occ=0.43 ... (46 atoms not shown) pdb="HH22BARG C 151 " occ=0.57 residue: pdb=" N AARG D 151 " occ=0.41 ... (46 atoms not shown) pdb="HH22BARG D 151 " occ=0.59 residue: pdb=" N AARG E 151 " occ=0.42 ... (46 atoms not shown) pdb="HH22BARG E 151 " occ=0.58 residue: pdb=" N AARG F 151 " occ=0.41 ... (46 atoms not shown) pdb="HH22BARG F 151 " occ=0.59 residue: pdb=" N AARG G 151 " occ=0.39 ... (46 atoms not shown) pdb="HH22BARG G 151 " occ=0.61 residue: pdb=" N AARG H 151 " occ=0.40 ... (46 atoms not shown) pdb="HH22BARG H 151 " occ=0.60 Time building chain proxies: 12.17, per 1000 atoms: 0.29 Number of scatterers: 42432 At special positions: 0 Unit cell: (130.872, 130.872, 98.952, 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 120 16.00 P 16 15.00 O 4096 8.00 N 4016 7.00 C 13792 6.00 H 20392 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.55 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5312 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 16 sheets defined 44.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 removed outlier: 3.861A pdb=" N GLU A 14 " --> pdb=" O PRO A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 29 Processing helix chain 'A' and resid 30 through 38 Processing helix chain 'A' and resid 47 through 58 removed outlier: 4.676A pdb=" N THR A 54 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N GLY A 55 " --> pdb=" O CYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 80 removed outlier: 4.275A pdb=" N GLU A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 92 Proline residue: A 86 - end of helix Processing helix chain 'A' and resid 142 through 159 removed outlier: 3.757A pdb=" N GLY A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 160 through 164 removed outlier: 7.421A pdb=" N ASP A 163 " --> pdb=" O LEU A 160 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU A 164 " --> pdb=" O LYS A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 160 through 164' Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 194 through 201 removed outlier: 3.573A pdb=" N THR A 198 " --> pdb=" O SER A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 262 removed outlier: 3.564A pdb=" N ARG A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 294 through 299 removed outlier: 4.038A pdb=" N LYS A 299 " --> pdb=" O PRO A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 340 through 358 Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.852A pdb=" N GLU B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 38 Processing helix chain 'B' and resid 47 through 58 removed outlier: 4.663A pdb=" N THR B 54 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLY B 55 " --> pdb=" O CYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 74 through 80 removed outlier: 4.275A pdb=" N GLU B 78 " --> pdb=" O GLU B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 92 Proline residue: B 86 - end of helix Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.762A pdb=" N GLY B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 removed outlier: 7.425A pdb=" N ASP B 163 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU B 164 " --> pdb=" O LYS B 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 160 through 164' Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 194 through 200 Processing helix chain 'B' and resid 240 through 262 removed outlier: 3.574A pdb=" N ARG B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 294 through 299 removed outlier: 3.979A pdb=" N LYS B 299 " --> pdb=" O PRO B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 340 through 359 Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.863A pdb=" N GLU C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 29 Processing helix chain 'C' and resid 30 through 38 Processing helix chain 'C' and resid 47 through 58 removed outlier: 4.677A pdb=" N THR C 54 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N GLY C 55 " --> pdb=" O CYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 80 removed outlier: 4.312A pdb=" N TYR C 77 " --> pdb=" O ASP C 73 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU C 78 " --> pdb=" O GLU C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 92 Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 142 through 159 removed outlier: 3.761A pdb=" N GLY C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 164 removed outlier: 7.425A pdb=" N ASP C 163 " --> pdb=" O LEU C 160 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU C 164 " --> pdb=" O LYS C 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 160 through 164' Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 194 through 200 Processing helix chain 'C' and resid 240 through 262 removed outlier: 3.563A pdb=" N ARG C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 294 through 299 removed outlier: 3.881A pdb=" N LYS C 299 " --> pdb=" O PRO C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 311 Processing helix chain 'C' and resid 340 through 358 Processing helix chain 'D' and resid 10 through 15 removed outlier: 3.847A pdb=" N GLU D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 29 Processing helix chain 'D' and resid 30 through 38 Processing helix chain 'D' and resid 47 through 58 removed outlier: 4.678A pdb=" N THR D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLY D 55 " --> pdb=" O CYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 74 through 80 removed outlier: 4.282A pdb=" N GLU D 78 " --> pdb=" O GLU D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 92 Proline residue: D 86 - end of helix Processing helix chain 'D' and resid 142 through 159 removed outlier: 3.766A pdb=" N GLY D 159 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 160 through 164 removed outlier: 7.434A pdb=" N ASP D 163 " --> pdb=" O LEU D 160 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU D 164 " --> pdb=" O LYS D 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 160 through 164' Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 194 through 201 Processing helix chain 'D' and resid 240 through 262 removed outlier: 3.534A pdb=" N ARG D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 Processing helix chain 'D' and resid 294 through 299 removed outlier: 3.895A pdb=" N LYS D 299 " --> pdb=" O PRO D 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 310 Processing helix chain 'D' and resid 340 through 358 Processing helix chain 'E' and resid 10 through 15 removed outlier: 3.830A pdb=" N GLU E 14 " --> pdb=" O PRO E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 25 through 29 Processing helix chain 'E' and resid 30 through 38 Processing helix chain 'E' and resid 47 through 58 removed outlier: 4.696A pdb=" N THR E 54 " --> pdb=" O GLN E 50 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLY E 55 " --> pdb=" O CYS E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 80 removed outlier: 4.319A pdb=" N TYR E 77 " --> pdb=" O ASP