Starting phenix.real_space_refine on Sat Mar 7 13:58:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jjp_22358/03_2026/7jjp_22358_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jjp_22358/03_2026/7jjp_22358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jjp_22358/03_2026/7jjp_22358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jjp_22358/03_2026/7jjp_22358.map" model { file = "/net/cci-nas-00/data/ceres_data/7jjp_22358/03_2026/7jjp_22358_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jjp_22358/03_2026/7jjp_22358_trim.cif" } resolution = 1.94 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= 0.001 sd= 0.016 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: 5 Type Number sf(0) Gaussians S 120 5.16 5 C 14832 2.51 5 N 3204 2.21 5 O 3660 1.98 5 H 19104 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40920 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "B" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "C" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "D" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "E" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "F" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "G" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "H" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "I" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "J" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "K" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "L" Number of atoms: 3197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 3197 Classifications: {'peptide': 196} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 188} Chain breaks: 1 Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 15, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 110 Chain: "B" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 15, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 110 Chain: "C" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 15, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 110 Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 15, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 110 Chain: "E" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 15, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 110 Chain: "F" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 15, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 110 Chain: "G" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 15, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 110 Chain: "H" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 15, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 110 Chain: "I" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 15, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 110 Chain: "J" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 15, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 110 Chain: "K" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 15, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 110 Chain: "L" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 180 Unusual residues: {'MC3': 15} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 510 Unresolved non-hydrogen angles: 645 Unresolved non-hydrogen dihedrals: 450 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'MC3:plan-1': 15, 'MC3:plan-2': 15} Unresolved non-hydrogen planarities: 110 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Time building chain proxies: 7.10, per 1000 atoms: 0.17 Number of scatterers: 40920 At special positions: 0 Unit cell: (97.999, 99.297, 165.495, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 O 3660 8.00 N 3204 7.00 C 14832 6.00 H 19104 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 201 " distance=2.04 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 190 " distance=2.04 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 201 " distance=2.04 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 195 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 190 " distance=2.04 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 201 " distance=2.04 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 195 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 190 " distance=2.04 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 201 " distance=2.04 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 195 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 190 " distance=2.04 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 201 " distance=2.04 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 195 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 190 " distance=2.04 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 201 " distance=2.04 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 195 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 190 " distance=2.04 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 201 " distance=2.04 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 195 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 190 " distance=2.04 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 201 " distance=2.04 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 195 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 190 " distance=2.04 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 201 " distance=2.04 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 195 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 190 " distance=2.04 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 201 " distance=2.04 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 195 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 190 " distance=2.04 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 201 " distance=2.04 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 195 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 190 " distance=2.04 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 201 " distance=2.04 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 190 " distance=2.04 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: 4.58 