Starting phenix.real_space_refine on Wed Aug 27 00:26:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b14_44068/08_2025/9b14_44068_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b14_44068/08_2025/9b14_44068.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9b14_44068/08_2025/9b14_44068_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b14_44068/08_2025/9b14_44068_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9b14_44068/08_2025/9b14_44068.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b14_44068/08_2025/9b14_44068.map" } resolution = 2.2 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 16 5.49 5 Mg 8 5.21 5 S 120 5.16 5 C 14216 2.51 5 N 4152 2.21 5 O 4312 1.98 5 H 21216 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 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: 44040 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5443 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, 5443 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: 5477 Chain: "B" Number of atoms: 5468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5443 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, 5443 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: 5477 Chain: "C" Number of atoms: 5468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5443 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, 5443 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: 5477 Chain: "D" Number of atoms: 5468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5443 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, 5443 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: 5477 Chain: "E" Number of atoms: 5468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5443 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, 5443 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: 5477 Chain: "F" Number of atoms: 5468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5443 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, 5443 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: 5477 Chain: "G" Number of atoms: 5468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5443 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, 5443 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: 5477 Chain: "H" Number of atoms: 5468 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 368, 5443 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, 5443 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: 5477 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {' MG': 1, 'ADP': 1, 'CRN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N AARG A 151 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG A 151 " occ=0.50 residue: pdb=" N AARG B 151 " occ=0.52 ... (46 atoms not shown) pdb="HH22BARG B 151 " occ=0.48 residue: pdb=" N AARG C 151 " occ=0.52 ... (46 atoms not shown) pdb="HH22BARG C 151 " occ=0.48 residue: pdb=" N AARG D 151 " occ=0.52 ... (46 atoms not shown) pdb="HH22BARG D 151 " occ=0.48 residue: pdb=" N AARG E 151 " occ=0.52 ... (46 atoms not shown) pdb="HH22BARG E 151 " occ=0.48 residue: pdb=" N AARG F 151 " occ=0.52 ... (46 atoms not shown) pdb="HH22BARG F 151 " occ=0.48 residue: pdb=" N AARG G 151 " occ=0.52 ... (46 atoms not shown) pdb="HH22BARG G 151 " occ=0.48 residue: pdb=" N AARG H 151 " occ=0.51 ... (46 atoms not shown) pdb="HH22BARG H 151 " occ=0.49 Time building chain proxies: 11.31, per 1000 atoms: 0.26 Number of scatterers: 44040 At special positions: 0 Unit cell: (154.28, 154.28, 96.824, 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 16 15.00 Mg 8 11.99 O 4312 8.00 N 4152 7.00 C 14216 6.00 H 21216 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=0, symmetry=0 Time building additional restraints: 3.34 Conformation dependent library (CDL) restraints added in 1.8 seconds Enol-peptide restraints added in 476.8 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 44.5% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 removed outlier: 3.774A 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: 5.053A pdb=" N THR A 54 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 5.361A 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 107 through 111 removed outlier: 3.589A pdb=" N LYS A 110 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE A 111 " --> pdb=" O ALA A 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 107 through 111' 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: 3.729A 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: 3.844A pdb=" N ARG A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 removed outlier: 3.597A pdb=" N LEU A 282 " --> pdb=" O PRO A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 302 through 310 removed outlier: 3.586A pdb=" N ILE A 306 " --> pdb=" O ARG A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 359 Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.769A 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: 5.056A pdb=" N THR B 54 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 5.347A 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 107 through 111 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: 3.660A 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 201 Processing helix chain 'B' and resid 240 through 262 removed outlier: 3.850A pdb=" N ARG B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 removed outlier: 3.606A pdb=" N LEU B 282 " --> pdb=" O PRO B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 300 removed outlier: 3.509A pdb=" N ASP B 300 " --> pdb=" O LEU B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 310 removed outlier: 3.585A pdb=" N ILE B 306 " --> pdb=" O ARG B 302 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 