Starting phenix.real_space_refine on Wed Aug 27 00:51:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b0u_44058/08_2025/9b0u_44058_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b0u_44058/08_2025/9b0u_44058.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b0u_44058/08_2025/9b0u_44058_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b0u_44058/08_2025/9b0u_44058_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b0u_44058/08_2025/9b0u_44058.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b0u_44058/08_2025/9b0u_44058.map" } resolution = 2.44 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= 0.029 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: 7 Type Number sf(0) Gaussians P 24 5.49 5 Mg 8 5.21 5 S 120 5.16 5 C 14216 2.51 5 N 4160 2.21 5 O 4336 1.98 5 H 21231 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s 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: 44095 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5470 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5445 Classifications: {'peptide': 368} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 349} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 85 Conformer: "B" Number of residues, atoms: 368, 5445 Classifications: {'peptide': 368} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 349} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 85 bond proxies already assigned to first conformer: 5479 Chain: "B" Number of atoms: 5470 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5445 Classifications: {'peptide': 368} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 349} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 85 Conformer: "B" Number of residues, atoms: 368, 5445 Classifications: {'peptide': 368} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 349} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 85 bond proxies already assigned to first conformer: 5479 Chain: "C" Number of atoms: 5470 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5445 Classifications: {'peptide': 368} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 349} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 85 Conformer: "B" Number of residues, atoms: 368, 5445 Classifications: {'peptide': 368} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 349} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 85 bond proxies already assigned to first conformer: 5479 Chain: "D" Number of atoms: 5470 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5445 Classifications: {'peptide': 368} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 349} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 85 Conformer: "B" Number of residues, atoms: 368, 5445 Classifications: {'peptide': 368} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 349} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 85 bond proxies already assigned to first conformer: 5479 Chain: "E" Number of atoms: 5470 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5445 Classifications: {'peptide': 368} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 349} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 85 Conformer: "B" Number of residues, atoms: 368, 5445 Classifications: {'peptide': 368} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 349} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 85 bond proxies already assigned to first conformer: 5479 Chain: "F" Number of atoms: 5470 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5445 Classifications: {'peptide': 368} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 349} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 85 Conformer: "B" Number of residues, atoms: 368, 5445 Classifications: {'peptide': 368} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 349} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 85 bond proxies already assigned to first conformer: 5479 Chain: "G" Number of atoms: 5470 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5445 Classifications: {'peptide': 368} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 349} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 85 Conformer: "B" Number of residues, atoms: 368, 5445 Classifications: {'peptide': 368} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 349} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 85 bond proxies already assigned to first conformer: 5479 Chain: "H" Number of atoms: 5469 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5444 Classifications: {'peptide': 368} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 349} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 85 Conformer: "B" Number of residues, atoms: 368, 5444 Classifications: {'peptide': 368} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 349} Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 8, 'ARG:plan': 7, 'GLN:plan1': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 85 bond proxies already assigned to first conformer: 5478 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 42 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N AARG A 151 " occ=0.57 ... (46 atoms not shown) pdb="HH22BARG A 151 " occ=0.43 residue: pdb=" N AARG B 151 " occ=0.55 ... (46 atoms not shown) pdb="HH22BARG B 151 " occ=0.45 residue: pdb=" N AARG C 151 " occ=0.58 ... (46 atoms not shown) pdb="HH22BARG C 151 " occ=0.42 residue: pdb=" N AARG D 151 " occ=0.55 ... (46 atoms not shown) pdb="HH22BARG D 151 " occ=0.45 residue: pdb=" N AARG E 151 " occ=0.55 ... (46 atoms not shown) pdb="HH22BARG E 151 " occ=0.45 residue: pdb=" N AARG F 151 " occ=0.54 ... (46 atoms not shown) pdb="HH22BARG F 151 " occ=0.46 residue: pdb=" N AARG G 151 " occ=0.54 ... (46 atoms not shown) pdb="HH22BARG G 151 " occ=0.46 residue: pdb=" N AARG H 151 " occ=0.56 ... (46 atoms not shown) pdb="HH22BARG H 151 " occ=0.44 Time building chain proxies: 13.82, per 1000 atoms: 0.31 Number of scatterers: 44095 At special positions: 0 Unit cell: (154.28, 153.216, 97.888, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 120 16.00 P 24 15.00 Mg 8 11.99 O 4336 8.00 N 4160 7.00 C 14216 6.00 H 21231 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.37 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 953.7 nanoseconds 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5424 Finding SS restraints... Secondary structure from input PDB file: 142 helices and 16 sheets defined 44.6% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 removed outlier: 3.757A pdb=" N GLU A 14 " --> pdb=" O PRO A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 29 Processing helix chain 'A' and resid 30 through 38 Processing helix chain 'A' and resid 47 through 58 removed outlier: 5.040A pdb=" N THR A 54 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLY A 55 " --> pdb=" O CYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 92 Proline residue: A 86 - end of helix Processing helix chain 'A' and resid 108 through 112 removed outlier: 3.849A pdb=" N ILE A 111 " --> pdb=" O ALA A 108 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ARG A 112 " --> pdb=" O SER A 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 108 through 112' Processing helix chain 'A' and resid 142 through 158 Processing helix chain 