E 73 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLU E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 92 Proline residue: E 86 - end of helix Processing helix chain 'E' and resid 142 through 159 removed outlier: 3.766A pdb=" N GLY E 159 " --> pdb=" O ASP E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 164 removed outlier: 7.424A pdb=" N ASP E 163 " --> pdb=" O LEU E 160 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N LEU E 164 " --> pdb=" O LYS E 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 160 through 164' Processing helix chain 'E' and resid 172 through 174 No H-bonds generated for 'chain 'E' and resid 172 through 174' Processing helix chain 'E' and resid 175 through 185 Processing helix chain 'E' and resid 194 through 200 Processing helix chain 'E' and resid 240 through 262 removed outlier: 3.568A pdb=" N ARG E 262 " --> pdb=" O LEU E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 282 Processing helix chain 'E' and resid 294 through 299 removed outlier: 3.870A pdb=" N LYS E 299 " --> pdb=" O PRO E 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 311 Processing helix chain 'E' and resid 340 through 358 Processing helix chain 'F' and resid 10 through 15 removed outlier: 3.832A pdb=" N GLU F 14 " --> pdb=" O PRO F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 38 Processing helix chain 'F' and resid 47 through 58 removed outlier: 4.676A pdb=" N THR F 54 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLY F 55 " --> pdb=" O CYS F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 80 removed outlier: 4.352A pdb=" N TYR F 77 " --> pdb=" O ASP F 73 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU F 78 " --> pdb=" O GLU F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 80 through 92 Proline residue: F 86 - end of helix Processing helix chain 'F' and resid 142 through 159 removed outlier: 3.759A pdb=" N GLY F 159 " --> pdb=" O ASP F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 164 removed outlier: 7.423A pdb=" N ASP F 163 " --> pdb=" O LEU F 160 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N LEU F 164 " --> pdb=" O LYS F 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 160 through 164' Processing helix chain 'F' and resid 172 through 174 No H-bonds generated for 'chain 'F' and resid 172 through 174' Processing helix chain 'F' and resid 175 through 185 Processing helix chain 'F' and resid 194 through 201 removed outlier: 3.572A pdb=" N THR F 198 " --> pdb=" O SER F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 262 removed outlier: 3.570A pdb=" N ARG F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 282 Processing helix chain 'F' and resid 294 through 299 removed outlier: 3.949A pdb=" N LYS F 299 " --> pdb=" O PRO F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 311 Processing helix chain 'F' and resid 340 through 358 Processing helix chain 'G' and resid 10 through 15 removed outlier: 3.849A pdb=" N GLU G 14 " --> pdb=" O PRO G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 29 Processing helix chain 'G' and resid 30 through 38 Processing helix chain 'G' and resid 47 through 58 removed outlier: 4.663A pdb=" N THR G 54 " --> pdb=" O GLN G 50 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N GLY G 55 " --> pdb=" O CYS G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 80 removed outlier: 4.313A pdb=" N TYR G 77 " --> pdb=" O ASP G 73 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLU G 78 " --> pdb=" O GLU G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 92 Proline residue: G 86 - end of helix Processing helix chain 'G' and resid 142 through 159 removed outlier: 3.758A pdb=" N GLY G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 164 removed outlier: 7.425A pdb=" N ASP G 163 " --> pdb=" O LEU G 160 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU G 164 " --> pdb=" O LYS G 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 160 through 164' Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 175 through 185 Processing helix chain 'G' and resid 194 through 200 Processing helix chain 'G' and resid 240 through 262 removed outlier: 3.560A pdb=" N ARG G 262 " --> pdb=" O LEU G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 282 Processing helix chain 'G' and resid 294 through 299 removed outlier: 3.988A pdb=" N LYS G 299 " --> pdb=" O PRO G 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 311 Processing helix chain 'G' and resid 340 through 358 Processing helix chain 'H' and resid 10 through 15 removed outlier: 3.845A pdb=" N GLU H 14 " --> pdb=" O PRO H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 29 Processing helix chain 'H' and resid 30 through 38 Processing helix chain 'H' and resid 47 through 58 removed outlier: 4.683A pdb=" N THR H 54 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLY H 55 " --> pdb=" O CYS H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 80 removed outlier: 4.281A pdb=" N GLU H 78 " --> pdb=" O GLU H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 92 Proline residue: H 86 - end of helix Processing helix chain 'H' and resid 142 through 159 removed outlier: 3.759A pdb=" N GLY H 159 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 164 removed outlier: 7.421A pdb=" N ASP H 163 " --> pdb=" O LEU H 160 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N LEU H 164 " --> pdb=" O LYS H 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 160 through 164' Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 175 through 185 Processing helix chain 'H' and resid 194 through 201 removed outlier: 3.591A pdb=" N THR H 198 " --> pdb=" O SER H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 262 removed outlier: 3.565A pdb=" N ARG H 262 " --> pdb=" O LEU H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 282 Processing helix chain 'H' and resid 294 through 299 removed outlier: 3.977A pdb=" N LYS H 299 " --> pdb=" O PRO H 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 311 Processing helix chain 'H' and resid 340 through 358 Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 170 removed outlier: 5.802A pdb=" N PHE A 220 " --> pdb=" O ASN A 215 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 268 through 269 Processing sheet with id=AA3, first strand: chain 'B' and resid 166 through 170 removed outlier: 5.802A pdb=" N PHE B 220 " --> pdb=" O ASN B 215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 268 through 269 Processing sheet with id=AA5, first strand: chain 'C' and resid 166 through 170 removed outlier: 5.802A pdb=" N PHE C 220 " --> pdb=" O ASN C 215 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 268 through 269 Processing sheet with id=AA7, first strand: chain 'D' and resid 166 through 170 removed outlier: 5.793A pdb=" N PHE D 220 " --> pdb=" O ASN D 215 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 268 through 269 Processing sheet with id=AA9, first strand: chain 'E' and resid 166 through 170 removed outlier: 5.802A pdb=" N PHE E 220 " --> pdb=" O ASN E 215 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 268 through 269 Processing sheet with id=AB2, first strand: chain 'F' and resid 166 through 170 removed outlier: 5.802A pdb=" N PHE F 220 " --> pdb=" O ASN F 215 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 268 through 269 Processing sheet with id=AB4, first strand: chain 'G' and resid 166 through 170 removed outlier: 5.801A pdb=" N PHE G 220 " --> pdb=" O ASN G 215 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 268 through 269 Processing sheet with id=AB6, first strand: chain 'H' and resid 166 through 170 removed outlier: 5.794A pdb=" N PHE H 220 " --> pdb=" O ASN H 215 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 268 through 269 969 hydrogen bonds defined for protein. 