Conformation dependent library (CDL) restraints added in 992.7 milliseconds 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4416 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 12 sheets defined 77.6% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 Creating SS restraints... Processing helix chain 'A' and resid 4 through 16 removed outlier: 4.013A pdb=" N GLU A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 33 removed outlier: 3.508A pdb=" N ARG A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 40 Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 109 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 152 through 181 removed outlier: 3.655A pdb=" N ARG A 156 " --> pdb=" O GLY A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 236 Processing helix chain 'B' and resid 4 through 16 removed outlier: 4.012A pdb=" N GLU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 33 removed outlier: 3.508A pdb=" N ARG B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 40 Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 109 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 152 through 181 removed outlier: 3.655A pdb=" N ARG B 156 " --> pdb=" O GLY B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 236 Processing helix chain 'C' and resid 4 through 16 removed outlier: 4.013A pdb=" N GLU C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 33 removed outlier: 3.509A pdb=" N ARG C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 109 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 152 through 181 removed outlier: 3.654A pdb=" N ARG C 156 " --> pdb=" O GLY C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 236 Processing helix chain 'D' and resid 4 through 16 removed outlier: 4.012A pdb=" N GLU D 16 " --> pdb=" O GLU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 33 removed outlier: 3.508A pdb=" N ARG D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 40 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 73 through 109 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 152 through 181 removed outlier: 3.654A pdb=" N ARG D 156 " --> pdb=" O GLY D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 236 Processing helix chain 'E' and resid 4 through 16 removed outlier: 4.012A pdb=" N GLU E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 33 removed outlier: 3.508A pdb=" N ARG E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 40 Processing helix chain 'E' and resid 40 through 45 Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 73 through 109 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 152 through 181 removed outlier: 3.654A pdb=" N ARG E 156 " --> pdb=" O GLY E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 236 Processing helix chain 'F' and resid 4 through 16 removed outlier: 4.011A pdb=" N GLU F 16 " --> pdb=" O GLU F 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 33 removed outlier: 3.508A pdb=" N ARG F 33 " --> pdb=" O LEU F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 40 Processing helix chain 'F' and resid 40 through 45 Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 73 through 109 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 152 through 181 removed outlier: 3.654A pdb=" N ARG F 156 " --> pdb=" O GLY F 152 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 236 Processing helix chain 'G' and resid 4 through 16 removed outlier: 4.012A pdb=" N GLU G 16 " --> pdb=" O GLU G 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 33 removed outlier: 3.508A pdb=" N ARG G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 40 Processing helix chain 'G' and resid 40 through 45 Processing helix chain 'G' and resid 60 through 70 Processing helix chain 'G' and resid 73 through 109 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 152 through 181 removed outlier: 3.654A pdb=" N ARG G 156 " --> pdb=" O GLY G 152 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 236 Processing helix chain 'H' and resid 4 through 16 removed outlier: 4.012A pdb=" N GLU H 16 " --> pdb=" O GLU H 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 33 removed outlier: 3.508A pdb=" N ARG H 33 " --> pdb=" O LEU H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 40 Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 73 through 109 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 152 through 181 removed outlier: 3.654A pdb=" N ARG H 156 " --> pdb=" O GLY H 152 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 236 Processing helix chain 'I' and resid 4 through 16 removed outlier: 4.012A pdb=" N GLU I 16 " --> pdb=" O GLU I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 33 removed outlier: 3.508A pdb=" N ARG I 33 " --> pdb=" O LEU I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 40 Processing helix chain 'I' and resid 40 through 45 Processing helix chain 'I' and resid 60 through 70 Processing helix chain 'I' and resid 73 through 109 Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 152 through 181 removed outlier: 3.654A pdb=" N ARG I 156 " --> pdb=" O GLY I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 236 Processing helix chain 'J' and resid 4 through 16 removed outlier: 4.012A pdb=" N GLU J 16 " --> pdb=" O GLU J 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 33 removed outlier: 3.508A pdb=" N ARG J 33 " --> pdb=" O LEU J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 40 Processing helix chain 'J' and resid 40 through 45 Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 73 through 109 Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 152 through 181 removed outlier: 3.654A pdb=" N ARG J 156 " --> pdb=" O GLY J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 236 Processing helix chain 'K' and resid 4 through 16 removed outlier: 4.012A pdb=" N GLU K 16 " --> pdb=" O GLU K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 33 removed outlier: 3.508A pdb=" N ARG K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 40 Processing helix chain 'K' and resid 40 through 45 Processing helix chain 'K' and resid 60 through 70 