359 Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.772A 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: 5.053A pdb=" N THR C 54 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 5.350A 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 107 through 111 removed outlier: 3.616A pdb=" N LYS C 110 " --> pdb=" O ASP C 107 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE C 111 " --> pdb=" O ALA C 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 107 through 111' 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: 3.588A 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 201 Processing helix chain 'C' and resid 240 through 262 removed outlier: 3.827A pdb=" N ARG C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 removed outlier: 3.600A pdb=" N LEU C 282 " --> pdb=" O PRO C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 298 removed outlier: 4.032A pdb=" N LEU C 297 " --> pdb=" O LYS C 293 " (cutoff:3.500A) removed outlier: 3.659A 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 310 removed outlier: 3.589A pdb=" N ILE C 306 " --> pdb=" O ARG C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 360 removed outlier: 3.504A pdb=" N ARG C 360 " --> pdb=" O ILE C 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 removed outlier: 3.774A 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: 5.044A pdb=" N THR D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 5.367A 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 107 through 111 removed outlier: 3.594A pdb=" N LYS D 110 " --> pdb=" O ASP D 107 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE D 111 " --> pdb=" O ALA D 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 107 through 111' 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: 3.782A 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 201 Processing helix chain 'D' and resid 240 through 262 removed outlier: 3.839A pdb=" N ARG D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 removed outlier: 3.572A pdb=" N LEU D 282 " --> pdb=" O PRO D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 298 removed outlier: 4.221A pdb=" N LEU D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) removed outlier: 3.929A 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 310 removed outlier: 3.590A pdb=" N ILE D 306 " --> pdb=" O ARG D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 358 Processing helix chain 'E' and resid 10 through 15 removed outlier: 3.772A 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: 5.054A pdb=" N THR E 54 " --> pdb=" O GLN E 50 " (cutoff:3.500A) removed outlier: 5.359A 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 107 through 111 removed outlier: 3.625A pdb=" N LYS E 110 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ILE E 111 " --> pdb=" O ALA E 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 107 through 111' 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: 3.616A 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 201 Processing helix chain 'E' and resid 240 through 262 removed outlier: 3.856A pdb=" N ARG E 262 " --> pdb=" O LEU E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 282 removed outlier: 3.573A pdb=" N LEU E 282 " --> pdb=" O PRO E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 296 through 300 Processing helix chain 'E' and resid 302 through 310 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: 3.771A 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: 5.049A pdb=" N THR F 54 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 5.357A 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 107 through 112 removed outlier: 3.813A pdb=" N ARG F 112 " --> pdb=" O SER F 109 " (cutoff:3.500A) 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: 3.642A 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 201 Processing helix chain 'F' and resid 240 through 262 removed outlier: 3.837A pdb=" N ARG F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 282 removed outlier: 3.570A pdb=" N LEU F 282 " --> pdb=" O PRO F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 300 Processing helix chain 'F' and resid 302 through 310 removed outlier: 3.576A pdb=" N ILE F 306 " --> pdb=" O ARG F 302 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 358 Processing helix chain 'G' and resid 10 through 15 removed outlier: 3.774A 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: 5.054A pdb=" N THR G 54 " --> pdb=" O GLN G 50 " (cutoff:3.500A) removed outlier: 5.364A 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 107 through 112 removed outlier: 3.778A pdb=" N ARG G 112 " --> pdb=" O SER G 109 " (cutoff:3.500A) 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: 3.637A 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: 3.846A pdb=" N ARG G 262 " --> pdb=" O LEU G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 282 removed outlier: 3.571A pdb=" N LEU G 282 " --> pdb=" O PRO G 279 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 310 removed outlier: 3.542A pdb=" N ILE G 306 " --> pdb=" O ARG G 302 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 359 Processing helix chain 'H' and resid 10 through 15 removed outlier: 3.770A 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: 5.058A pdb=" N THR H 54 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 5.361A 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 107 through 111 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: 3.728A 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: 3.844A pdb=" N ARG H 262 " --> pdb=" O LEU H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 282 removed outlier: 3.588A pdb=" N LEU H 282 " --> pdb=" O PRO H 279 " (cutoff:3.500A) Processing