2723 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: 9.93 Time building geometry restraints manager: 4.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 20344 1.03 - 1.23: 307 1.23 - 1.43: 9253 1.43 - 1.62: 12816 1.62 - 1.82: 184 Bond restraints: 42904 Sorted by residual: bond pdb=" C4 KLU B 402 " pdb=" C5 KLU B 402 " ideal model delta sigma weight residual 1.524 1.572 -0.048 2.00e-02 2.50e+03 5.73e+00 bond pdb=" C4 KLU D 402 " pdb=" C5 KLU D 402 " ideal model delta sigma weight residual 1.524 1.572 -0.048 2.00e-02 2.50e+03 5.72e+00 bond pdb=" C4 KLU G 402 " pdb=" C5 KLU G 402 " ideal model delta sigma weight residual 1.524 1.572 -0.048 2.00e-02 2.50e+03 5.70e+00 bond pdb=" C4 KLU C 402 " pdb=" C5 KLU C 402 " ideal model delta sigma weight residual 1.524 1.572 -0.048 2.00e-02 2.50e+03 5.65e+00 bond pdb=" C4 KLU H 402 " pdb=" C5 KLU H 402 " ideal model delta sigma weight residual 1.524 1.572 -0.048 2.00e-02 2.50e+03 5.64e+00 ... (remaining 42899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 73001 1.17 - 2.34: 3499 2.34 - 3.51: 280 3.51 - 4.68: 144 4.68 - 5.85: 60 Bond angle restraints: 76984 Sorted by residual: angle pdb=" CA PHE A 303 " pdb=" C PHE A 303 " pdb=" N PRO A 304 " ideal model delta sigma weight residual 118.44 122.47 -4.03 1.59e+00 3.96e-01 6.41e+00 angle pdb=" CA GLU E 78 " pdb=" CB GLU E 78 " pdb=" CG GLU E 78 " ideal model delta sigma weight residual 114.10 118.77 -4.67 2.00e+00 2.50e-01 5.45e+00 angle pdb=" CA GLU F 78 " pdb=" CB GLU F 78 " pdb=" CG GLU F 78 " ideal model delta sigma weight residual 114.10 118.74 -4.64 2.00e+00 2.50e-01 5.38e+00 angle pdb=" N PHE A 303 " pdb=" CA PHE A 303 " pdb=" C PHE A 303 " ideal model delta sigma weight residual 109.81 114.41 -4.60 2.21e+00 2.05e-01 4.33e+00 angle pdb=" N LEU H 294 " pdb=" CA LEU H 294 " pdb=" C LEU H 294 " ideal model delta sigma weight residual 109.81 114.25 -4.44 2.21e+00 2.05e-01 4.04e+00 ... (remaining 76979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 18131 17.92 - 35.84: 1463 35.84 - 53.76: 562 53.76 - 71.68: 172 71.68 - 89.61: 32 Dihedral angle restraints: 20360 sinusoidal: 10872 harmonic: 9488 Sorted by residual: dihedral pdb=" CA LEU F 294 " pdb=" C LEU F 294 " pdb=" N PRO F 295 " pdb=" CA PRO F 295 " ideal model delta harmonic sigma weight residual -180.00 -158.78 -21.22 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CA LEU B 294 " pdb=" C LEU B 294 " pdb=" N PRO B 295 " pdb=" CA PRO B 295 " ideal model delta harmonic sigma weight residual -180.00 -159.22 -20.78 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA LEU H 294 " pdb=" C LEU H 294 " pdb=" N PRO H 295 " pdb=" CA PRO H 295 " ideal model delta harmonic sigma weight residual 180.00 -159.33 -20.67 0 5.00e+00 4.00e-02 1.71e+01 ... (remaining 20357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2288 0.030 - 0.060: 741 0.060 - 0.090: 231 0.090 - 0.119: 171 0.119 - 0.149: 9 Chirality restraints: 3440 Sorted by residual: chirality pdb=" CA PHE A 303 " pdb=" N PHE A 303 " pdb=" C PHE A 303 " pdb=" CB PHE A 303 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA PRO B 295 " pdb=" N PRO B 295 " pdb=" C PRO B 295 " pdb=" CB PRO B 295 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.24e-01 chirality pdb=" CA ILE E 64 " pdb=" N ILE E 64 " pdb=" C ILE E 64 " pdb=" CB ILE E 64 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 ... (remaining 3437 not shown) Planarity restraints: 6712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 303 " -0.016 2.00e-02 2.50e+03 7.17e-03 1.54e+00 pdb=" CG PHE A 303 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 PHE A 303 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE A 303 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 303 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 303 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 303 " -0.004 2.00e-02 2.50e+03 pdb=" HD1 PHE A 303 " 0.001 2.00e-02 2.50e+03 pdb=" HD2 PHE A 303 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE A 303 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 303 " -0.001 2.00e-02 2.50e+03 pdb=" HZ PHE A 303 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS F 278 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO F 279 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO F 279 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO F 279 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 278 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO D 279 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 279 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 279 " 0.016 5.00e-02 4.00e+02 ... (remaining 6709 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 2124 2.17 - 2.78: 81068 2.78 - 3.39: 120224 3.39 - 3.99: 156323 3.99 - 4.60: 244263 Nonbonded interactions: 604002 Sorted by model distance: nonbonded pdb=" H GLY B 68 " pdb=" O1 KLU B 402 " model vdw 1.563 2.450 nonbonded pdb=" H GLY F 68 " pdb=" O1 KLU F 402 " model vdw 1.591 2.450 nonbonded pdb=" OE1 GLU E 341 " pdb=" H GLU E 341 " model vdw 1.614 2.450 nonbonded pdb=" OE1 GLU F 341 " pdb=" H GLU F 341 " model vdw 1.614 2.450 nonbonded pdb=" OE1 GLU C 341 " pdb=" H GLU C 341 " model vdw 1.614 2.450 ... (remaining 603997 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 150 or resid 153 through 402)) selection = (chain 'B' and (resid 3 through 150 or resid 153 through 402)) selection = (chain 'C' and (resid 3 through 150 or resid 153 through 402)) selection = (chain 'D' and (resid 3 through 150 or resid 153 through 402)) selection = (chain 'E' and (resid 3 through 150 or resid 153 through 402)) selection = (chain 'F' and (resid 3 through 150 or resid 153 through 402)) selection = (chain 'G' and (resid 3 through 150 or resid 153 through 402)) selection = (chain 'H' and (resid 3 through 150 or resid 153 through 402)) } 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=0.39 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.270 Extract box with map and model: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 42.650 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.080 