'A' and resid 159 through 160 No H-bonds generated for 'chain 'A' and resid 159 through 160' Processing helix chain 'A' and resid 161 through 164 removed outlier: 3.877A pdb=" N LEU A 164 " --> pdb=" O LYS A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 161 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 200 Processing helix chain 'A' and resid 240 through 262 removed outlier: 3.801A pdb=" N ARG A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.630A pdb=" N LEU A 282 " --> pdb=" O PRO A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 298 removed outlier: 4.341A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N SER A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 298' 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: 3.759A pdb=" N GLU B 14 " --> pdb=" O PRO B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 29 Processing helix chain 'B' and resid 30 through 38 Processing helix chain 'B' and resid 47 through 58 removed outlier: 5.040A pdb=" N THR B 54 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N GLY B 55 " --> pdb=" O CYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 80 through 92 Proline residue: B 86 - end of helix Processing helix chain 'B' and resid 117 through 122 removed outlier: 4.220A pdb=" N LEU B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 158 Processing helix chain 'B' and resid 159 through 160 No H-bonds generated for 'chain 'B' and resid 159 through 160' Processing helix chain 'B' and resid 161 through 164 removed outlier: 3.902A pdb=" N LEU B 164 " --> pdb=" O LYS B 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 161 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: 3.818A pdb=" N ARG B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.628A pdb=" N LEU B 282 " --> pdb=" O PRO B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 298 removed outlier: 4.398A pdb=" N LEU B 297 " --> pdb=" O LYS B 293 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N SER B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 293 through 298' Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 340 through 358 Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.761A pdb=" N GLU C 14 " --> pdb=" O PRO C 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 29 Processing helix chain 'C' and resid 30 through 38 Processing helix chain 'C' and resid 47 through 58 removed outlier: 5.041A pdb=" N THR C 54 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLY C 55 " --> pdb=" O CYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 80 through 92 Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 108 through 112 removed outlier: 3.851A pdb=" N ILE C 111 " --> pdb=" O ALA C 108 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ARG C 112 " --> pdb=" O SER C 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 108 through 112' Processing helix chain 'C' and resid 117 through 122 removed outlier: 4.223A pdb=" N LEU C 122 " --> pdb=" O GLU C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 158 Processing helix chain 'C' and resid 159 through 160 No H-bonds generated for 'chain 'C' and resid 159 through 160' Processing helix chain 'C' and resid 161 through 164 removed outlier: 3.900A pdb=" N LEU C 164 " --> pdb=" O LYS C 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 161 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: 3.815A pdb=" N ARG C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.632A pdb=" N LEU C 282 " --> pdb=" O PRO C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 298 removed outlier: 4.551A pdb=" N LEU C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N SER C 298 " --> pdb=" O LEU C 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 293 through 298' 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: 3.760A pdb=" N GLU D 14 " --> pdb=" O PRO D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 29 Processing helix chain 'D' and resid 30 through 38 Processing helix chain 'D' and resid 47 through 58 removed outlier: 5.041A pdb=" N THR D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLY D 55 " --> pdb=" O CYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'D' and resid 80 through 92 Proline residue: D 86 - end of helix Processing helix chain 'D' and resid 142 through 158 Processing helix chain 'D' and resid 159 through 160 No H-bonds generated for 'chain 'D' and resid 159 through 160' Processing helix chain 'D' and resid 161 through 164 removed outlier: 3.895A pdb=" N LEU D 164 " --> pdb=" O LYS D 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 161 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 200 Processing helix chain 'D' and resid 240 through 262 removed outlier: 3.821A pdb=" N ARG D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 removed outlier: 3.629A pdb=" N LEU D 282 " --> pdb=" O PRO D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 298 removed outlier: 4.355A pdb=" N LEU D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N SER D 298 " --> pdb=" O LEU D 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 293 through 298' Processing helix chain 'D' and resid 302 through 311 removed outlier: 3.517A pdb=" N ILE D 306 " --> pdb=" O ARG D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 359 Processing helix chain 'E' and resid 10 through 15 removed outlier: 3.757A pdb=" N GLU E 14 " --> pdb=" O PRO E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 29 Processing helix chain 'E' and resid 30 through 38 Processing helix chain 'E' and resid 47 through 58 removed outlier: 5.040A pdb=" N THR E 54 " --> pdb=" O GLN E 50 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLY E 55 " --> pdb=" O CYS E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 80 Processing helix chain 'E' and resid 80 through 92 Proline residue: E 86 - end of helix Processing helix chain 'E' and resid 142 through 158 Processing helix chain 'E' and resid 159 through 160 No H-bonds generated for 'chain 'E' and resid 159 through 160' Processing helix chain 'E' and resid 161 through 164 removed outlier: 3.896A pdb=" N LEU E 164 " --> pdb=" O LYS E 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 161 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: 3.824A pdb=" N ARG E 262 " --> pdb=" O LEU E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 282 removed outlier: 3.634A pdb=" N LEU E 282 " --> pdb=" O PRO E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 293 through 298 removed outlier: 4.445A pdb=" N LEU E 297 " --> pdb=" O LYS E 293 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N SER E 298 " --> pdb=" O LEU E 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 293 through 298' Processing helix chain 'E' and resid 302 through 311 removed outlier: 3.550A pdb=" N ILE E 306 " --> pdb=" O ARG E 302 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 358 Processing helix chain 'F' and resid 10 through 15 removed outlier: 3.759A pdb=" N GLU F 14 " --> pdb=" O PRO F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 29 Processing helix chain 'F' and resid 30 through 38 Processing helix chain 'F' and resid 47 through 58 removed outlier: 5.041A pdb=" N THR F 54 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLY F 55 " --> pdb=" O CYS