Processing helix chain 'K' and resid 73 through 109 Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 152 through 181 removed outlier: 3.655A pdb=" N ARG K 156 " --> pdb=" O GLY K 152 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 236 Processing helix chain 'L' and resid 4 through 16 removed outlier: 4.012A pdb=" N GLU L 16 " --> pdb=" O GLU L 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 33 removed outlier: 3.508A pdb=" N ARG L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 33 through 40 Processing helix chain 'L' and resid 40 through 45 Processing helix chain 'L' and resid 60 through 70 Processing helix chain 'L' and resid 73 through 109 Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 152 through 181 removed outlier: 3.655A pdb=" N ARG L 156 " --> pdb=" O GLY L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 236 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 1440 hydrogen bonds defined for protein. 4248 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: 9.95 Time building geometry restraints manager: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 19092 1.03 - 1.22: 45 1.22 - 1.42: 8619 1.42 - 1.62: 12972 1.62 - 1.82: 156 Bond restraints: 40884 Sorted by residual: bond pdb=" CG1 ILE B 36 " pdb=" CD1 ILE B 36 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.29e+00 bond pdb=" CG1 ILE L 36 " pdb=" CD1 ILE L 36 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.29e+00 bond pdb=" CG1 ILE F 36 " pdb=" CD1 ILE F 36 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.29e+00 bond pdb=" CG1 ILE C 36 " pdb=" CD1 ILE C 36 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.29e+00 bond pdb=" CG1 ILE K 36 " pdb=" CD1 ILE K 36 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.28e+00 ... (remaining 40879 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 68532 1.69 - 3.38: 3090 3.38 - 5.07: 282 5.07 - 6.77: 27 6.77 - 8.46: 21 Bond angle restraints: 71952 Sorted by residual: angle pdb=" N ALA I 41 " pdb=" CA ALA I 41 " pdb=" C ALA I 41 " ideal model delta sigma weight residual 111.11 114.29 -3.18 1.20e+00 6.94e-01 7.01e+00 angle pdb=" N ALA H 41 " pdb=" CA ALA H 41 " pdb=" C ALA H 41 " ideal model delta sigma weight residual 111.11 114.28 -3.17 1.20e+00 6.94e-01 6.97e+00 angle pdb=" N ALA L 41 " pdb=" CA ALA L 41 " pdb=" C ALA L 41 " ideal model delta sigma weight residual 111.11 114.28 -3.17 1.20e+00 6.94e-01 6.96e+00 angle pdb=" N ALA J 41 " pdb=" CA ALA J 41 " pdb=" C ALA J 41 " ideal model delta sigma weight residual 111.11 114.26 -3.15 1.20e+00 6.94e-01 6.88e+00 angle pdb=" N ALA D 41 " pdb=" CA ALA D 41 " pdb=" C ALA D 41 " ideal model delta sigma weight residual 111.11 114.26 -3.15 1.20e+00 6.94e-01 6.88e+00 ... (remaining 71947 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.80: 17453 15.80 - 31.59: 1671 31.59 - 47.39: 457 47.39 - 63.19: 339 63.19 - 78.98: 48 Dihedral angle restraints: 19968 sinusoidal: 11256 harmonic: 8712 Sorted by residual: dihedral pdb=" CA VAL L 14 " pdb=" C VAL L 14 " pdb=" N ASN L 15 " pdb=" CA ASN L 15 " ideal model delta harmonic sigma weight residual 180.00 159.81 20.19 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA VAL I 14 " pdb=" C VAL I 14 " pdb=" N ASN I 15 " pdb=" CA ASN I 15 " ideal model delta harmonic sigma weight residual 180.00 159.82 20.18 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA VAL E 14 " pdb=" C VAL E 14 " pdb=" N ASN E 15 " pdb=" CA ASN E 15 " ideal model delta harmonic sigma weight residual 180.00 159.83 20.17 0 5.00e+00 4.00e-02 1.63e+01 ... (remaining 19965 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1442 0.043 - 0.086: 1052 0.086 - 0.129: 375 0.129 - 0.172: 142 0.172 - 0.216: 37 Chirality restraints: 3048 Sorted by residual: chirality pdb=" CA ASP C 47 " pdb=" N ASP C 47 " pdb=" C ASP C 47 " pdb=" CB ASP C 47 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ASP D 47 " pdb=" N ASP D 47 " pdb=" C ASP D 47 " pdb=" CB ASP D 47 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 chirality pdb=" CA ASP B 47 " pdb=" N ASP B 47 " pdb=" C ASP B 47 " pdb=" CB ASP B 47 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 3045 not shown) Planarity restraints: 5568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 49 " 0.004 2.00e-02 2.50e+03 2.21e-02 7.31e+00 pdb=" CD GLN A 49 " -0.042 2.00e-02 2.50e+03 pdb=" OE1 GLN A 49 " 0.026 2.00e-02 2.50e+03 pdb=" NE2 GLN A 49 " 0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 49 " 0.020 2.00e-02 2.50e+03 pdb="HE22 GLN A 49 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN J 49 " -0.003 2.00e-02 2.50e+03 2.19e-02 7.21e+00 pdb=" CD GLN J 49 " 0.041 2.00e-02 2.50e+03 pdb=" OE1 GLN J 49 " -0.026 2.00e-02 2.50e+03 pdb=" NE2 GLN J 49 " -0.005 2.00e-02 2.50e+03 pdb="HE21 GLN J 49 " -0.019 2.00e-02 2.50e+03 pdb="HE22 GLN J 49 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 10 " -0.013 2.00e-02 2.50e+03 2.59e-02 6.68e+00 pdb=" C ILE H 10 " 0.045 2.00e-02 2.50e+03 pdb=" O ILE H 10 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU H 11 " -0.015 2.00e-02 2.50e+03 ... (remaining 5565 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 4561 2.25 - 2.83: 84667 2.83 - 3.42: 107244 3.42 - 4.01: 151240 4.01 - 4.60: 230875 Nonbonded interactions: 578587 Sorted by model distance: nonbonded pdb=" HG1 THR D 56 " pdb=" O HOH D 607 " model vdw 1.657 2.450 nonbonded pdb=" HG1 THR C 56 " pdb=" O HOH C 607 " model vdw 1.657 2.450 nonbonded pdb=" HG1 THR F 56 " pdb=" O HOH F 607 " model vdw 1.658 2.450 nonbonded pdb=" HG1 THR E 56 " pdb=" O HOH E 607 " model vdw 1.659 2.450 nonbonded pdb=" HG1 THR L 56 " pdb=" O HOH L 607 " model vdw 1.660 2.450 ... (remaining 578582 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 2 through 236 or (resid 503 and (name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23)) or (resid 504 and (name C13 or name C14 or \ name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C2 \ 1 or name C22 or name C23 or name C24)) or (resid 506 through 507 and (name C15 \ or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name \ C22 or name C23 or name C24)) or resid 509 