helix chain 'H' and resid 302 through 310 removed outlier: 3.584A pdb=" N ILE H 306 " --> pdb=" O ARG H 302 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 359 Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 170 removed outlier: 5.747A pdb=" N PHE A 220 " --> pdb=" O ASN A 215 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A 123 " --> pdb=" O HIS A 291 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N ALA A 288 " --> pdb=" O ASN A 333 " (cutoff:3.500A) removed outlier: 3.601A 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: 5.752A pdb=" N PHE B 220 " --> pdb=" O ASN B 215 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER B 123 " --> pdb=" O HIS B 291 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ALA B 288 " --> pdb=" O ASN B 333 " (cutoff:3.500A) removed outlier: 3.552A 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: 5.729A pdb=" N PHE C 220 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N SER C 123 " --> pdb=" O HIS C 291 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ALA C 288 " --> pdb=" O ASN C 333 " (cutoff:3.500A) removed outlier: 3.589A 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: 5.724A pdb=" N PHE D 220 " --> pdb=" O ASN D 215 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N ALA D 288 " --> pdb=" O ASN D 333 " (cutoff:3.500A) removed outlier: 3.541A 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: 5.753A pdb=" N PHE E 220 " --> pdb=" O ASN E 215 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N SER E 123 " --> pdb=" O HIS E 291 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ALA E 288 " --> pdb=" O ASN E 333 " (cutoff:3.500A) removed outlier: 3.585A 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: 5.753A pdb=" N PHE F 220 " --> pdb=" O ASN F 215 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N SER F 123 " --> pdb=" O HIS F 291 " (cutoff:3.500A) removed outlier: 6.061A pdb=" N ALA F 288 " --> pdb=" O ASN F 333 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN F 333 " --> pdb=" O ALA F 288 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N PHE F 329 " --> pdb=" O ILE F 292 " (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: 5.747A pdb=" N PHE G 220 " --> pdb=" O ASN G 215 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER G 123 " --> pdb=" O HIS G 291 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N ALA G 288 " --> pdb=" O ASN G 333 " (cutoff:3.500A) removed outlier: 3.539A 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: 5.746A pdb=" N PHE H 220 " --> pdb=" O ASN H 215 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N ALA H 288 " --> pdb=" O ASN H 333 " (cutoff:3.500A) removed outlier: 3.556A 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 269 984 hydrogen bonds defined for protein. 2780 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: 9.34 Time building geometry restraints manager: 4.34 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: 21160 1.03 - 1.23: 66 1.23 - 1.42: 9912 1.42 - 1.62: 13206 1.62 - 1.81: 184 Bond restraints: 44528 Sorted by residual: bond pdb=" C4 ADP A 402 " pdb=" C5 ADP A 402 " ideal model delta sigma weight residual 1.490 1.463 0.027 2.00e-02 2.50e+03 1.84e+00 bond pdb=" C4 ADP H 402 " pdb=" C5 ADP H 402 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.74e+00 bond pdb=" C4 ADP C 402 " pdb=" C5 ADP C 402 " ideal model delta sigma weight residual 1.490 1.464 0.026 2.00e-02 2.50e+03 1.74e+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 1.70e+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 ... (remaining 44523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.28: 76662 1.28 - 2.56: 2835 2.56 - 3.84: 282 3.84 - 5.12: 74 5.12 - 6.40: 43 Bond angle restraints: 79896 Sorted by residual: angle pdb=" N LEU H 296 " pdb=" CA LEU H 296 " pdb=" CB LEU H 296 " ideal model delta sigma weight residual 114.17 110.28 3.89 1.14e+00 7.69e-01 1.16e+01 angle pdb=" N LEU G 296 " pdb=" CA LEU G 296 " pdb=" CB LEU G 296 " ideal model delta sigma weight residual 114.17 110.47 3.70 1.14e+00 7.69e-01 1.05e+01 angle pdb=" N GLY A 319 " pdb=" CA GLY A 319 " pdb=" C GLY A 319 " ideal model delta sigma weight residual 112.04 115.24 -3.20 1.02e+00 9.61e-01 9.85e+00 angle pdb=" N SER E 123 " pdb=" CA SER E 123 " pdb=" C SER E 123 " ideal model delta sigma weight residual 108.52 112.39 -3.87 1.52e+00 4.33e-01 6.49e+00 angle pdb=" N SER D 123 " pdb=" CA SER D 123 " pdb=" C SER D 123 " ideal model delta sigma weight residual 108.52 112.18 -3.66 1.52e+00 4.33e-01 5.80e+00 ... (remaining 79891 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.93: 18640 15.93 - 31.86: 1584 31.86 - 47.79: 561 47.79 - 63.72: 225 63.72 - 79.64: 38 Dihedral angle restraints: 21048 sinusoidal: 11248 harmonic: 9800 Sorted by residual: dihedral pdb=" CA VAL G 290 " pdb=" C VAL G 290 " pdb=" N HIS G 291 " pdb=" CA HIS G 291 " ideal model delta harmonic sigma weight residual 180.00 157.55 22.45 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA VAL F 290 " pdb=" C VAL F 290 " pdb=" N HIS F 291 " pdb=" CA HIS F 291 " ideal model delta harmonic sigma weight residual 180.00 157.65 22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" C5' ADP A 402 " pdb=" O5' ADP A 402 " pdb=" PA ADP A 402 " pdb=" O2A ADP A 402 " ideal model delta sinusoidal sigma weight residual -60.00 19.65 -79.64 1 2.00e+01 2.50e-03 1.97e+01 ... (remaining 21045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1970 0.025 - 0.051: 956 0.051 - 0.076: 346 0.076 - 0.102: 144 0.102 - 0.127: 96 Chirality restraints: 3512 Sorted by residual: chirality pdb=" CA ILE C 233 " pdb=" N ILE C 233 " pdb=" C ILE C 233 " pdb=" CB ILE C 233 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA ILE