F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 80 Processing helix chain 'F' and resid 80 through 92 Proline residue: F 86 - end of helix Processing helix chain 'F' and resid 142 through 158 Processing helix chain 'F' and resid 159 through 160 No H-bonds generated for 'chain 'F' and resid 159 through 160' Processing helix chain 'F' and resid 161 through 164 removed outlier: 3.885A pdb=" N LEU F 164 " --> pdb=" O LYS F 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 161 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 200 Processing helix chain 'F' and resid 240 through 262 removed outlier: 3.812A pdb=" N ARG F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 282 removed outlier: 3.634A pdb=" N LEU F 282 " --> pdb=" O PRO F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 293 through 298 removed outlier: 4.419A pdb=" N LEU F 297 " --> pdb=" O LYS F 293 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N SER F 298 " --> pdb=" O LEU F 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 293 through 298' 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: 3.762A pdb=" N GLU G 14 " --> pdb=" O PRO G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 29 Processing helix chain 'G' and resid 30 through 38 Processing helix chain 'G' and resid 47 through 58 removed outlier: 5.040A pdb=" N THR G 54 " --> pdb=" O GLN G 50 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLY G 55 " --> pdb=" O CYS G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 80 Processing helix chain 'G' and resid 80 through 92 Proline residue: G 86 - end of helix Processing helix chain 'G' and resid 108 through 112 removed outlier: 3.851A pdb=" N ILE G 111 " --> pdb=" O ALA G 108 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ARG G 112 " --> pdb=" O SER G 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 108 through 112' Processing helix chain 'G' and resid 142 through 158 Processing helix chain 'G' and resid 159 through 160 No H-bonds generated for 'chain 'G' and resid 159 through 160' Processing helix chain 'G' and resid 161 through 164 removed outlier: 3.897A pdb=" N LEU G 164 " --> pdb=" O LYS G 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 161 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: 3.823A pdb=" N ARG G 262 " --> pdb=" O LEU G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 282 removed outlier: 3.626A pdb=" N LEU G 282 " --> pdb=" O PRO G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 298 removed outlier: 4.419A pdb=" N LEU G 297 " --> pdb=" O LYS G 293 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N SER G 298 " --> pdb=" O LEU G 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 293 through 298' 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: 3.758A pdb=" N GLU H 14 " --> pdb=" O PRO H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 29 Processing helix chain 'H' and resid 30 through 38 Processing helix chain 'H' and resid 47 through 58 removed outlier: 5.040A pdb=" N THR H 54 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLY H 55 " --> pdb=" O CYS H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 80 Processing helix chain 'H' and resid 80 through 92 Proline residue: H 86 - end of helix Processing helix chain 'H' and resid 108 through 112 removed outlier: 3.868A pdb=" N ILE H 111 " --> pdb=" O ALA H 108 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG H 112 " --> pdb=" O SER H 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 108 through 112' Processing helix chain 'H' and resid 142 through 158 Processing helix chain 'H' and resid 159 through 160 No H-bonds generated for 'chain 'H' and resid 159 through 160' Processing helix chain 'H' and resid 161 through 164 removed outlier: 3.898A pdb=" N LEU H 164 " --> pdb=" O LYS H 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 161 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 200 Processing helix chain 'H' and resid 240 through 262 removed outlier: 3.821A pdb=" N ARG H 262 " --> pdb=" O LEU H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 282 removed outlier: 3.629A pdb=" N LEU H 282 " --> pdb=" O PRO H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 293 through 298 removed outlier: 4.411A pdb=" N LEU H 297 " --> pdb=" O LYS H 293 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER H 298 " --> pdb=" O LEU H 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 293 through 298' Processing helix chain 'H' and resid 302 through 310 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: 5.716A pdb=" N PHE A 220 " --> pdb=" O ASN A 215 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ALA A 288 " --> pdb=" O ASN A 333 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 333 " --> pdb=" O ALA A 288 " (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: 5.715A pdb=" N PHE B 220 " --> pdb=" O ASN B 215 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ALA B 288 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN B 333 " --> pdb=" O ALA B 288 " (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: 5.714A pdb=" N PHE C 220 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N ALA C 288 " --> pdb=" O ASN C 333 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN C 333 " --> pdb=" O ALA C 288 " (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: 5.714A pdb=" N PHE D 220 " --> pdb=" O ASN D 215 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ALA D 288 " --> pdb=" O ASN D 333 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN D 333 " --> pdb=" O ALA D 288 " (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: 5.707A pdb=" N PHE E 220 " --> pdb=" O ASN E 215 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N ALA E 288 " --> pdb=" O ASN E 333 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASN E 333 " --> pdb=" O ALA E 288 " (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: 5.714A pdb=" N PHE F 220 " --> pdb=" O ASN F 215 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ALA F 288 " --> pdb=" O ASN F 333 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASN F 333 " --> pdb=" O ALA F 288 " (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: 5.707A pdb=" N PHE G 220 " --> pdb=" O ASN G 215 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ALA G 288 " --> pdb=" O ASN G 333 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ASN G 333 " --> pdb=" O ALA G 288 " (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: 5.715A pdb=" N PHE H 220 " --> pdb=" O ASN H 215 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N ALA H 288 " --> pdb=" O ASN H 333 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASN H 333 " --> pdb=" O ALA H 288 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 268 through 269 968 hydrogen bonds defined for protein. 