through 512 or resid 514 through 515) \ ) selection = (chain 'B' and (resid 2 through 236 or resid 503 through 504 or resid 506 throug \ h 507 or resid 509 through 510 or (resid 511 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23)) or resid 512 or resid 514 through 515)) selection = (chain 'C' and (resid 2 through 236 or resid 503 through 504 or resid 506 throug \ h 507 or resid 509 through 510 or (resid 511 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23)) or resid 512 or resid 514 through 515)) selection = (chain 'D' and (resid 2 through 236 or resid 503 through 504 or resid 506 throug \ h 507 or resid 509 through 510 or (resid 511 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23)) or resid 512 or resid 514 through 515)) selection = (chain 'E' and (resid 2 through 236 or resid 503 through 504 or resid 506 throug \ h 507 or resid 509 through 510 or (resid 511 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23)) or resid 512 or resid 514 through 515)) selection = (chain 'F' and (resid 2 through 236 or resid 503 through 504 or resid 506 throug \ h 507 or resid 509 through 510 or (resid 511 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23)) or resid 512 or resid 514 through 515)) selection = (chain 'G' and (resid 2 through 236 or (resid 503 and (name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23)) or (resid 504 and (name C13 or name C14 or \ name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C2 \ 1 or name C22 or name C23 or name C24)) or (resid 506 through 507 and (name C15 \ or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or name \ C22 or name C23 or name C24)) or resid 509 through 512 or resid 514 through 515) \ ) selection = (chain 'H' and (resid 2 through 236 or resid 503 through 504 or resid 506 throug \ h 507 or resid 509 through 510 or (resid 511 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23)) or resid 512 or resid 514 through 515)) selection = (chain 'I' and (resid 2 through 236 or resid 503 through 504 or resid 506 throug \ h 507 or resid 509 through 510 or (resid 511 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23)) or resid 512 or resid 514 through 515)) selection = (chain 'J' and (resid 2 through 236 or resid 503 through 504 or resid 506 throug \ h 507 or resid 509 through 510 or (resid 511 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23)) or resid 512 or resid 514 through 515)) selection = (chain 'K' and (resid 2 through 236 or resid 503 through 504 or resid 506 throug \ h 507 or resid 509 through 510 or (resid 511 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23)) or resid 512 or resid 514 through 515)) selection = (chain 'L' and (resid 2 through 236 or resid 503 through 504 or resid 506 throug \ h 507 or resid 509 through 510 or (resid 511 and (name C12 or name C13 or name C \ 14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or na \ me C21 or name C22 or name C23)) or resid 512 or resid 514 through 515)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 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: 0.220 Extract box with map and model: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 35.770 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 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:8.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 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 : 0.011 0.073 21816 Z= 0.438 Angle : 0.876 8.458 28776 Z= 0.457 Chirality : 0.067 0.216 3048 Planarity : 0.006 0.026 3324 Dihedral : 13.339 61.154 8580 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 0.56 % Allowed : 6.56 % Favored : 92.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.16), residues: 2304 helix: 0.85 (0.12), residues: 1752 sheet: -0.86 (0.30), residues: 204 loop : -1.67 (0.26), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG C 189 TYR 0.017 0.003 TYR L 66 PHE 0.028 0.004 PHE I 84 TRP 0.030 0.004 TRP E 193 HIS 0.007 0.002 HIS F 95 Details of bonding type rmsd covalent geometry : bond 0.01146 (21780) covalent geometry : angle 0.87346 (28704) SS BOND : bond 0.00602 ( 36) SS BOND : angle 1.61665 ( 72) hydrogen bonds : bond 0.08996 ( 1440) hydrogen bonds : angle 5.33642 ( 4248) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 324 time to evaluate : 1.028 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 12 residues processed: 335 average time/residue: 1.2779 time to fit residues: 484.8951 Evaluate side-chains 300 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 288 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 30.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.167560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.110617 restraints weight = 48250.035| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.18 r_work: 0.3163 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 2.66 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 21816 Z= 0.121 Angle : 0.534 5.068 28776 Z= 0.285 Chirality : 0.039 0.119 3048 Planarity : 0.004 0.041 3324 Dihedral : 6.699 55.701 4188 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.02 % Allowed : 7.59 % Favored : 91.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.17), residues: 2304 helix: 2.33 (0.12), residues: 1752 sheet: -0.03 (0.36), residues: 132 loop : -1.06 (0.24), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 101 TYR 0.014 0.002 TYR J 66 PHE 0.015 0.002 PHE J 212 TRP 0.007 0.001 TRP K 193 HIS 0.003 0.001 HIS H 176 Details of bonding type rmsd covalent geometry : bond 0.00239 (21780) covalent geometry : angle 0.53134 (28704) SS BOND : bond 0.00150 ( 36) SS BOND : angle 1.21464 ( 72) hydrogen bonds : bond 0.04648 ( 1440) hydrogen bonds : angle 4.60509 ( 4248) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 303 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 13 GLU cc_start: 0.7685 (tt0) cc_final: 0.7149 (mt-10) REVERT: J 13 GLU cc_start: 0.7791 (tt0) cc_final: 0.7242 (mt-10) REVERT: K 13 GLU cc_start: 0.7670 (tt0) cc_final: 0.7006 (mt-10) outliers start: 22 outliers final: 13 residues processed: 317 average time/residue: 1.3178 