H 233 " pdb=" N ILE H 233 " pdb=" C ILE H 233 " pdb=" CB ILE H 233 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 chirality pdb=" CA ILE E 233 " pdb=" N ILE E 233 " pdb=" C ILE E 233 " pdb=" CB ILE E 233 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.99e-01 ... (remaining 3509 not shown) Planarity restraints: 6992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS C 61 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO C 62 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO C 62 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 62 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 61 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO B 62 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO B 62 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 62 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 61 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO F 62 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO F 62 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO F 62 " 0.023 5.00e-02 4.00e+02 ... (remaining 6989 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 2535 2.19 - 2.79: 87684 2.79 - 3.39: 124517 3.39 - 4.00: 168724 4.00 - 4.60: 260360 Nonbonded interactions: 643820 Sorted by model distance: nonbonded pdb=" O ARG E 112 " pdb=" HG SER E 113 " model vdw 1.584 2.450 nonbonded pdb=" OE1 GLU E 270 " pdb=" H GLU E 270 " model vdw 1.592 2.450 nonbonded pdb=" O ARG H 112 " pdb=" HG SER H 113 " model vdw 1.618 2.450 nonbonded pdb=" OE1 GLU G 270 " pdb=" H GLU G 270 " model vdw 1.634 2.450 nonbonded pdb=" OE1 GLU H 270 " pdb=" H GLU H 270 " model vdw 1.634 2.450 ... (remaining 643815 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 150 or resid 153 through 403)) selection = (chain 'B' and (resid 3 through 150 or resid 153 through 403)) selection = (chain 'C' and (resid 3 through 150 or resid 153 through 403)) selection = (chain 'D' and (resid 3 through 150 or resid 153 through 403)) selection = (chain 'E' and (resid 3 through 150 or resid 153 through 403)) selection = (chain 'F' and (resid 3 through 150 or resid 153 through 403)) selection = (chain 'G' and (resid 3 through 150 or resid 153 through 403)) selection = (chain 'H' and (resid 3 through 150 or resid 153 through 403)) } 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=0.48 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: 1.210 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: 0.230 Extract box with map and model: 0.440 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 39.620 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.120 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:7.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 23312 Z= 0.147 Angle : 0.613 6.404 31760 Z= 0.301 Chirality : 0.039 0.127 3512 Planarity : 0.004 0.042 4176 Dihedral : 15.593 79.645 8384 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.64 % Favored : 94.19 % Rotamer: Outliers : 0.44 % Allowed : 16.49 % Favored : 83.07 % 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: 0.16 (0.15), residues: 2952 helix: 2.00 (0.16), residues: 1064 sheet: -1.07 (0.19), residues: 432 loop : -0.97 (0.16), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 7 TYR 0.004 0.001 TYR E 274 PHE 0.006 0.001 PHE A 189 TRP 0.006 0.001 TRP A 46 HIS 0.005 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00330 (23312) covalent geometry : angle 0.61345 (31760) hydrogen bonds : bond 0.10712 ( 984) hydrogen bonds : angle 5.16045 ( 2780) *********************** 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 186 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 176 time to evaluate : 1.008 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 10 residues processed: 186 average time/residue: 1.1271 time to fit residues: 241.6712 Evaluate side-chains 186 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 176 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 CYS Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 362 LEU Chi-restraints excluded: chain H residue 104 THR 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: 4.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 4.9990 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 260 GLN B 260 GLN C 260 GLN D 260 GLN E 260 GLN F 260 GLN G 260 GLN H 260 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.088622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.063317 restraints weight = 221345.769| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.61 r_work: 0.2639 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.0422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 23312 Z= 0.263 Angle : 0.651 6.929 31760 Z= 0.324 Chirality : 0.043 0.122 3512 Planarity : 0.005 0.046 4176 Dihedral : 6.514 79.012 3403 Min Nonbonded Distance : 1.758 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 6.42 % Favored : 93.41 % Rotamer: Outliers : 0.92 % Allowed : 16.14 % Favored : 82.94 % 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: -0.06 (0.15), residues: 2952 helix: 2.15 (0.16), residues: 1024 sheet: -0.98 (0.20), residues: 432 loop : -1.36 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 315 TYR 0.006 0.001 TYR E 120 PHE 0.007 0.001 PHE B 303 TRP 0.008 0.001 TRP E 46 HIS 0.007 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00595 (23312) covalent geometry : angle 0.65073 (31760) hydrogen bonds : bond 0.04428 ( 984) hydrogen bonds : angle 4.74451 ( 2780) *********************** 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 205 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 1.200 Fit side-chains outliers start: 21 outliers final: 15 residues processed: 196 average time/residue: 1.1318 time to fit residues: 259.0385 Evaluate side-chains 190 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 175 time to evaluate : 1.