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 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 : 0.003 0.058 22520 Z= 0.148 Angle : 0.618 5.852 30680 Z= 0.282 Chirality : 0.038 0.149 3440 Planarity : 0.003 0.030 3992 Dihedral : 17.246 89.605 8128 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 1.44 % Allowed : 26.02 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 0.54 (0.17), residues: 2840 helix: 2.28 (0.17), residues: 1064 sheet: -1.39 (0.24), residues: 392 loop : -0.63 (0.18), residues: 1384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 271 TYR 0.011 0.001 TYR A 354 PHE 0.017 0.001 PHE A 303 TRP 0.005 0.001 TRP E 268 HIS 0.004 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00280 (22512) covalent geometry : angle 0.61789 (30680) hydrogen bonds : bond 0.12708 ( 969) hydrogen bonds : angle 5.42946 ( 2723) Misc. bond : bond 0.03885 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Evaluate side-chains 212 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 210 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8353 (mmt-90) REVERT: H 210 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.8372 (mmt-90) outliers start: 31 outliers final: 27 residues processed: 211 average time/residue: 1.3088 time to fit residues: 313.7420 Evaluate side-chains 200 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 171 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 66 THR Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 226 GLU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 52 ILE Chi-restraints excluded: chain E residue 210 ARG Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 210 ARG Chi-restraints excluded: chain G residue 226 GLU Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 52 ILE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 210 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.121735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.089086 restraints weight = 263411.625| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 4.68 r_work: 0.3040 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3045 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3045 r_free = 0.3045 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3045 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.0586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 22520 Z= 0.158 Angle : 0.603 5.975 30680 Z= 0.289 Chirality : 0.040 0.127 3440 Planarity : 0.004 0.042 3992 Dihedral : 6.491 53.305 3456 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 1.57 % Allowed : 25.37 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 0.39 (0.17), residues: 2840 helix: 2.04 (0.16), residues: 1072 sheet: -1.26 (0.24), residues: 392 loop : -0.69 (0.18), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 146 TYR 0.011 0.001 TYR C 354 PHE 0.027 0.001 PHE A 303 TRP 0.003 0.001 TRP F 46 HIS 0.003 0.001 HIS E 28 Details of bonding type rmsd covalent geometry : bond 0.00359 (22512) covalent geometry : angle 0.60313 (30680) hydrogen bonds : bond 0.03524 ( 969) hydrogen bonds : angle 4.57331 ( 2723) Misc. bond : bond 0.00112 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Evaluate side-chains 220 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 186 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8684 (tp30) cc_final: 0.8479 (tp30) REVERT: A 227 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7237 (tm-30) REVERT: A 231 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8209 (ttm110) REVERT: B 227 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7318 (tm-30) REVERT: C 227 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7389 (tm-30) REVERT: D 78 GLU cc_start: 0.8673 (tp30) cc_final: 0.8466 (tp30) REVERT: D 227 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7388 (tm-30) REVERT: E 227 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7192 (tm-30) REVERT: G 227 GLU cc_start: 0.7648 (OUTLIER) cc_final: 0.7330 (tm-30) REVERT: H 69 MET cc_start: 0.9084 (mtp) cc_final: 0.8716 (mtp) REVERT: H 227 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.7247 (tm-30) outliers start: 34 outliers final: 12 residues processed: 218 average time/residue: 1.3051 time to fit residues: 325.6155 Evaluate side-chains 197 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 303 PHE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 227 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 4 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 141 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 165 optimal weight: 0.7980 chunk 156 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.120332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.087816 restraints weight = 243834.683| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 4.52 r_work: 0.3016 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3025 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.0866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 22520 Z= 0.202 Angle : 0.610 6.162 30680 Z= 0.292 Chirality : 0.040 0.132 3440 Planarity : 0.004 0.033 3992 Dihedral : 5.796 43.066 3404 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.36 % Favored : 93.50 % Rotamer: Outliers : 2.45 % Allowed : 24.26 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 0.27 (0.17), residues: 2840 helix: 1.95 (0.16), residues: 1072 sheet: -1.28 (0.24), residues: 392 loop : -0.79 (0.18), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 147 TYR 0.012 0.001 TYR G 354 PHE 0.024 0.001 PHE G 303 TRP 0.003 0.001 TRP H 46 HIS 0.008 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00461 (22512) covalent geometry : angle 0.60980 (30680) hydrogen bonds : bond 0.03577 ( 969) hydrogen bonds : angle 4.51998 ( 2723) Misc. bond : bond 0.00156 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Evaluate side-chains 230 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 177 time to evaluate : 0.809 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8718 (tp30) cc_final: 0.8492 (tp30) REVERT: A 227 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7179 (tm-30) REVERT: A 231 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.8184 (ttm110) REVERT: B 227 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7145 (tm-30) REVERT: C 227 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7425 (tm-30) REVERT: D 78 GLU cc_start: 0.8693 (tp30) cc_final: 0.8465 (tp30) REVERT: D 227 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7206 (tm-30) REVERT: E 78 GLU cc_start: 0.8699 (tp30) cc_final: 0.8476 (tp30) REVERT: E 227 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.7161 (tm-30) REVERT: F 69 MET cc_start: 0.9058 (mtp) cc_final: 0.8708 (mtp) REVERT: F 78 GLU cc_start: 0.8714 (tp30) cc_final: 0.8492 (tp30) REVERT: G 227 GLU cc_start: 0.7701 (OUTLIER) cc_final: 0.7410 (tm-30) REVERT: H 69 MET cc_start: 0.9117 (mtp) cc_final: 0.8739 (mtp) outliers