time to fit residues: 472.6555 Evaluate side-chains 310 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 297 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 127 optimal weight: 0.9990 chunk 221 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 224 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 108 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 138 optimal weight: 4.9990 chunk 144 optimal weight: 2.9990 chunk 189 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 GLN E 58 GLN F 58 GLN H 58 GLN I 58 GLN L 58 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.164963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.107079 restraints weight = 47839.106| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.18 r_work: 0.3110 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 21816 Z= 0.138 Angle : 0.524 4.168 28776 Z= 0.278 Chirality : 0.040 0.122 3048 Planarity : 0.004 0.051 3324 Dihedral : 6.438 55.428 4188 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.35 % Allowed : 7.91 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.17), residues: 2304 helix: 2.81 (0.12), residues: 1752 sheet: -0.29 (0.34), residues: 132 loop : -0.98 (0.25), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 33 TYR 0.017 0.002 TYR G 66 PHE 0.020 0.002 PHE J 212 TRP 0.007 0.001 TRP A 193 HIS 0.004 0.001 HIS K 161 Details of bonding type rmsd covalent geometry : bond 0.00309 (21780) covalent geometry : angle 0.52191 (28704) SS BOND : bond 0.00360 ( 36) SS BOND : angle 1.07914 ( 72) hydrogen bonds : bond 0.04533 ( 1440) hydrogen bonds : angle 4.38784 ( 4248) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 329 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 13 GLU cc_start: 0.7071 (OUTLIER) cc_final: 0.6665 (mt-10) REVERT: C 51 ASP cc_start: 0.8734 (m-30) cc_final: 0.8415 (m-30) REVERT: C 231 MET cc_start: 0.8227 (OUTLIER) cc_final: 0.7477 (mpp) REVERT: D 13 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6600 (mt-10) REVERT: D 156 ARG cc_start: 0.7458 (mmt180) cc_final: 0.7241 (tpt-90) REVERT: E 13 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6747 (mt-10) REVERT: F 51 ASP cc_start: 0.8741 (m-30) cc_final: 0.8407 (m-30) REVERT: F 231 MET cc_start: 0.8310 (OUTLIER) cc_final: 0.7536 (mpp) REVERT: G 156 ARG cc_start: 0.7274 (mmt180) cc_final: 0.7014 (mmt180) REVERT: I 13 GLU cc_start: 0.7714 (tt0) cc_final: 0.7068 (mt-10) REVERT: I 51 ASP cc_start: 0.8752 (m-30) cc_final: 0.8392 (m-30) REVERT: J 13 GLU cc_start: 0.7727 (tt0) cc_final: 0.7154 (mt-10) REVERT: J 231 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7550 (mpp) REVERT: K 13 GLU cc_start: 0.7646 (tt0) cc_final: 0.7021 (mt-10) REVERT: K 231 MET cc_start: 0.8212 (OUTLIER) cc_final: 0.7676 (mpp) REVERT: L 13 GLU cc_start: 0.7675 (tt0) cc_final: 0.7046 (mt-10) REVERT: L 51 ASP cc_start: 0.8739 (m-30) cc_final: 0.8432 (m-30) outliers start: 29 outliers final: 13 residues processed: 338 average time/residue: 1.3237 time to fit residues: 506.2861 Evaluate side-chains 341 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 321 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 231 MET Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 231 MET Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 11 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 221 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 162 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN C 58 GLN D 58 GLN G 58 GLN J 58 GLN K 58 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.164250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.106589 restraints weight = 48345.001| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.17 r_work: 0.3104 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 21816 Z= 0.141 Angle : 0.516 4.097 28776 Z= 0.276 Chirality : 0.040 0.122 3048 Planarity : 0.004 0.073 3324 Dihedral : 6.458 55.604 4188 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.54 % Allowed : 8.05 % Favored : 90.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.13 (0.17), residues: 2304 helix: 2.96 (0.12), residues: 1740 sheet: -0.40 (0.33), residues: 132 loop : -1.06 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 183 TYR 0.017 0.002 TYR J 66 PHE 0.020 0.002 PHE J 212 TRP 0.006 0.001 TRP G 193 HIS 0.004 0.001 HIS H 161 Details of bonding type rmsd covalent geometry : bond 0.00302 (21780) covalent geometry : angle 0.51330 (28704) SS BOND : bond 0.00402 ( 36) SS BOND : angle 1.15340 ( 72) hydrogen bonds : bond 0.04405 ( 1440) hydrogen bonds : angle 4.31697 ( 4248) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 332 time to evaluate : 1.017 Fit side-chains REVERT: A 13 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6753 (mt-10) REVERT: B 102 MET cc_start: 0.6004 (OUTLIER) cc_final: 0.5318 (mpt) REVERT: B 225 PHE cc_start: 0.8285 (t80) cc_final: 0.8036 (t80) REVERT: B 231 MET cc_start: 0.8217 (OUTLIER) cc_final: 0.7751 (mpp) REVERT: C 51 ASP cc_start: 0.8780 (m-30) cc_final: 0.8476 (m-30) REVERT: C 225 PHE cc_start: 0.8316 (t80) cc_final: 0.8070 (t80) REVERT: D 13 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.6685 (mt-10) REVERT: D 156 ARG cc_start: 0.7565 (mmt180) cc_final: 0.7361 (tpt-90) REVERT: E 13 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6783 (mt-10) REVERT: E 102 MET cc_start: 0.6028 (OUTLIER) cc_final: 0.5416 (mpt) REVERT: F 51 ASP cc_start: 0.8778 (m-30) cc_final: 0.8487 (m-30) REVERT: F 225 PHE cc_start: 0.8299 (t80) cc_final: 0.8057 (t80) REVERT: F 231 MET cc_start: 0.8340 (OUTLIER) cc_final: 0.7477 (mpp) REVERT: G 156 ARG cc_start: 0.7362 (mmt180) cc_final: 0.7107 (mmt180) REVERT: H 102 MET cc_start: 0.5755 (OUTLIER) cc_final: 0.5330 (mpt) REVERT: I 13 GLU cc_start: 0.7691 (tt0) cc_final: 0.7138 (mt-10) REVERT: I 51 ASP cc_start: 0.8790 (m-30) cc_final: 0.8490 (m-30) REVERT: I 225 PHE cc_start: 0.8310 (t80) cc_final: 0.8063 (t80) REVERT: J 13 GLU cc_start: 0.7663 (tt0) cc_final: 0.7220 (mt-10) REVERT: J 102 MET cc_start: 0.6161 (OUTLIER) cc_final: 0.5530 (mpt) REVERT: K 13 GLU cc_start: 0.7602 (tt0) cc_final: 0.7093 (mt-10) REVERT: K 102 