2744 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: 9.72 Time building geometry restraints manager: 4.70 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: 21175 1.03 - 1.23: 136 1.23 - 1.42: 9848 1.42 - 1.62: 13232 1.62 - 1.81: 184 Bond restraints: 44575 Sorted by residual: bond pdb=" C4 ADP G 402 " pdb=" C5 ADP G 402 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.71e+00 bond pdb=" C4 ADP F 402 " pdb=" C5 ADP F 402 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.68e+00 bond pdb=" C4 ADP B 402 " pdb=" C5 ADP B 402 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.67e+00 bond pdb=" C4 ADP E 402 " pdb=" C5 ADP E 402 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.67e+00 bond pdb=" C4 ADP A 402 " pdb=" C5 ADP A 402 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.66e+00 ... (remaining 44570 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 76381 1.23 - 2.47: 3156 2.47 - 3.70: 293 3.70 - 4.94: 75 4.94 - 6.17: 61 Bond angle restraints: 79966 Sorted by residual: angle pdb=" N GLY A 285 " pdb=" CA GLY A 285 " pdb=" C GLY A 285 " ideal model delta sigma weight residual 115.30 111.50 3.80 1.44e+00 4.82e-01 6.95e+00 angle pdb=" N GLY B 285 " pdb=" CA GLY B 285 " pdb=" C GLY B 285 " ideal model delta sigma weight residual 115.30 111.52 3.78 1.44e+00 4.82e-01 6.90e+00 angle pdb=" CB ARG E 360 " pdb=" CG ARG E 360 " pdb=" CD ARG E 360 " ideal model delta sigma weight residual 111.30 116.71 -5.41 2.30e+00 1.89e-01 5.53e+00 angle pdb=" N GLY F 326 " pdb=" CA GLY F 326 " pdb=" C GLY F 326 " ideal model delta sigma weight residual 113.18 107.88 5.30 2.37e+00 1.78e-01 5.01e+00 angle pdb=" N GLY D 326 " pdb=" CA GLY D 326 " pdb=" C GLY D 326 " ideal model delta sigma weight residual 113.18 108.01 5.17 2.37e+00 1.78e-01 4.77e+00 ... (remaining 79961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 18768 17.97 - 35.95: 1663 35.95 - 53.92: 485 53.92 - 71.90: 120 71.90 - 89.87: 19 Dihedral angle restraints: 21055 sinusoidal: 11255 harmonic: 9800 Sorted by residual: dihedral pdb=" CA GLY E 326 " pdb=" C GLY E 326 " pdb=" N GLY E 327 " pdb=" CA GLY E 327 " ideal model delta harmonic sigma weight residual -180.00 -151.10 -28.90 0 5.00e+00 4.00e-02 3.34e+01 dihedral pdb=" CA GLY F 326 " pdb=" C GLY F 326 " pdb=" N GLY F 327 " pdb=" CA GLY F 327 " ideal model delta harmonic sigma weight residual -180.00 -151.40 -28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA GLY B 326 " pdb=" C GLY B 326 " pdb=" N GLY B 327 " pdb=" CA GLY B 327 " ideal model delta harmonic sigma weight residual -180.00 -151.40 -28.60 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 21052 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2093 0.028 - 0.056: 919 0.056 - 0.084: 276 0.084 - 0.112: 180 0.112 - 0.140: 44 Chirality restraints: 3512 Sorted by residual: chirality pdb=" CA VAL H 328 " pdb=" N VAL H 328 " pdb=" C VAL H 328 " pdb=" CB VAL H 328 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.93e-01 chirality pdb=" CA VAL C 328 " pdb=" N VAL C 328 " pdb=" C VAL C 328 " pdb=" CB VAL C 328 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.83e-01 chirality pdb=" CA VAL B 328 " pdb=" N VAL B 328 " pdb=" C VAL B 328 " pdb=" CB VAL B 328 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 3509 not shown) Planarity restraints: 6992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU C 137 " -0.028 5.00e-02 4.00e+02 4.16e-02 2.77e+00 pdb=" N PRO C 138 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 138 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 138 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU H 137 " -0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO H 138 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO H 138 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 138 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU G 137 " 0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO G 138 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO G 138 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO G 138 " 0.022 5.00e-02 4.00e+02 ... (remaining 6989 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 5014 2.23 - 2.82: 95414 2.82 - 3.42: 118649 3.42 - 4.01: 166393 4.01 - 4.60: 254862 Nonbonded interactions: 640332 Sorted by model distance: nonbonded pdb=" O ARG A 112 " pdb=" HG SER A 113 " model vdw 1.640 2.450 nonbonded pdb=" O ARG C 112 " pdb=" HG SER C 113 " model vdw 1.640 2.450 nonbonded pdb="HH21 ARG F 127 " pdb=" O1B ADP F 402 " model vdw 1.641 2.450 nonbonded pdb=" O ARG H 112 " pdb=" HG SER H 113 " model vdw 1.642 2.450 nonbonded pdb=" O ARG G 112 " pdb=" HG SER G 113 " model vdw 1.644 2.450 ... (remaining 640327 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 150 or resid 153 through 314 or (resid 315 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name N \ E or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB \ 3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or nam \ e HH21 or name HH22)) or resid 316 through 370 or resid 404)) selection = (chain 'B' and (resid 3 through 150 or resid 153 through 314 or (resid 315 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name N \ E or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB \ 3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or nam \ e HH21 or name HH22)) or resid 316 through 370 or resid 404)) selection = (chain 'C' and (resid 3 through 150 or resid 153 through 314 or (resid 315 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name N \ E or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB \ 3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or nam \ e HH21 or name HH22)) or resid 316 through 370 or resid 404)) selection = (chain 'D' and (resid 3 through 150 or resid 153 through 314 or (resid 315 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name N \ E or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB \ 3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or nam \ e HH21 or name HH22)) or resid 316 through 370 or resid 404)) selection = (chain 'E' and (resid 3 through 150 or resid 153 through 314 or (resid 315 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name N \ E or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB \ 3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or nam \ e HH21 or name HH22)) or resid 316 through 370 or resid 404)) selection = (chain 'F' and (resid 3 through 150 or resid 153 through 314 or (resid 315 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name N \ E or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB \ 3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or nam \ e HH21 or name HH22)) or resid 316 through 370 or resid 404)) selection = (chain 'G' and (resid 3 through 150 or resid 153 through 314 or (resid 315 and ( \ name N or name CA or name C or name O or name CB or name CG or name CD or name N \ E or name CZ or name NH1 or name NH2 or name H or name HA or name HB2 or name HB \ 3 or name HG2 or name HG3 or name HD2 or name HD3 or name HE or name HH11 or nam \ e HH21 or name HH22)) or resid 316 through 370 or resid 404)) selection = (chain 'H' and (resid 3 through 150 or resid 153 through 370 or resid 404)) } 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=0.42 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.240 Extract box with map and model: 0.550 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 44.950 Find NCS groups from input model: 0.830 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 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 : 0.009 0.891 23347 Z= 0.824 Angle : 0.608 6.174 31808 Z= 0.292 Chirality : 0.040 0.140 3512 Planarity : 0.004 0.042 4176 Dihedral : 15.713 89.871 8384 