start: 53 outliers final: 12 residues processed: 229 average time/residue: 1.2391 time to fit residues: 327.1419 Evaluate side-chains 190 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 41 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 161 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 114 optimal weight: 3.9990 chunk 41 optimal weight: 5.9990 chunk 254 optimal weight: 2.9990 chunk 194 optimal weight: 0.0670 chunk 108 optimal weight: 3.9990 chunk 209 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.119141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.087021 restraints weight = 227828.858| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 4.34 r_work: 0.3030 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3036 r_free = 0.3036 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22520 Z= 0.194 Angle : 0.605 6.141 30680 Z= 0.290 Chirality : 0.040 0.136 3440 Planarity : 0.004 0.034 3992 Dihedral : 5.796 43.960 3403 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.86 % Favored : 93.89 % Rotamer: Outliers : 2.55 % Allowed : 24.35 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 0.26 (0.17), residues: 2840 helix: 1.96 (0.16), residues: 1072 sheet: -1.20 (0.24), residues: 392 loop : -0.84 (0.18), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 147 TYR 0.015 0.001 TYR B 354 PHE 0.028 0.001 PHE G 303 TRP 0.003 0.001 TRP H 46 HIS 0.005 0.001 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00441 (22512) covalent geometry : angle 0.60516 (30680) hydrogen bonds : bond 0.03374 ( 969) hydrogen bonds : angle 4.46227 ( 2723) Misc. bond : bond 0.00157 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Evaluate side-chains 233 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 178 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8705 (tp30) cc_final: 0.8467 (tp30) REVERT: A 227 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7389 (tm-30) REVERT: A 231 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8185 (ttm110) REVERT: B 227 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7147 (tm-30) REVERT: C 78 GLU cc_start: 0.8699 (tp30) cc_final: 0.8451 (tp30) REVERT: C 227 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7461 (tm-30) REVERT: D 78 GLU cc_start: 0.8663 (tp30) cc_final: 0.8425 (tp30) REVERT: D 227 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7170 (tm-30) REVERT: E 78 GLU cc_start: 0.8659 (tp30) cc_final: 0.8410 (tp30) REVERT: E 227 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7175 (tm-30) REVERT: F 69 MET cc_start: 0.9079 (mtp) cc_final: 0.8725 (mtp) REVERT: F 78 GLU cc_start: 0.8679 (tp30) cc_final: 0.8431 (tp30) REVERT: G 78 GLU cc_start: 0.8687 (tp30) cc_final: 0.8436 (tp30) REVERT: G 227 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: H 227 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7399 (tm-30) REVERT: H 287 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8674 (ttt90) outliers start: 55 outliers final: 23 residues processed: 232 average time/residue: 1.2557 time to fit residues: 333.9052 Evaluate side-chains 207 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 202 MET Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 210 ARG Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 210 ARG Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 210 ARG Chi-restraints excluded: chain H residue 227 GLU Chi-restraints excluded: chain H residue 287 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 273 optimal weight: 4.9990 chunk 263 optimal weight: 0.9980 chunk 223 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 191 optimal weight: 4.9990 chunk 146 optimal weight: 3.9990 chunk 242 optimal weight: 5.9990 chunk 241 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 256 optimal weight: 0.7980 chunk 157 optimal weight: 5.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.120557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.088255 restraints weight = 237972.985| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 4.48 r_work: 0.3046 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3054 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3054 r_free = 0.3054 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3054 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22520 Z= 0.131 Angle : 0.583 5.806 30680 Z= 0.276 Chirality : 0.039 0.134 3440 Planarity : 0.004 0.032 3992 Dihedral : 5.540 41.728 3403 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.33 % Favored : 94.39 % Rotamer: Outliers : 2.31 % Allowed : 24.17 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 0.40 (0.17), residues: 2840 helix: 2.10 (0.16), residues: 1072 sheet: -1.13 (0.24), residues: 392 loop : -0.78 (0.18), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 133 TYR 0.012 0.001 TYR B 354 PHE 0.026 0.001 PHE G 303 TRP 0.003 0.001 TRP E 268 HIS 0.005 0.001 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00301 (22512) covalent geometry : angle 0.58296 (30680) hydrogen bonds : bond 0.03021 ( 969) hydrogen bonds : angle 4.31238 ( 2723) Misc. bond : bond 0.00122 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Evaluate side-chains 234 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 184 time to evaluate : 1.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8704 (tp30) cc_final: 0.8460 (tp30) REVERT: A 227 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7117 (tm-30) REVERT: A 231 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8138 (ttm110) REVERT: A 287 ARG cc_start: 0.8969 (OUTLIER) cc_final: 0.8590 (ttt90) REVERT: B 78 GLU cc_start: 0.8696 (tp30) cc_final: 0.8443 (tp30) REVERT: C 78 GLU cc_start: 0.8701 (tp30) cc_final: 0.8433 (tp30) REVERT: C 227 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7480 (tm-30) REVERT: D 78 GLU cc_start: 0.8668 (tp30) cc_final: 0.8421 (tp30) REVERT: D 227 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7258 (tm-30) REVERT: E 78 GLU cc_start: 0.8638 (tp30) cc_final: 0.8370 (tp30) REVERT: E 227 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7118 (tm-30) REVERT: F 69 MET cc_start: 0.9078 (mtp) cc_final: 0.8695 (mtp) REVERT: F 78 GLU cc_start: 0.8690 (tp30) cc_final: 0.8423 (tp30) REVERT: G 78 GLU cc_start: 0.8690 (tp30) cc_final: 0.8420 (tp30) REVERT: H 69 MET cc_start: 0.9100 (mtp) cc_final: 0.8757 (mtp) REVERT: H 78 GLU cc_start: 0.8712 (tp30) cc_final: 0.8509 (tp30) REVERT: H 227 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7324 (tm-30) outliers start: 50 outliers final: 24 residues processed: 232 average time/residue: 1.2266 time to fit residues: 326.5047 Evaluate side-chains 210 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 179 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 287 ARG Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 210 ARG Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 210 ARG Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 210 ARG Chi-restraints excluded: chain H residue 227 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 60 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 261 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 249 optimal weight: 2.9990 chunk 75 optimal weight: 0.1980 chunk 240 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.120769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.088088 restraints weight = 265936.381| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 4.73 r_work: 0.3025 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 22520 Z= 0.160 Angle : 0.591 5.889 30680 Z= 0.281 Chirality : 0.040 0.156 3440 Planarity : 0.004 0.033 3992 Dihedral : 5.589 41.559 3403 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.61 % Favored : 94.11 % Rotamer: Outliers : 2.36 % Allowed : 22.87 % Favored : 74.