MET cc_start: 0.5830 (OUTLIER) cc_final: 0.5364 (mpt) REVERT: L 13 GLU cc_start: 0.7632 (tt0) cc_final: 0.7144 (mt-10) REVERT: L 51 ASP cc_start: 0.8782 (m-30) cc_final: 0.8495 (m-30) REVERT: L 225 PHE cc_start: 0.8305 (t80) cc_final: 0.8056 (t80) outliers start: 33 outliers final: 12 residues processed: 337 average time/residue: 1.2872 time to fit residues: 492.4069 Evaluate side-chains 345 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 323 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain F residue 231 MET Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 102 MET Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 153 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 47 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 124 optimal weight: 20.0000 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 210 optimal weight: 7.9990 chunk 193 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.163273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.105414 restraints weight = 48456.575| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 1.16 r_work: 0.3067 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2938 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 21816 Z= 0.197 Angle : 0.574 4.406 28776 Z= 0.306 Chirality : 0.042 0.126 3048 Planarity : 0.004 0.063 3324 Dihedral : 7.470 56.347 4188 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.68 % Allowed : 8.43 % Favored : 89.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.02 (0.17), residues: 2304 helix: 2.89 (0.12), residues: 1740 sheet: -0.55 (0.32), residues: 132 loop : -1.10 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 183 TYR 0.019 0.002 TYR J 66 PHE 0.022 0.003 PHE H 212 TRP 0.008 0.002 TRP H 193 HIS 0.005 0.001 HIS H 161 Details of bonding type rmsd covalent geometry : bond 0.00450 (21780) covalent geometry : angle 0.57095 (28704) SS BOND : bond 0.00594 ( 36) SS BOND : angle 1.34222 ( 72) hydrogen bonds : bond 0.04844 ( 1440) hydrogen bonds : angle 4.39926 ( 4248) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 334 time to evaluate : 0.958 Fit side-chains REVERT: A 13 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6800 (mt-10) REVERT: A 102 MET cc_start: 0.6162 (OUTLIER) cc_final: 0.5475 (mpt) REVERT: B 225 PHE cc_start: 0.8309 (t80) cc_final: 0.8056 (t80) REVERT: B 231 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7750 (mpp) REVERT: C 51 ASP cc_start: 0.8814 (m-30) cc_final: 0.8506 (m-30) REVERT: C 225 PHE cc_start: 0.8365 (t80) cc_final: 0.8144 (t80) REVERT: C 231 MET cc_start: 0.8204 (OUTLIER) cc_final: 0.7513 (mpp) REVERT: D 13 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6696 (mt-10) REVERT: D 156 ARG cc_start: 0.7644 (mmt180) cc_final: 0.7441 (tpt-90) REVERT: E 13 GLU cc_start: 0.7208 (OUTLIER) cc_final: 0.6769 (mt-10) REVERT: E 231 MET cc_start: 0.8254 (OUTLIER) cc_final: 0.7698 (mpp) REVERT: F 51 ASP cc_start: 0.8820 (m-30) cc_final: 0.8515 (m-30) REVERT: F 225 PHE cc_start: 0.8325 (t80) cc_final: 0.8091 (t80) REVERT: G 102 MET cc_start: 0.5865 (OUTLIER) cc_final: 0.5292 (mpt) REVERT: H 102 MET cc_start: 0.5841 (OUTLIER) cc_final: 0.5306 (mpt) REVERT: H 225 PHE cc_start: 0.8304 (t80) cc_final: 0.8071 (t80) REVERT: H 231 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7741 (mpp) REVERT: I 13 GLU cc_start: 0.7695 (tt0) cc_final: 0.7121 (mt-10) REVERT: I 51 ASP cc_start: 0.8823 (m-30) cc_final: 0.8525 (m-30) REVERT: I 225 PHE cc_start: 0.8338 (t80) cc_final: 0.8097 (t80) REVERT: J 13 GLU cc_start: 0.7643 (tt0) cc_final: 0.7197 (mt-10) REVERT: K 13 GLU cc_start: 0.7634 (tt0) cc_final: 0.7072 (mt-10) REVERT: K 102 MET cc_start: 0.5875 (OUTLIER) cc_final: 0.5379 (mpt) REVERT: K 231 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7600 (mpp) REVERT: L 13 GLU cc_start: 0.7670 (tt0) cc_final: 0.7129 (mt-10) REVERT: L 51 ASP cc_start: 0.8823 (m-30) cc_final: 0.8525 (m-30) REVERT: L 225 PHE cc_start: 0.8355 (t80) cc_final: 0.8129 (t80) outliers start: 36 outliers final: 12 residues processed: 337 average time/residue: 1.2390 time to fit residues: 473.9902 Evaluate side-chains 351 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 327 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 231 MET Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 102 MET Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 231 MET Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 102 MET Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 231 MET Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 169 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 117 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 173 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 178 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 55 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.165067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.107710 restraints weight = 48636.996| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.17 r_work: 0.3102 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 21816 Z= 0.124 Angle : 0.496 3.891 28776 Z= 0.265 Chirality : 0.039 0.122 3048 Planarity : 0.004 0.058 3324 Dihedral : 6.549 57.111 4188 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.16 % Allowed : 9.40 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.18 (0.17), residues: 2304 helix: 3.00 (0.12), residues: 1740 sheet: -0.40 (0.33), residues: 132 loop : -1.05 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 183 TYR 0.015 0.002 TYR A 66 PHE 0.018 0.002 PHE J 212 TRP 0.005 0.001 TRP H 193 HIS 0.003 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00263 (21780) covalent geometry : angle 0.49402 (28704) SS BOND : bond 0.00340 ( 36) SS BOND : angle 1.04425 ( 72) hydrogen bonds : bond 0.04143 ( 1440) hydrogen bonds : angle 4.22075 ( 4248) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 340 time to evaluate : 0.829 Fit side-chains REVERT: A 13 GLU cc_start: 0.7178 (OUTLIER) cc_final: 0.6795 (mt-10) REVERT: B 102 MET cc_start: 0.6017 (OUTLIER) cc_final: 0.5404 (mpt) REVERT: B 225 PHE cc_start: 0.8304 (t80) cc_final: 0.8079 (t80) REVERT: C 51 ASP cc_start: 0.8783 (m-30) cc_final: 0.8476 (m-30) REVERT: C 225 PHE cc_start: 0.8353 (t80) cc_final: 0.8133 (t80) REVERT: D 13 GLU cc_start: 0.7063 (OUTLIER) cc_final: 0.6697 (mt-10) REVERT: D 102 MET cc_start: 0.6008 (OUTLIER) cc_final: 0.5407 (mpt) REVERT: D 156 ARG cc_start: 0.7620 (mmt180) cc_final: 0.7418 (tpt-90) REVERT: E 13 GLU cc_start: 0.7215 (OUTLIER) cc_final: 0.6818 (mt-10) REVERT: E 102 MET cc_start: 0.6036 (OUTLIER) cc_final: 0.5410 (mpt) REVERT: F 51 ASP cc_start: 0.8790 (m-30) cc_final: 0.8487 (m-30) REVERT: F 225 PHE cc_start: 0.8325 (t80) cc_final: 0.8110 (t80) REVERT: H 102 MET cc_start: 0.5849 (OUTLIER) cc_final: 0.5292 (mpt) REVERT: H 225 PHE cc_start: 0.8299 (t80) cc_final: 0.8054 (t80) REVERT: I 13 GLU cc_start: 0.7643 (tt0) cc_final: 0.7088 (mt-10) REVERT: I 51 ASP cc_start: 0.8807 (m-30) cc_final: 0.8505 (m-30) REVERT: I 225 PHE cc_start: 0.8330 (t80) cc_final: 0.8109 (t80) REVERT: J 13 GLU cc_start: 0.7608 (tt0) cc_final: 0.7178 (mt-10) REVERT: J 102 MET cc_start: 0.6168 (OUTLIER) cc_final: 0.5480 (mpt) REVERT: K 13 GLU cc_start: 0.7570 (tt0) cc_final: 0.7039 (mt-10) REVERT: K 102 MET cc_start: 0.5890 (OUTLIER) cc_final: 0.5369 (mpt) REVERT: L 51 ASP cc_start: 0.8788 (m-30) cc_final: 0.8492 (m-30) REVERT: L 225 PHE cc_start: 0.8346 (t80) cc_final: 0.8122 (t80) outliers start: 25 outliers final: 12 residues processed: 343 average time/residue: 1.1405 time to fit residues: 446.8658 Evaluate side-chains 354 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 333 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 102 MET Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 50 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 39 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 151 optimal weight: 7.9990 chunk 83 optimal weight: 2.9990 chunk 121 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.165007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.107544 restraints weight = 48580.077| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.17 r_work: 0.3101 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 21816 Z= 0.128 Angle : 0.502 4.033 28776 Z= 0.267 Chirality : 0.039 0.123 3048 Planarity : 0.004 0.068 3324 Dihedral : 6.438 57.195 4188 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.07 % Allowed : 10.01 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.30 (0.17), residues: 2304 helix: 3.10 (0.12), residues: 1740 sheet: -0.48 (0.33), residues: 132 loop : -1.04 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 183 TYR 0.016 0.002 TYR J 66 PHE 0.018 0.002 PHE J 212 TRP 0.005 0.001 TRP H 193 HIS 0.003 0.001 HIS G 161 Details of bonding type rmsd covalent geometry : bond 0.00278 (21780) covalent geometry : angle 0.49936 (28704) SS BOND : bond 0.00346 ( 36) SS BOND : angle 1.06509 ( 72) hydrogen bonds : bond 0.04116 ( 1440) hydrogen bonds : angle 4.18048 ( 4248) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 338 time to evaluate : 0.893 Fit side-chains REVERT: A 13 GLU cc_start: 0.7175 (OUTLIER) cc_final: 0.6819 (mt-10) REVERT: B 102 MET cc_start: 0.6058 (OUTLIER) cc_final: 0.5430 (mpt) REVERT: B 225 PHE cc_start: 0.8307 (t80) cc_final: 0.8072 (t80) REVERT: C 51 ASP cc_start: 0.8799 (m-30) cc_final: 0.8487 (m-30) REVERT: D 13 GLU cc_start: 0.7065 (OUTLIER) cc_final: 0.6728 (mt-10) REVERT: D 102 MET cc_start: 0.6042 (OUTLIER) cc_final: 0.5435 (mpt) REVERT: E 13 GLU cc_start: 0.7202 (OUTLIER) cc_final: 0.6810 (mt-10) REVERT: E 102 MET cc_start: 0.6013 (OUTLIER) cc_final: 0.5385 (mpt) REVERT: F 51 ASP cc_start: 0.8796 (m-30) cc_final: 0.8490 (m-30) REVERT: F 225 PHE cc_start: 0.8337 (t80) cc_final: 0.8113 (t80) REVERT: H 225 PHE cc_start: 0.8305 (t80) cc_final: 0.8081 (t80) REVERT: I 13 GLU cc_start: 0.7597 (tt0) cc_final: 0.7099 (mt-10) REVERT: I 51 ASP cc_start: 0.8813 (m-30) cc_final: 0.8508 (m-30) REVERT: I 225 PHE cc_start: 0.8346 (t80) cc_final: 0.8117 (t80) REVERT: J 13 GLU cc_start: 0.7593 (tt0) cc_final: 0.7171 (mt-10) REVERT: K 13 GLU cc_start: 0.7567 (tt0) cc_final: 0.7038 (mt-10) REVERT: K 102 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.5335 (mpt) REVERT: K 225 PHE cc_start: 0.8324 (t80) cc_final: 0.8085 (t80) REVERT: L 51 ASP cc_start: 0.8810 (m-30) cc_final: 0.8507 (m-30) REVERT: L 225 PHE cc_start: 0.8363 (t80) cc_final: 0.8159 (t80) outliers start: 23 outliers final: 12 residues processed: 342 average time/residue: 0.9861 time to fit residues: 386.3073 Evaluate side-chains 354 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 335 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 102 MET Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 102 MET Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 74 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 96 optimal weight: 7.9990 chunk 107 optimal weight: 4.9990 chunk 205 optimal weight: 0.6980 chunk 181 optimal weight: 8.9990 chunk 126 optimal weight: 3.9990 chunk 153 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.162824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.104854 restraints weight = 48172.824| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 1.16 r_work: 0.3060 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 21816 Z= 0.218 Angle : 0.593 4.423 28776 Z= 0.316 Chirality : 0.043 0.123 3048 Planarity : 0.004 0.069 3324 Dihedral : 7.735 57.505 4188 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.07 % Allowed : 9.87 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.17), residues: 2304 helix: 2.91 (0.12), residues: 1740 sheet: -0.50 (0.32), residues: 132 loop : -1.13 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 183 TYR 0.020 0.002 TYR J 66 PHE 0.024 0.003 PHE H 212 TRP 0.009 0.002 TRP H 193 HIS 0.005 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00501 (21780) covalent geometry : angle 0.58978 (28704) SS BOND : bond 0.00676 ( 36) SS BOND : angle 1.42745 ( 72) hydrogen bonds : bond 0.04894 ( 1440) hydrogen bonds : angle 4.37800 ( 4248) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 338 time to evaluate : 0.621 Fit side-chains REVERT: A 13 