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.08 % Favored : 93.65 % Rotamer: Outliers : 0.83 % Allowed : 20.31 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.28 % 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: 0.28 (0.16), residues: 2952 helix: 2.29 (0.17), residues: 1016 sheet: -1.43 (0.21), residues: 448 loop : -0.78 (0.17), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 204 TYR 0.009 0.001 TYR F 115 PHE 0.006 0.001 PHE D 303 TRP 0.005 0.001 TRP F 46 HIS 0.005 0.001 HIS D 61 Details of bonding type rmsd covalent geometry : bond 0.00342 (23344) covalent geometry : angle 0.60753 (31808) hydrogen bonds : bond 0.11893 ( 968) hydrogen bonds : angle 5.00857 ( 2744) Misc. bond : bond 0.71418 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 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 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 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 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 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 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 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 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 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 260 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 241 time to evaluate : 1.164 Fit side-chains REVERT: A 107 ASP cc_start: 0.9172 (m-30) cc_final: 0.8725 (t0) outliers start: 19 outliers final: 18 residues processed: 260 average time/residue: 1.3124 time to fit residues: 389.7067 Evaluate side-chains 258 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 240 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 367 ASP Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain D residue 367 ASP Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain E residue 367 ASP Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain G residue 367 ASP Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 367 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.097623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.065009 restraints weight = 213558.423| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 4.10 r_work: 0.2574 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.0555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 23347 Z= 0.279 Angle : 0.660 7.176 31808 Z= 0.324 Chirality : 0.044 0.141 3512 Planarity : 0.004 0.047 4176 Dihedral : 6.952 82.484 3427 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.93 % Favored : 92.73 % Rotamer: Outliers : 1.80 % Allowed : 18.82 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.28 % 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: -0.11 (0.16), residues: 2952 helix: 1.94 (0.17), residues: 1048 sheet: -1.48 (0.21), residues: 448 loop : -1.13 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 125 TYR 0.007 0.001 TYR B 9 PHE 0.009 0.001 PHE H 303 TRP 0.006 0.001 TRP C 46 HIS 0.008 0.002 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00626 (23344) covalent geometry : angle 0.65974 (31808) hydrogen bonds : bond 0.04450 ( 968) hydrogen bonds : angle 4.70343 ( 2744) Misc. bond : bond 0.00283 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 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 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 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 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 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 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 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 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 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 285 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 244 time to evaluate : 1.185 Fit side-chains revert: symmetry clash REVERT: A 107 ASP cc_start: 0.9170 (m-30) cc_final: 0.8743 (t0) outliers start: 41 outliers final: 14 residues processed: 269 average time/residue: 1.2904 time to fit residues: 399.5895 Evaluate side-chains 253 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 239 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 362 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain F residue 367 ASP Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 367 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 0.0870 chunk 224 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 252 optimal weight: 1.9990 chunk 183 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 83 optimal weight: 6.9990 overall best weight: 1.3564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.099610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.067112 restraints weight = 210132.006| |-----------------------------------------------------------------------------| r_work (start): 0.2766 rms_B_bonded: 4.09 r_work: 0.2611 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.0598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23347 Z= 0.128 Angle : 0.606 6.288 31808 Z= 0.290 Chirality : 0.041 0.136 3512 Planarity : 0.004 0.043 4176 Dihedral : 6.658 80.673 3417 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.27 % Allowed : 6.39 % Favored : 93.34 % Rotamer: Outliers : 1.49 % Allowed : 19.04 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.28 % 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: 0.02 (0.16), residues: 2952 helix: 2.11 (0.17), residues: 1048 sheet: -1.49 (0.21), residues: 448 loop : -1.07 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 360 TYR 0.015 0.001 TYR C 354 PHE 0.006 0.001 PHE B 303 TRP 0.004 0.001 TRP C 46 HIS 0.007 0.001 HIS D 61 Details of bonding type rmsd covalent geometry : bond 0.00289 (23344) covalent geometry : angle 0.60559 (31808) hydrogen bonds : bond 0.03613 ( 968) hydrogen bonds : angle 4.46227 ( 2744) Misc. bond : bond 0.00141 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 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 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 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 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 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 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 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 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 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 297 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 263 time to evaluate : 1.244 Fit side-chains revert: symmetry clash REVERT: A 107 ASP cc_start: 0.9162 (m-30) cc_final: 0.8737 (t0) REVERT: A 360 ARG cc_start: 0.6325 (mmp-170) cc_final: 0.5749 (mmp80) outliers start: 34 outliers final: 11 residues processed: 281 average time/residue: 1.2483 time to fit residues: 402.6687 Evaluate side-chains 260 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 249 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain H residue 171 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 59 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 280 optimal weight: 3.9990 chunk 214 optimal weight: 5.9990 chunk 157 optimal weight: 0.9980 chunk 220 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 282 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 181 