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain C residue 100 MET Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain E residue 100 MET Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 104 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 246 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 207 optimal weight: 1.9990 chunk 224 optimal weight: 2.9990 chunk 208 optimal weight: 1.9990 chunk 233 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 275 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 chunk 205 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN B 260 GLN C 260 GLN D 260 GLN E 260 GLN F 260 GLN G 260 GLN H 260 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.089359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.063722 restraints weight = 212283.367| |-----------------------------------------------------------------------------| r_work (start): 0.2811 rms_B_bonded: 3.65 r_work: 0.2667 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2673 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2673 r_free = 0.2673 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2673 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23312 Z= 0.152 Angle : 0.616 6.696 31760 Z= 0.302 Chirality : 0.041 0.124 3512 Planarity : 0.004 0.044 4176 Dihedral : 6.240 74.708 3400 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.70 % Favored : 94.16 % Rotamer: Outliers : 0.75 % Allowed : 16.32 % Favored : 82.94 % 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 (0.15), residues: 2952 helix: 2.33 (0.16), residues: 1024 sheet: -1.00 (0.20), residues: 432 loop : -1.39 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 243 TYR 0.009 0.001 TYR C 354 PHE 0.006 0.001 PHE C 189 TRP 0.006 0.001 TRP B 46 HIS 0.005 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00343 (23312) covalent geometry : angle 0.61629 (31760) hydrogen bonds : bond 0.03805 ( 984) hydrogen bonds : angle 4.59971 ( 2780) *********************** 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 200 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 183 time to evaluate : 1.200 Fit side-chains REVERT: A 78 GLU cc_start: 0.8994 (tt0) cc_final: 0.8755 (tm-30) REVERT: B 40 LYS cc_start: 0.9140 (mttp) cc_final: 0.8674 (mttt) REVERT: D 78 GLU cc_start: 0.8973 (tt0) cc_final: 0.8730 (tm-30) REVERT: G 78 GLU cc_start: 0.8976 (tt0) cc_final: 0.8746 (tm-30) outliers start: 17 outliers final: 8 residues processed: 199 average time/residue: 1.3689 time to fit residues: 316.8593 Evaluate side-chains 185 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 177 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 104 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 11 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 269 optimal weight: 7.9990 chunk 212 optimal weight: 7.9990 chunk 230 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 143 optimal weight: 8.9990 chunk 220 optimal weight: 2.9990 chunk 167 optimal weight: 6.9990 chunk 209 optimal weight: 0.0570 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN B 260 GLN C 260 GLN D 260 GLN E 260 GLN F 260 GLN G 260 GLN H 260 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.088262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.062873 restraints weight = 210113.264| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 3.58 r_work: 0.2649 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2653 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2653 r_free = 0.2653 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2653 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.0649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 23312 Z= 0.229 Angle : 0.633 6.440 31760 Z= 0.312 Chirality : 0.042 0.123 3512 Planarity : 0.005 0.046 4176 Dihedral : 6.329 75.252 3400 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.01 % Favored : 93.85 % Rotamer: Outliers : 1.10 % Allowed : 16.32 % Favored : 82.59 % 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: -0.16 (0.15), residues: 2952 helix: 1.90 (0.16), residues: 1072 sheet: -1.03 (0.20), residues: 432 loop : -1.39 (0.15), residues: 1448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 6 TYR 0.006 0.001 TYR B 77 PHE 0.006 0.001 PHE F 303 TRP 0.007 0.001 TRP B 46 HIS 0.006 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00524 (23312) covalent geometry : angle 0.63309 (31760) hydrogen bonds : bond 0.03953 ( 984) hydrogen bonds : angle 4.63565 ( 2780) *********************** 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 207 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 1.091 Fit side-chains REVERT: C 19 ARG cc_start: 0.9298 (OUTLIER) cc_final: 0.8585 (mtm110) REVERT: D 19 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.8585 (mtm110) REVERT: G 19 ARG cc_start: 0.9299 (OUTLIER) cc_final: 0.8584 (mtm110) outliers start: 25 outliers final: 8 residues processed: 199 average time/residue: 1.1962 time to fit residues: 271.7592 Evaluate side-chains 185 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 174 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 104 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 4 optimal weight: 0.9980 chunk 199 optimal weight: 0.6980 chunk 281 optimal weight: 10.0000 chunk 27 optimal weight: 2.9990 chunk 284 optimal weight: 0.9980 chunk 261 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 255 optimal weight: 3.9990 chunk 163 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 139 optimal weight: 6.