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 0.37 (0.17), residues: 2840 helix: 2.08 (0.16), residues: 1072 sheet: -1.12 (0.24), residues: 392 loop : -0.83 (0.18), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 287 TYR 0.012 0.001 TYR B 354 PHE 0.028 0.001 PHE F 303 TRP 0.003 0.001 TRP G 46 HIS 0.005 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00366 (22512) covalent geometry : angle 0.59075 (30680) hydrogen bonds : bond 0.03134 ( 969) hydrogen bonds : angle 4.36021 ( 2723) Misc. bond : bond 0.00138 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Evaluate side-chains 229 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 178 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8727 (tp30) cc_final: 0.8477 (tp30) REVERT: A 227 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7127 (tm-30) REVERT: A 231 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8181 (ttm110) REVERT: B 78 GLU cc_start: 0.8721 (tp30) cc_final: 0.8461 (tp30) REVERT: C 78 GLU cc_start: 0.8737 (tp30) cc_final: 0.8467 (tp30) REVERT: C 227 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7520 (tm-30) REVERT: D 78 GLU cc_start: 0.8693 (tp30) cc_final: 0.8445 (tp30) REVERT: D 227 GLU cc_start: 0.7708 (OUTLIER) cc_final: 0.7077 (tm-30) REVERT: E 78 GLU cc_start: 0.8704 (tp30) cc_final: 0.8432 (tp30) REVERT: E 227 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7457 (tm-30) REVERT: F 69 MET cc_start: 0.9086 (mtp) cc_final: 0.8716 (mtp) REVERT: F 78 GLU cc_start: 0.8729 (tp30) cc_final: 0.8459 (tp30) REVERT: G 78 GLU cc_start: 0.8739 (tp30) cc_final: 0.8471 (tp30) REVERT: G 227 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: H 69 MET cc_start: 0.9110 (mtp) cc_final: 0.8768 (mtp) REVERT: H 78 GLU cc_start: 0.8745 (tp30) cc_final: 0.8529 (tp30) REVERT: H 227 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7331 (tm-30) outliers start: 51 outliers final: 27 residues processed: 223 average time/residue: 1.3394 time to fit residues: 341.0651 Evaluate side-chains 207 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 210 ARG Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 202 MET Chi-restraints excluded: chain G residue 210 ARG Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 210 ARG Chi-restraints excluded: chain H residue 227 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 85 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 222 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 chunk 190 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 264 optimal weight: 2.9990 chunk 260 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.120021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.087971 restraints weight = 228581.317| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 4.37 r_work: 0.3031 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3037 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3037 r_free = 0.3037 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3037 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 22520 Z= 0.194 Angle : 0.604 6.020 30680 Z= 0.289 Chirality : 0.040 0.160 3440 Planarity : 0.004 0.034 3992 Dihedral : 5.726 42.701 3403 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.39 % Favored : 93.32 % Rotamer: Outliers : 2.18 % Allowed : 23.33 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 0.29 (0.17), residues: 2840 helix: 2.01 (0.16), residues: 1072 sheet: -1.13 (0.25), residues: 392 loop : -0.88 (0.18), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 287 TYR 0.013 0.001 TYR A 120 PHE 0.028 0.001 PHE E 303 TRP 0.004 0.001 TRP G 206 HIS 0.005 0.001 HIS G 214 Details of bonding type rmsd covalent geometry : bond 0.00441 (22512) covalent geometry : angle 0.60354 (30680) hydrogen bonds : bond 0.03298 ( 969) hydrogen bonds : angle 4.40263 ( 2723) Misc. bond : bond 0.00159 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Evaluate side-chains 219 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 172 time to evaluate : 1.284 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8693 (tp30) cc_final: 0.8435 (tp30) REVERT: A 227 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7379 (tm-30) REVERT: A 231 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.8203 (ttm110) REVERT: B 78 GLU cc_start: 0.8699 (tp30) cc_final: 0.8468 (tp30) REVERT: B 227 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7104 (tm-30) REVERT: C 78 GLU cc_start: 0.8704 (tp30) cc_final: 0.8434 (tp30) REVERT: C 227 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7483 (tm-30) REVERT: D 78 GLU cc_start: 0.8653 (tp30) cc_final: 0.8394 (tp30) REVERT: D 227 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7389 (tm-30) REVERT: E 78 GLU cc_start: 0.8659 (tp30) cc_final: 0.8391 (tp30) REVERT: E 227 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7149 (tm-30) REVERT: F 78 GLU cc_start: 0.8698 (tp30) cc_final: 0.8431 (tp30) REVERT: G 69 MET cc_start: 0.9228 (mtm) cc_final: 0.9025 (ptp) REVERT: G 78 GLU cc_start: 0.8697 (tp30) cc_final: 0.8429 (tp30) REVERT: G 227 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7470 (tm-30) REVERT: H 69 MET cc_start: 0.9105 (mtp) cc_final: 0.8743 (mtp) REVERT: H 78 GLU cc_start: 0.8724 (tp30) cc_final: 0.8500 (tp30) REVERT: H 227 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7403 (tm-30) outliers start: 47 outliers final: 26 residues processed: 216 average time/residue: 1.3503 time to fit residues: 333.1214 Evaluate side-chains 207 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 210 ARG Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 202 MET Chi-restraints excluded: chain G residue 210 ARG Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 210 ARG Chi-restraints excluded: chain H residue 227 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 61 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 214 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 259 optimal weight: 1.9990 chunk 225 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 139 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 23 optimal weight: 10.0000 