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.099322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.066650 restraints weight = 211324.670| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 4.11 r_work: 0.2605 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2605 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2605 r_free = 0.2605 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2605 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23347 Z= 0.153 Angle : 0.609 9.876 31808 Z= 0.292 Chirality : 0.041 0.253 3512 Planarity : 0.004 0.044 4176 Dihedral : 6.533 77.828 3411 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.27 % Allowed : 7.00 % Favored : 92.73 % Rotamer: Outliers : 1.75 % Allowed : 18.86 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.28 % 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: -0.01 (0.16), residues: 2952 helix: 2.11 (0.17), residues: 1048 sheet: -1.52 (0.21), residues: 448 loop : -1.10 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 210 TYR 0.012 0.001 TYR C 354 PHE 0.005 0.001 PHE A 248 TRP 0.005 0.001 TRP D 46 HIS 0.006 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00346 (23344) covalent geometry : angle 0.60892 (31808) hydrogen bonds : bond 0.03505 ( 968) hydrogen bonds : angle 4.42010 ( 2744) Misc. bond : bond 0.00082 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 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 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 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 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 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 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 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 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 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 285 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 245 time to evaluate : 1.238 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.9152 (m-30) cc_final: 0.8729 (t0) outliers start: 40 outliers final: 13 residues processed: 263 average time/residue: 1.3010 time to fit residues: 391.2321 Evaluate side-chains 254 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 241 time to evaluate : 1.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 171 LEU Chi-restraints excluded: chain H residue 347 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 27 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 108 optimal weight: 0.0020 chunk 214 optimal weight: 5.9990 chunk 67 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 235 optimal weight: 0.6980 chunk 268 optimal weight: 5.9990 chunk 234 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 overall best weight: 1.4992 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.099680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.067223 restraints weight = 201271.809| |-----------------------------------------------------------------------------| r_work (start): 0.2771 rms_B_bonded: 4.05 r_work: 0.2618 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2616 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2616 r_free = 0.2616 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2616 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.0739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 23347 Z= 0.134 Angle : 0.600 7.716 31808 Z= 0.286 Chirality : 0.040 0.137 3512 Planarity : 0.004 0.042 4176 Dihedral : 6.368 75.454 3409 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.86 % Favored : 92.83 % Rotamer: Outliers : 1.01 % Allowed : 19.65 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.28 % 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: 0.04 (0.16), residues: 2952 helix: 2.17 (0.17), residues: 1048 sheet: -1.54 (0.21), residues: 448 loop : -1.07 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 210 TYR 0.013 0.001 TYR C 354 PHE 0.005 0.001 PHE A 248 TRP 0.004 0.001 TRP G 46 HIS 0.006 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00301 (23344) covalent geometry : angle 0.60001 (31808) hydrogen bonds : bond 0.03331 ( 968) hydrogen bonds : angle 4.34169 ( 2744) Misc. bond : bond 0.00085 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 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 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 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 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 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 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 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 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 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 283 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 260 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.9184 (m-30) cc_final: 0.8753 (t0) REVERT: A 360 ARG cc_start: 0.6295 (mmp-170) cc_final: 0.5708 (mmp80) REVERT: C 107 ASP cc_start: 0.9127 (m-30) cc_final: 0.8739 (t0) outliers start: 23 outliers final: 13 residues processed: 272 average time/residue: 1.2851 time to fit residues: 403.0915 Evaluate side-chains 264 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 251 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 171 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 81 optimal weight: 0.8980 chunk 153 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 238 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 17 optimal weight: 3.9990 chunk 267 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 176 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- 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 = 0.3351 r_free = 0.3351 target = 0.098633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.066186 restraints weight = 200647.409| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 4.02 r_work: 0.2596 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23347 Z= 0.194 Angle : 0.614 6.544 31808 Z= 0.296 Chirality : 0.041 0.141 3512 Planarity : 0.004 0.045 4176 Dihedral : 6.444 73.645 3409 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.31 % Allowed : 7.07 % Favored : 92.62 % Rotamer: Outliers : 0.79 % Allowed : 19.61 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.28 % 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: -0.04 (0.16), residues: 2952 helix: 2.13 (0.17), residues: 1048 sheet: -1.58 (0.21), residues: 448 loop : -1.14 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 210 TYR 0.009 0.001 TYR A 115 PHE 0.006 0.001 PHE A 248 TRP 0.005 0.001 TRP G 46 HIS 0.006 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00439 (23344) covalent geometry : angle 0.61435 (31808) hydrogen bonds : bond 0.03529 ( 968) hydrogen bonds : angle 4.39157 ( 2744) Misc. bond : bond 0.00097 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 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 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 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 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 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 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 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 