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN B 260 GLN C 260 GLN D 260 GLN E 260 GLN F 260 GLN G 260 GLN H 260 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.090273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.064589 restraints weight = 229742.711| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 3.76 r_work: 0.2681 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2688 r_free = 0.2688 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.0717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23312 Z= 0.116 Angle : 0.596 6.245 31760 Z= 0.289 Chirality : 0.040 0.125 3512 Planarity : 0.004 0.042 4176 Dihedral : 5.970 68.340 3400 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.74 % Favored : 94.13 % Rotamer: Outliers : 0.61 % Allowed : 17.28 % Favored : 82.11 % 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: 0.18 (0.15), residues: 2952 helix: 2.53 (0.16), residues: 1024 sheet: -1.04 (0.20), residues: 432 loop : -1.32 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 243 TYR 0.006 0.001 TYR F 120 PHE 0.006 0.001 PHE C 189 TRP 0.005 0.001 TRP E 46 HIS 0.005 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00263 (23312) covalent geometry : angle 0.59565 (31760) hydrogen bonds : bond 0.03388 ( 984) hydrogen bonds : angle 4.45678 ( 2780) *********************** 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 194 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 180 time to evaluate : 0.884 Fit side-chains REVERT: A 78 GLU cc_start: 0.8961 (tt0) cc_final: 0.8746 (tm-30) REVERT: C 78 GLU cc_start: 0.9011 (tt0) cc_final: 0.8767 (tm-30) REVERT: D 78 GLU cc_start: 0.9001 (tt0) cc_final: 0.8758 (tm-30) REVERT: E 78 GLU cc_start: 0.9001 (tt0) cc_final: 0.8756 (tm-30) REVERT: G 78 GLU cc_start: 0.8999 (tt0) cc_final: 0.8796 (tm-30) REVERT: H 78 GLU cc_start: 0.9004 (tt0) cc_final: 0.8763 (tm-30) outliers start: 14 outliers final: 8 residues processed: 193 average time/residue: 1.0441 time to fit residues: 234.4863 Evaluate side-chains 184 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 176 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 104 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 87 optimal weight: 3.9990 chunk 139 optimal weight: 6.9990 chunk 270 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 97 optimal weight: 1.9990 chunk 225 optimal weight: 0.7980 chunk 246 optimal weight: 0.7980 chunk 140 optimal weight: 3.9990 chunk 265 optimal weight: 1.9990 chunk 108 optimal weight: 0.0370 chunk 193 optimal weight: 2.9990 overall best weight: 1.1262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN B 260 GLN C 260 GLN D 260 GLN E 260 GLN F 260 GLN G 260 GLN H 260 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.090547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.065146 restraints weight = 212202.242| |-----------------------------------------------------------------------------| r_work (start): 0.2836 rms_B_bonded: 3.63 r_work: 0.2693 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.0837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 23312 Z= 0.121 Angle : 0.588 6.043 31760 Z= 0.285 Chirality : 0.040 0.125 3512 Planarity : 0.004 0.041 4176 Dihedral : 5.847 64.418 3400 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.67 % Favored : 94.19 % Rotamer: Outliers : 0.61 % Allowed : 17.19 % Favored : 82.19 % 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: 0.26 (0.15), residues: 2952 helix: 2.59 (0.16), residues: 1024 sheet: -1.09 (0.20), residues: 432 loop : -1.23 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 6 TYR 0.005 0.001 TYR B 77 PHE 0.005 0.001 PHE F 303 TRP 0.005 0.001 TRP B 46 HIS 0.006 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00273 (23312) covalent geometry : angle 0.58825 (31760) hydrogen bonds : bond 0.03297 ( 984) hydrogen bonds : angle 4.40589 ( 2780) *********************** 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 195 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 181 time to evaluate : 1.156 Fit side-chains REVERT: A 19 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.8575 (mtm110) REVERT: B 78 GLU cc_start: 0.8989 (tt0) cc_final: 0.8744 (tm-30) REVERT: C 78 GLU cc_start: 0.8990 (tt0) cc_final: 0.8749 (tm-30) REVERT: D 78 GLU cc_start: 0.8976 (tt0) cc_final: 0.8735 (tm-30) REVERT: E 19 ARG cc_start: 0.9275 (OUTLIER) cc_final: 0.8556 (mtm110) REVERT: E 78 GLU cc_start: 0.9011 (tt0) cc_final: 0.8759 (tm-30) REVERT: F 19 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.8573 (mtm110) REVERT: H 19 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.8567 (mtm110) REVERT: H 78 GLU cc_start: 0.8981 (tt0) cc_final: 0.8742 (tm-30) outliers start: 14 outliers final: 7 residues processed: 194 average time/residue: 1.4323 time to fit residues: 317.9126 Evaluate side-chains 186 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 175 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 104 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 215 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 249 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 262 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN B 260 GLN C 260 GLN D 260 GLN E 260 GLN F 260 GLN G 260 GLN H 260 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.088969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.063539 restraints weight = 217419.393| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 3.63 r_work: 0.2659 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 23312 Z= 0.198 Angle : 0.614 6.327 31760 Z= 0.300 Chirality : 0.041 0.125 3512 Planarity : 0.004 0.044 4176 Dihedral : 6.047 68.832 3399 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.45 % Favored : 93.41 % Rotamer: Outliers : 0.96 % Allowed : 16.80 % Favored : 82.24 % 