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.119957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.087792 restraints weight = 225599.814| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 4.39 r_work: 0.3045 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3049 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3049 r_free = 0.3049 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3049 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22520 Z= 0.157 Angle : 0.590 5.890 30680 Z= 0.281 Chirality : 0.040 0.153 3440 Planarity : 0.004 0.033 3992 Dihedral : 5.610 41.912 3403 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.61 % Favored : 94.11 % Rotamer: Outliers : 1.76 % Allowed : 24.03 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 0.35 (0.17), residues: 2840 helix: 2.12 (0.16), residues: 1072 sheet: -1.11 (0.24), residues: 392 loop : -0.88 (0.18), residues: 1376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 287 TYR 0.012 0.001 TYR B 354 PHE 0.027 0.001 PHE E 303 TRP 0.003 0.001 TRP D 268 HIS 0.005 0.001 HIS G 214 Details of bonding type rmsd covalent geometry : bond 0.00359 (22512) covalent geometry : angle 0.58973 (30680) hydrogen bonds : bond 0.03101 ( 969) hydrogen bonds : angle 4.33940 ( 2723) Misc. bond : bond 0.00140 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8681 (tp30) cc_final: 0.8411 (tp30) REVERT: A 227 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7380 (tm-30) REVERT: A 231 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8186 (ttm110) REVERT: B 78 GLU cc_start: 0.8675 (tp30) cc_final: 0.8434 (tp30) REVERT: C 78 GLU cc_start: 0.8662 (tp30) cc_final: 0.8389 (tp30) REVERT: C 227 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7477 (tm-30) REVERT: C 313 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7656 (tm-30) REVERT: D 78 GLU cc_start: 0.8650 (tp30) cc_final: 0.8385 (tp30) REVERT: D 227 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7261 (tm-30) REVERT: E 78 GLU cc_start: 0.8621 (tp30) cc_final: 0.8372 (tp30) REVERT: E 227 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7375 (tm-30) REVERT: F 69 MET cc_start: 0.9098 (mtp) cc_final: 0.8800 (mtp) REVERT: F 78 GLU cc_start: 0.8653 (tp30) cc_final: 0.8403 (tp30) REVERT: G 78 GLU cc_start: 0.8666 (tp30) cc_final: 0.8397 (tp30) REVERT: G 227 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7436 (tm-30) REVERT: H 69 MET cc_start: 0.9113 (mtp) cc_final: 0.8757 (mtp) REVERT: H 78 GLU cc_start: 0.8690 (tp30) cc_final: 0.8465 (tp30) REVERT: H 227 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7362 (tm-30) outliers start: 38 outliers final: 27 residues processed: 211 average time/residue: 1.4632 time to fit residues: 356.0772 Evaluate side-chains 206 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 171 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 227 GLU Chi-restraints excluded: chain A residue 231 ARG Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 329 PHE Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 202 MET Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 313 GLN Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain D residue 227 GLU Chi-restraints excluded: chain E residue 41 THR Chi-restraints excluded: chain E residue 210 ARG Chi-restraints excluded: chain E residue 227 GLU Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 41 THR Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 202 MET Chi-restraints excluded: chain G residue 210 ARG Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 41 THR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 210 ARG Chi-restraints excluded: chain H residue 227 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 118 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 115 optimal weight: 9.9990 chunk 264 optimal weight: 0.7980 chunk 178 optimal weight: 0.9980 chunk 119 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 265 optimal weight: 3.9990 chunk 270 optimal weight: 0.6980 chunk 158 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.122030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.089540 restraints weight = 246118.659| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 4.65 r_work: 0.3064 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22520 Z= 0.099 Angle : 0.575 5.657 30680 Z= 0.270 Chirality : 0.039 0.140 3440 Planarity : 0.004 0.032 3992 Dihedral : 5.238 39.860 3403 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.43 % Favored : 94.39 % Rotamer: Outliers : 0.97 % Allowed : 24.58 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 0.57 (0.17), residues: 2840 helix: 2.30 (0.16), residues: 1080 sheet: -1.08 (0.24), residues: 392 loop : -0.74 (0.19), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 287 TYR 0.011 0.001 TYR H 120 PHE 0.023 0.001 PHE E 303 TRP 0.005 0.001 TRP H 213 HIS 0.005 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00228 (22512) covalent geometry : angle 0.57531 (30680) hydrogen bonds : bond 0.02723 ( 969) hydrogen bonds : angle 4.21498 ( 2723) Misc. bond : bond 0.00099 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Evaluate side-chains 216 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8684 (tp30) cc_final: 0.8411 (tp30) REVERT: A 267 MET cc_start: 0.8389 (mtt) cc_final: 0.8178 (mtt) REVERT: B 78 GLU cc_start: 0.8666 (tp30) cc_final: 0.8433 (tp30) REVERT: B 227 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7307 (tm-30) REVERT: C 78 GLU cc_start: 0.8647 (tp30) cc_final: 0.8394 (tp30) REVERT: C 227 GLU cc_start: 0.7726 (OUTLIER) cc_final: 0.7418 (tm-30) REVERT: C 267 MET cc_start: 0.8397 (mtt) cc_final: 0.8179 (mtt) REVERT: D 69 MET cc_start: 0.9233 (mtm) cc_final: 0.8976 (ptp) REVERT: D 78 GLU cc_start: 0.8661 (tp30) cc_final: 0.8392 (tp30) REVERT: D 91 ARG cc_start: 0.8692 (mmm160) cc_final: 0.8405 (tpp-160) REVERT: E 78 GLU cc_start: 0.8623 (tp30) cc_final: 0.8371 (tp30) REVERT: E 91 ARG cc_start: 0.8684 (mmm160) cc_final: 0.8404 (tpp-160) REVERT: F 69 MET cc_start: 0.9081 (mtp) cc_final: 0.8736 (mtp) REVERT: F 78 GLU cc_start: 0.8654 (tp30) cc_final: 0.8404 (tp30) REVERT: F 91 ARG cc_start: 0.8685 (mmm160) cc_final: 0.8387 (tpp-160) REVERT: F 267 MET cc_start: 0.8377 (mtt) cc_final: 0.8167 (mtt) REVERT: G 78 GLU cc_start: 0.8655 (tp30) cc_final: 0.8401 (tp30) REVERT: G 227 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7393 (tm-30) REVERT: G 267 MET cc_start: 0.8403 (mtt) cc_final: 0.8184 (mtt) REVERT: H 69 MET cc_start: 0.9095 (mtp) cc_final: 0.8710 (mtp) REVERT: H 78 GLU cc_start: 0.8675 (tp30) cc_final: 0.8465 (tp30) REVERT: H 227 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7228 (tm-30) outliers start: 21 outliers final: 14 residues processed: 214 average time/residue: 1.5358 time to fit residues: 374.5252 Evaluate side-chains 196 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 178 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain D residue 210 ARG Chi-restraints