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 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 258 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 240 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.9149 (m-30) cc_final: 0.8728 (t0) REVERT: A 360 ARG cc_start: 0.6265 (mmp-170) cc_final: 0.5692 (mmp80) outliers start: 18 outliers final: 10 residues processed: 253 average time/residue: 1.3222 time to fit residues: 382.6599 Evaluate side-chains 245 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 235 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 171 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 41 optimal weight: 1.9990 chunk 192 optimal weight: 5.9990 chunk 57 optimal weight: 2.9990 chunk 268 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 253 optimal weight: 0.9990 chunk 201 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 252 optimal weight: 0.9990 chunk 68 optimal weight: 0.0070 chunk 5 optimal weight: 2.9990 overall best weight: 0.9804 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.100229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.067612 restraints weight = 227548.634| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 4.27 r_work: 0.2622 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2622 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2622 r_free = 0.2622 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2622 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.0864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 23347 Z= 0.110 Angle : 0.591 6.306 31808 Z= 0.281 Chirality : 0.040 0.136 3512 Planarity : 0.004 0.041 4176 Dihedral : 6.253 73.448 3409 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.52 % Favored : 93.14 % Rotamer: Outliers : 0.57 % Allowed : 20.00 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.28 % 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: 0.11 (0.16), residues: 2952 helix: 2.25 (0.17), residues: 1048 sheet: -1.57 (0.21), residues: 448 loop : -1.03 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 247 TYR 0.008 0.001 TYR E 115 PHE 0.006 0.001 PHE D 303 TRP 0.004 0.001 TRP B 46 HIS 0.005 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00245 (23344) covalent geometry : angle 0.59089 (31808) hydrogen bonds : bond 0.03163 ( 968) hydrogen bonds : angle 4.26362 ( 2744) Misc. bond : bond 0.00079 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 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 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 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 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 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 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 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 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 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 275 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 262 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.9173 (m-30) cc_final: 0.8739 (t0) REVERT: A 360 ARG cc_start: 0.6220 (mmp-170) cc_final: 0.5653 (mmp80) REVERT: C 107 ASP cc_start: 0.9083 (m-30) cc_final: 0.8695 (t0) REVERT: H 107 ASP cc_start: 0.9087 (m-30) cc_final: 0.8741 (t0) outliers start: 13 outliers final: 10 residues processed: 274 average time/residue: 1.2890 time to fit residues: 405.0989 Evaluate side-chains 268 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 258 time to evaluate : 1.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 171 LEU Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain E residue 171 LEU Chi-restraints excluded: chain F residue 171 LEU Chi-restraints excluded: chain G residue 171 LEU Chi-restraints excluded: chain H residue 171 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 280 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 62 optimal weight: 0.0870 chunk 162 optimal weight: 2.9990 chunk 254 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 overall best weight: 0.9360 ------------------------------------------------------------------------------- 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 = 0.3380 r_free = 0.3380 target = 0.100445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.068001 restraints weight = 218300.362| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 4.18 r_work: 0.2633 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2632 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2632 r_free = 0.2632 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2632 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 23347 Z= 0.109 Angle : 0.588 6.637 31808 Z= 0.278 Chirality : 0.040 0.138 3512 Planarity : 0.004 0.041 4176 Dihedral : 6.109 68.801 3409 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.56 % Favored : 93.10 % Rotamer: Outliers : 0.53 % Allowed : 20.04 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.28 % 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: 0.17 (0.16), residues: 2952 helix: 2.30 (0.17), residues: 1048 sheet: -1.55 (0.21), residues: 448 loop : -0.99 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 143 TYR 0.008 0.001 TYR G 115 PHE 0.006 0.001 PHE A 248 TRP 0.004 0.001 TRP B 46 HIS 0.005 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00243 (23344) covalent geometry : angle 0.58760 (31808) hydrogen bonds : bond 0.03063 ( 968) hydrogen bonds : angle 4.22649 ( 2744) Misc. bond : bond 0.00065 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 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 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 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 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 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 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 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 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 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 282 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 270 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.9180 (m-30) cc_final: 0.8760 (t0) REVERT: A 360 ARG cc_start: 0.6208 (mmp-170) cc_final: 0.5628 (mmp80) REVERT: C 107 ASP cc_start: 0.9095 (m-30) cc_final: 0.8719 (t0) REVERT: D 107 ASP cc_start: 0.9158 (m-30) cc_final: 0.8784 (t0) REVERT: F 107 ASP cc_start: 0.9135 (m-30) cc_final: 0.8793 (t0) REVERT: G 107 ASP cc_start: 0.9148 (m-30) cc_final: 0.8769 (t0) REVERT: H 107 ASP cc_start: 0.9093 (m-30) cc_final: 0.8760 (t0) outliers start: 12 outliers final: 3 residues processed: 282 average time/residue: 1.2525 time to fit residues: 404.4920 Evaluate side-chains 260 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 257 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain H residue 171 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 234 optimal weight: 4.9990 chunk 256 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 131 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 277 optimal weight: 1.9990 chunk 118 optimal weight: 6.9990 chunk 211 optimal weight: 0.5980 chunk 120 optimal weight: 0.6980 chunk 200 optimal weight: 4.