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: 0.13 (0.15), residues: 2952 helix: 2.46 (0.16), residues: 1024 sheet: -1.08 (0.20), residues: 432 loop : -1.31 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 6 TYR 0.005 0.001 TYR A 77 PHE 0.007 0.001 PHE F 303 TRP 0.006 0.001 TRP B 46 HIS 0.006 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00453 (23312) covalent geometry : angle 0.61370 (31760) hydrogen bonds : bond 0.03658 ( 984) hydrogen bonds : angle 4.49249 ( 2780) *********************** 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 200 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 1.245 Fit side-chains REVERT: A 19 ARG cc_start: 0.9294 (OUTLIER) cc_final: 0.8585 (mtm110) REVERT: B 19 ARG cc_start: 0.9271 (OUTLIER) cc_final: 0.8549 (mtm110) REVERT: E 19 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.8569 (mtm110) REVERT: F 19 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.8582 (mtm110) REVERT: H 19 ARG cc_start: 0.9300 (OUTLIER) cc_final: 0.8589 (mtm110) outliers start: 22 outliers final: 7 residues processed: 192 average time/residue: 1.6710 time to fit residues: 364.4412 Evaluate side-chains 187 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 175 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 104 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 287 optimal weight: 8.9990 chunk 187 optimal weight: 3.9990 chunk 257 optimal weight: 2.9990 chunk 11 optimal weight: 6.9990 chunk 246 optimal weight: 0.5980 chunk 196 optimal weight: 5.9990 chunk 170 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 211 optimal weight: 5.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN B 260 GLN C 260 GLN D 260 GLN E 260 GLN F 260 GLN G 260 GLN H 260 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.088874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.063539 restraints weight = 206340.835| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 3.57 r_work: 0.2662 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2669 r_free = 0.2669 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 23312 Z= 0.191 Angle : 0.612 6.240 31760 Z= 0.300 Chirality : 0.041 0.124 3512 Planarity : 0.004 0.044 4176 Dihedral : 6.096 69.274 3399 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.84 % Favored : 94.02 % Rotamer: Outliers : 1.10 % Allowed : 16.75 % Favored : 82.15 % 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: 0.09 (0.15), residues: 2952 helix: 2.42 (0.16), residues: 1024 sheet: -1.08 (0.20), residues: 432 loop : -1.33 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 243 TYR 0.011 0.001 TYR C 354 PHE 0.006 0.001 PHE F 303 TRP 0.006 0.001 TRP B 46 HIS 0.006 0.001 HIS H 214 Details of bonding type rmsd covalent geometry : bond 0.00434 (23312) covalent geometry : angle 0.61186 (31760) hydrogen bonds : bond 0.03670 ( 984) hydrogen bonds : angle 4.49418 ( 2780) *********************** 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 201 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 1.323 Fit side-chains REVERT: A 19 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.8577 (mtm110) REVERT: A 78 GLU cc_start: 0.9046 (tt0) cc_final: 0.8787 (tm-30) REVERT: B 19 ARG cc_start: 0.9271 (OUTLIER) cc_final: 0.8551 (mtm110) REVERT: C 19 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.8573 (mtm110) REVERT: D 19 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.8576 (mtm110) REVERT: D 218 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8756 (mtpt) REVERT: E 19 ARG cc_start: 0.9270 (OUTLIER) cc_final: 0.8561 (mtm110) REVERT: F 19 ARG cc_start: 0.9297 (OUTLIER) cc_final: 0.8586 (mtm110) REVERT: G 19 ARG cc_start: 0.9291 (OUTLIER) cc_final: 0.8582 (mtm110) REVERT: H 19 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.8580 (mtm110) outliers start: 25 outliers final: 7 residues processed: 193 average time/residue: 1.7648 time to fit residues: 385.3445 Evaluate side-chains 191 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 104 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 9 optimal weight: 3.9990 chunk 257 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 256 optimal weight: 0.9980 chunk 195 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 253 optimal weight: 0.8980 chunk 208 optimal weight: 4.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN B 260 GLN C 260 GLN D 260 GLN E 260 GLN F 260 GLN G 260 GLN H 260 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.089595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.064278 restraints weight = 201760.887| |-----------------------------------------------------------------------------| r_work (start): 0.2823 rms_B_bonded: 3.55 r_work: 0.2680 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2686 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2686 r_free = 0.2686 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2686 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23312 Z= 0.146 Angle : 0.598 6.254 31760 Z= 0.291 Chirality : 0.040 0.124 3512 Planarity : 0.004 0.042 4176 Dihedral : 6.004 67.436 3399 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.35 % Favored : 93.51 % Rotamer: Outliers : 0.75 % Allowed : 17.15 % Favored : 82.11 % 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: 0.19 (0.15), residues: 2952 helix: 2.53 (0.16), residues: 1024 sheet: -1.09 (0.20), residues: 432 loop : -1.28 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 243 TYR 0.006 0.001 TYR E 120 PHE 0.005 0.001 PHE C 189 TRP 0.006 0.001 TRP B 46 HIS 0.006 0.001 HIS D 214 Details of bonding type rmsd covalent geometry : bond 0.00330 (23312) covalent geometry : angle 0.59772 (31760) hydrogen bonds : bond 0.03465 ( 984) hydrogen bonds : angle 4.43781 ( 