excluded: chain E residue 210 ARG Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain G residue 210 ARG Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 227 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 184 optimal weight: 0.9990 chunk 276 optimal weight: 9.9990 chunk 125 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 256 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 102 optimal weight: 7.9990 chunk 188 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.121450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.089303 restraints weight = 238462.668| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 4.51 r_work: 0.3059 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3070 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3070 r_free = 0.3070 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3070 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22520 Z= 0.113 Angle : 0.592 5.607 30680 Z= 0.280 Chirality : 0.039 0.154 3440 Planarity : 0.004 0.032 3992 Dihedral : 5.182 39.903 3395 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.61 % Favored : 94.25 % Rotamer: Outliers : 0.97 % Allowed : 24.91 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 0.59 (0.17), residues: 2840 helix: 2.30 (0.16), residues: 1080 sheet: -1.02 (0.24), residues: 392 loop : -0.74 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 287 TYR 0.010 0.001 TYR B 354 PHE 0.028 0.001 PHE E 303 TRP 0.004 0.001 TRP F 213 HIS 0.005 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00263 (22512) covalent geometry : angle 0.59222 (30680) hydrogen bonds : bond 0.02785 ( 969) hydrogen bonds : angle 4.24435 ( 2723) Misc. bond : bond 0.00104 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5680 Ramachandran restraints generated. 2840 Oldfield, 0 Emsley, 2840 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Residue LYS 20 is missing expected H atoms. Skipping. Residue LYS 65 is missing expected H atoms. Skipping. Residue THR 99 is missing expected H atoms. Skipping. Residue LYS 110 is missing expected H atoms. Skipping. Residue TYR 115 is missing expected H atoms. Skipping. Residue LYS 161 is missing expected H atoms. Skipping. Residue LEU 182 is missing expected H atoms. Skipping. Residue LYS 191 is missing expected H atoms. Skipping. Residue LYS 237 is missing expected H atoms. Skipping. Residue LYS 253 is missing expected H atoms. Skipping. Residue LYS 293 is missing expected H atoms. Skipping. Residue LEU 294 is missing expected H atoms. Skipping. Residue LEU 296 is missing expected H atoms. Skipping. Residue LYS 299 is missing expected H atoms. Skipping. Residue LYS 305 is missing expected H atoms. Skipping. Residue LYS 314 is missing expected H atoms. Skipping. Evaluate side-chains 203 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 182 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 GLU cc_start: 0.8674 (tp30) cc_final: 0.8398 (tp30) REVERT: B 78 GLU cc_start: 0.8646 (tp30) cc_final: 0.8407 (tp30) REVERT: B 227 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7297 (tm-30) REVERT: C 78 GLU cc_start: 0.8637 (tp30) cc_final: 0.8379 (tp30) REVERT: C 227 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7457 (tm-30) REVERT: D 69 MET cc_start: 0.9227 (mtm) cc_final: 0.8973 (ptp) REVERT: D 78 GLU cc_start: 0.8653 (tp30) cc_final: 0.8379 (tp30) REVERT: D 91 ARG cc_start: 0.8697 (mmm160) cc_final: 0.8394 (tpp-160) REVERT: E 78 GLU cc_start: 0.8610 (tp30) cc_final: 0.8351 (tp30) REVERT: E 91 ARG cc_start: 0.8684 (mmm160) cc_final: 0.8389 (tpp-160) REVERT: F 69 MET cc_start: 0.9093 (mtp) cc_final: 0.8759 (mtp) REVERT: F 78 GLU cc_start: 0.8626 (tp30) cc_final: 0.8373 (tp30) REVERT: F 91 ARG cc_start: 0.8683 (mmm160) cc_final: 0.8379 (tpp-160) REVERT: G 78 GLU cc_start: 0.8637 (tp30) cc_final: 0.8383 (tp30) REVERT: G 227 GLU cc_start: 0.7702 (OUTLIER) cc_final: 0.7399 (tm-30) REVERT: H 69 MET cc_start: 0.9094 (mtp) cc_final: 0.8713 (mtp) REVERT: H 78 GLU cc_start: 0.8655 (tp30) cc_final: 0.8441 (tp30) REVERT: H 227 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7112 (tm-30) outliers start: 21 outliers final: 14 residues processed: 201 average time/residue: 1.3898 time to fit residues: 321.5728 Evaluate side-chains 193 residues out of total 2496 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 175 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ARG Chi-restraints excluded: chain A residue 329 PHE Chi-restraints excluded: chain B residue 66 THR Chi-restraints excluded: chain B residue 210 ARG Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 210 ARG Chi-restraints excluded: chain C residue 227 GLU Chi-restraints excluded: chain C residue 329 PHE Chi-restraints excluded: chain E residue 210 ARG Chi-restraints excluded: chain E residue 329 PHE Chi-restraints excluded: chain F residue 210 ARG Chi-restraints excluded: chain F residue 329 PHE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 210 ARG Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 329 PHE Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 227 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 280 random chunks: chunk 127 optimal weight: 2.9990 chunk 167 optimal weight: 0.5980 chunk 133 optimal weight: 7.9990 chunk 246 optimal weight: 2.9990 chunk 237 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 255 optimal weight: 10.0000 chunk 100 optimal weight: 5.9990 chunk 264 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.119773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.087897 restraints weight = 227183.091| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 4.39 r_work: 0.3043 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3048 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3048 r_free = 0.3048 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3048 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22520 Z= 0.180 Angle : 0.616 5.763 30680 Z= 0.296 Chirality : 0.040 0.152 3440 Planarity : 0.004 0.033 3992 Dihedral : 5.378 40.158 3395 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.21 % Allowed : 6.50 % Favored : 93.29 % Rotamer: Outliers : 0.88 % Allowed : 25.14 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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 aren not related in a simple way. whole: 0.44 (0.17), residues: 2840 helix: 2.16 (0.16), residues: 1080 sheet: -1.04 (0.25), residues: 392 loop : -0.84 (0.18), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 287 TYR 0.015 0.001 TYR F 120 PHE 0.026 0.001 PHE G 303 TRP 0.004 0.001 TRP C 264 HIS 0.005 0.001 HIS C 214 Details of bonding type rmsd covalent geometry : bond 0.00412 (22512) covalent geometry : angle 0.61641 (30680) hydrogen bonds : bond 0.03142 ( 969) hydrogen bonds : angle 4.33181 ( 2723) Misc. bond : bond 0.00146 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11494.09 seconds wall clock time: 195 minutes 1.07 seconds (11701.07 seconds total)