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.3369 r_free = 0.3369 target = 0.099743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.067416 restraints weight = 213029.677| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 4.12 r_work: 0.2621 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.0955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 23347 Z= 0.144 Angle : 0.594 6.195 31808 Z= 0.283 Chirality : 0.040 0.138 3512 Planarity : 0.004 0.043 4176 Dihedral : 5.832 67.790 3395 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.83 % Favored : 92.83 % Rotamer: Outliers : 0.48 % Allowed : 20.48 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.28 % 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: 0.14 (0.16), residues: 2952 helix: 2.27 (0.17), residues: 1048 sheet: -1.57 (0.21), residues: 448 loop : -1.00 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 210 TYR 0.014 0.001 TYR C 354 PHE 0.006 0.001 PHE D 303 TRP 0.004 0.001 TRP H 46 HIS 0.005 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00324 (23344) covalent geometry : angle 0.59421 (31808) hydrogen bonds : bond 0.03182 ( 968) hydrogen bonds : angle 4.24955 ( 2744) Misc. bond : bond 0.00082 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 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 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 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 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 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 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 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 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 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 270 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 259 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.9171 (m-30) cc_final: 0.8741 (t0) REVERT: A 360 ARG cc_start: 0.6199 (mmp-170) cc_final: 0.5637 (mmp80) REVERT: C 107 ASP cc_start: 0.9087 (m-30) cc_final: 0.8702 (t0) REVERT: G 107 ASP cc_start: 0.9141 (m-30) cc_final: 0.8746 (t0) REVERT: H 107 ASP cc_start: 0.9090 (m-30) cc_final: 0.8750 (t0) outliers start: 11 outliers final: 4 residues processed: 267 average time/residue: 1.1438 time to fit residues: 351.9502 Evaluate side-chains 262 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 258 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 363 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 245 optimal weight: 0.0970 chunk 73 optimal weight: 2.9990 chunk 29 optimal weight: 0.0040 chunk 232 optimal weight: 1.9990 chunk 225 optimal weight: 0.0980 chunk 136 optimal weight: 0.3980 chunk 216 optimal weight: 2.9990 chunk 263 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 262 optimal weight: 6.9990 chunk 201 optimal weight: 0.9980 overall best weight: 0.3190 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.102107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2883 r_free = 0.2883 target = 0.069784 restraints weight = 228634.486| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 4.28 r_work: 0.2662 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2664 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2664 r_free = 0.2664 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2664 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 23347 Z= 0.092 Angle : 0.582 6.833 31808 Z= 0.274 Chirality : 0.040 0.137 3512 Planarity : 0.004 0.038 4176 Dihedral : 5.523 64.789 3393 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.39 % Favored : 93.27 % Rotamer: Outliers : 0.13 % Allowed : 20.75 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.28 % 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 (0.16), residues: 2952 helix: 2.36 (0.17), residues: 1048 sheet: -1.50 (0.21), residues: 448 loop : -0.90 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 204 TYR 0.010 0.001 TYR G 354 PHE 0.006 0.001 PHE A 248 TRP 0.006 0.001 TRP E 213 HIS 0.005 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00199 (23344) covalent geometry : angle 0.58215 (31808) hydrogen bonds : bond 0.02839 ( 968) hydrogen bonds : angle 4.13668 ( 2744) Misc. bond : bond 0.00071 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5904 Ramachandran restraints generated. 2952 Oldfield, 0 Emsley, 2952 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 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 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 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 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 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 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 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 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 279 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 276 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 ASP cc_start: 0.9168 (m-30) cc_final: 0.8765 (t0) REVERT: B 107 ASP cc_start: 0.9126 (m-30) cc_final: 0.8769 (t0) REVERT: B 242 LYS cc_start: 0.9441 (tptm) cc_final: 0.9190 (tptm) REVERT: D 107 ASP cc_start: 0.9149 (m-30) cc_final: 0.8793 (t0) REVERT: E 107 ASP cc_start: 0.9137 (m-30) cc_final: 0.8782 (t0) REVERT: F 107 ASP cc_start: 0.9132 (m-30) cc_final: 0.8796 (t0) REVERT: G 107 ASP cc_start: 0.9146 (m-30) cc_final: 0.8781 (t0) outliers start: 3 outliers final: 4 residues processed: 279 average time/residue: 0.9818 time to fit residues: 315.8610 Evaluate side-chains 276 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 272 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 363 GLU Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain E residue 347 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 210 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 251 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 238 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 276 optimal weight: 0.6980 chunk 233 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3371 r_free = 0.3371 target = 0.099950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.067410 restraints weight = 225151.006| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 4.25 r_work: 0.2621 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.115 23347 Z= 0.174 Angle : 0.693 28.093 31808 Z= 0.315 Chirality : 0.041 0.210 3512 Planarity : 0.004 0.043 4176 Dihedral : 5.632 62.775 3393 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 3.37 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.39 % Favored : 93.27 % Rotamer: Outliers : 0.18 % Allowed : 20.83 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.28 % 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: 0.20 (0.16), residues: 2952 helix: 2.30 (0.17), residues: 1048 sheet: -1.56 (0.21), residues: 448 loop : -0.94 (0.17), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 210 TYR 0.015 0.001 TYR C 354 PHE 0.006 0.001 PHE E 329 TRP 0.004 0.001 TRP H 46 HIS 0.005 0.001 HIS A 61 Details of bonding type rmsd covalent geometry : bond 0.00403 (23344) covalent geometry : angle 0.69262 (31808) hydrogen bonds : bond 0.03213 ( 968) hydrogen bonds : angle 4.21932 ( 2744) Misc. bond : bond 0.00082 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13739.35 seconds wall clock time: 232 minutes 18.22 seconds (13938.22 seconds total)