2780) *********************** 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 192 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 1.315 Fit side-chains REVERT: A 19 ARG cc_start: 0.9281 (OUTLIER) cc_final: 0.8568 (mtm110) REVERT: A 78 GLU cc_start: 0.9031 (tt0) cc_final: 0.8774 (tm-30) REVERT: B 19 ARG cc_start: 0.9261 (OUTLIER) cc_final: 0.8540 (mtm110) REVERT: C 19 ARG cc_start: 0.9280 (OUTLIER) cc_final: 0.8566 (mtm110) REVERT: D 19 ARG cc_start: 0.9284 (OUTLIER) cc_final: 0.8569 (mtm110) REVERT: D 78 GLU cc_start: 0.8945 (tt0) cc_final: 0.8712 (tm-30) REVERT: D 218 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8749 (mtpt) REVERT: E 19 ARG cc_start: 0.9273 (OUTLIER) cc_final: 0.8555 (mtm110) REVERT: F 19 ARG cc_start: 0.9288 (OUTLIER) cc_final: 0.8574 (mtm110) REVERT: H 19 ARG cc_start: 0.9293 (OUTLIER) cc_final: 0.8580 (mtm110) REVERT: H 78 GLU cc_start: 0.8953 (tt0) cc_final: 0.8720 (tm-30) outliers start: 17 outliers final: 8 residues processed: 192 average time/residue: 1.7360 time to fit residues: 380.2572 Evaluate side-chains 191 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 175 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 240 optimal weight: 2.9990 chunk 115 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 172 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 269 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 135 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN B 260 GLN C 260 GLN D 260 GLN E 260 GLN F 260 GLN G 260 GLN H 260 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.089356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.063952 restraints weight = 209821.279| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 3.61 r_work: 0.2672 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 23312 Z= 0.165 Angle : 0.602 6.124 31760 Z= 0.294 Chirality : 0.041 0.125 3512 Planarity : 0.004 0.043 4176 Dihedral : 6.021 67.050 3399 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.87 % Favored : 93.99 % Rotamer: Outliers : 0.75 % Allowed : 17.06 % Favored : 82.19 % 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: 0.16 (0.15), residues: 2952 helix: 2.50 (0.16), residues: 1024 sheet: -1.10 (0.20), residues: 432 loop : -1.28 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 243 TYR 0.005 0.001 TYR F 77 PHE 0.006 0.001 PHE F 303 TRP 0.006 0.001 TRP B 46 HIS 0.006 0.001 HIS G 214 Details of bonding type rmsd covalent geometry : bond 0.00377 (23312) covalent geometry : angle 0.60214 (31760) hydrogen bonds : bond 0.03523 ( 984) hydrogen bonds : angle 4.45437 ( 2780) ********************** 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 192 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 1.245 Fit side-chains REVERT: A 19 ARG cc_start: 0.9282 (OUTLIER) cc_final: 0.8568 (mtm110) REVERT: A 78 GLU cc_start: 0.9033 (tt0) cc_final: 0.8775 (tm-30) REVERT: B 19 ARG cc_start: 0.9267 (OUTLIER) cc_final: 0.8545 (mtm110) REVERT: C 19 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.8569 (mtm110) REVERT: D 19 ARG cc_start: 0.9285 (OUTLIER) cc_final: 0.8568 (mtm110) REVERT: D 78 GLU cc_start: 0.8953 (tt0) cc_final: 0.8720 (tm-30) REVERT: D 218 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8754 (mtpt) REVERT: E 19 ARG cc_start: 0.9277 (OUTLIER) cc_final: 0.8558 (mtm110) REVERT: F 19 ARG cc_start: 0.9289 (OUTLIER) cc_final: 0.8575 (mtm110) REVERT: G 19 ARG cc_start: 0.9286 (OUTLIER) cc_final: 0.8571 (mtm110) REVERT: H 19 ARG cc_start: 0.9294 (OUTLIER) cc_final: 0.8580 (mtm110) outliers start: 17 outliers final: 8 residues processed: 192 average time/residue: 1.7024 time to fit residues: 366.6759 Evaluate side-chains 192 residues out of total 2536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ARG Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 19 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 19 ARG Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain E residue 19 ARG Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 19 ARG Chi-restraints excluded: chain H residue 104 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 288 random chunks: chunk 278 optimal weight: 3.9990 chunk 187 optimal weight: 3.9990 chunk 272 optimal weight: 1.9990 chunk 165 optimal weight: 0.9990 chunk 129 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 154 optimal weight: 2.9990 chunk 180 optimal weight: 0.3980 chunk 256 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 260 GLN B 260 GLN C 260 GLN D 260 GLN E 260 GLN F 260 GLN G 260 GLN H 260 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.090034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.064685 restraints weight = 204513.258| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.58 r_work: 0.2686 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 23312 Z= 0.133 Angle : 0.591 6.187 31760 Z= 0.287 Chirality : 0.040 0.124 3512 Planarity : 0.004 0.041 4176 Dihedral : 5.932 65.038 3399 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.25 % Favored : 93.61 % Rotamer: Outliers : 1.10 % Allowed : 16.54 % Favored : 82.37 % 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: 0.24 (0.15), residues: 2952 helix: 2.57 (0.16), residues: 1024 sheet: -1.08 (0.21), residues: 432 loop : -1.24 (0.15), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 243 TYR 0.005 0.001 TYR F 77 PHE 0.005 0.001 PHE C 189 TRP 0.005 0.001 TRP B 46 HIS 0.005 0.001 HIS G 214 Details of bonding type rmsd covalent geometry : bond 0.00298 (23312) covalent geometry : angle 0.59147 (31760) hydrogen bonds : bond 0.03360 ( 984) hydrogen bonds : angle 4.39869 ( 2780) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14428.38 seconds wall clock time: 244 minutes 35.67 seconds (14675.67 seconds total)