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6808 (mt-10) REVERT: A 102 MET cc_start: 0.6180 (OUTLIER) cc_final: 0.5483 (mpt) REVERT: B 102 MET cc_start: 0.6071 (OUTLIER) cc_final: 0.5368 (mpt) REVERT: B 225 PHE cc_start: 0.8335 (t80) cc_final: 0.8109 (t80) REVERT: C 51 ASP cc_start: 0.8819 (m-30) cc_final: 0.8507 (m-30) REVERT: D 13 GLU cc_start: 0.7052 (OUTLIER) cc_final: 0.6702 (mt-10) REVERT: D 102 MET cc_start: 0.6079 (OUTLIER) cc_final: 0.5449 (mpt) REVERT: E 13 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6806 (mt-10) REVERT: F 51 ASP cc_start: 0.8832 (m-30) cc_final: 0.8539 (m-30) REVERT: H 102 MET cc_start: 0.5856 (OUTLIER) cc_final: 0.5343 (mpt) REVERT: H 225 PHE cc_start: 0.8330 (t80) cc_final: 0.8090 (t80) REVERT: I 13 GLU cc_start: 0.7669 (tt0) cc_final: 0.7124 (mt-10) REVERT: I 51 ASP cc_start: 0.8830 (m-30) cc_final: 0.8561 (m-30) REVERT: J 13 GLU cc_start: 0.7622 (tt0) cc_final: 0.7153 (mt-10) REVERT: K 13 GLU cc_start: 0.7618 (tt0) cc_final: 0.7066 (mt-10) REVERT: K 102 MET cc_start: 0.5932 (OUTLIER) cc_final: 0.5335 (mpt) REVERT: K 225 PHE cc_start: 0.8371 (t80) cc_final: 0.8143 (t80) REVERT: L 51 ASP cc_start: 0.8822 (m-30) cc_final: 0.8553 (m-30) REVERT: L 225 PHE cc_start: 0.8380 (t80) cc_final: 0.8161 (t80) outliers start: 23 outliers final: 12 residues processed: 344 average time/residue: 0.7853 time to fit residues: 311.9083 Evaluate side-chains 354 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 334 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 102 MET Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 102 MET Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 225 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 173 optimal weight: 5.9990 chunk 200 optimal weight: 20.0000 chunk 7 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.163635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.105754 restraints weight = 48386.685| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.17 r_work: 0.3075 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 2.59 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 21816 Z= 0.171 Angle : 0.550 4.208 28776 Z= 0.293 Chirality : 0.041 0.123 3048 Planarity : 0.004 0.070 3324 Dihedral : 7.439 58.161 4188 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.12 % Allowed : 10.20 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.08 (0.17), residues: 2304 helix: 2.93 (0.12), residues: 1740 sheet: -0.45 (0.33), residues: 132 loop : -1.11 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 183 TYR 0.019 0.002 TYR J 66 PHE 0.021 0.002 PHE J 212 TRP 0.007 0.001 TRP H 193 HIS 0.004 0.001 HIS H 74 Details of bonding type rmsd covalent geometry : bond 0.00382 (21780) covalent geometry : angle 0.54716 (28704) SS BOND : bond 0.00539 ( 36) SS BOND : angle 1.25975 ( 72) hydrogen bonds : bond 0.04545 ( 1440) hydrogen bonds : angle 4.30669 ( 4248) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 337 time to evaluate : 0.581 Fit side-chains REVERT: A 13 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6774 (mt-10) REVERT: A 102 MET cc_start: 0.6175 (OUTLIER) cc_final: 0.5476 (mpt) REVERT: B 225 PHE cc_start: 0.8337 (t80) cc_final: 0.8097 (t80) REVERT: C 51 ASP cc_start: 0.8806 (m-30) cc_final: 0.8486 (m-30) REVERT: D 13 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6678 (mt-10) REVERT: D 102 MET cc_start: 0.6082 (OUTLIER) cc_final: 0.5404 (mpt) REVERT: E 13 GLU cc_start: 0.7177 (OUTLIER) cc_final: 0.6787 (mt-10) REVERT: F 51 ASP cc_start: 0.8810 (m-30) cc_final: 0.8498 (m-30) REVERT: G 102 MET cc_start: 0.5974 (OUTLIER) cc_final: 0.5349 (mpt) REVERT: H 102 MET cc_start: 0.5844 (OUTLIER) cc_final: 0.5327 (mpt) REVERT: H 225 PHE cc_start: 0.8328 (t80) cc_final: 0.8103 (t80) REVERT: I 51 ASP cc_start: 0.8817 (m-30) cc_final: 0.8519 (m-30) REVERT: J 13 GLU cc_start: 0.7611 (tt0) cc_final: 0.7154 (mt-10) REVERT: J 102 MET cc_start: 0.6102 (OUTLIER) cc_final: 0.5436 (mpt) REVERT: K 13 GLU cc_start: 0.7614 (tt0) cc_final: 0.7054 (mt-10) REVERT: K 102 MET cc_start: 0.5912 (OUTLIER) cc_final: 0.5314 (mpt) REVERT: L 51 ASP cc_start: 0.8811 (m-30) cc_final: 0.8507 (m-30) outliers start: 24 outliers final: 12 residues processed: 342 average time/residue: 0.7209 time to fit residues: 284.2319 Evaluate side-chains 353 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 332 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 102 MET Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 102 MET Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 112 optimal weight: 4.9990 chunk 162 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 chunk 165 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 189 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 205 optimal weight: 2.9990 chunk 210 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.162092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.106130 restraints weight = 48287.116| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 1.12 r_work: 0.3063 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 21816 Z= 0.214 Angle : 0.596 5.420 28776 Z= 0.317 Chirality : 0.043 0.124 3048 Planarity : 0.005 0.090 3324 Dihedral : 7.986 59.777 4188 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.98 % Allowed : 10.71 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.97 (0.17), residues: 2304 helix: 2.85 (0.12), residues: 1740 sheet: -0.48 (0.32), residues: 132 loop : -1.13 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 183 TYR 0.020 0.002 TYR J 66 PHE 0.024 0.003 PHE H 212 TRP 0.008 0.002 TRP H 193 HIS 0.004 0.001 HIS K 161 Details of bonding type rmsd covalent geometry : bond 0.00490 (21780) covalent geometry : angle 0.59254 (28704) SS BOND : bond 0.00687 ( 36) SS BOND : angle 1.40905 ( 72) hydrogen bonds : bond 0.04870 ( 1440) hydrogen bonds : angle 4.37797 ( 4248) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4608 Ramachandran restraints generated. 2304 Oldfield, 0 Emsley, 2304 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 330 time to evaluate : 0.582 Fit side-chains REVERT: A 13 GLU cc_start: 0.7135 (OUTLIER) cc_final: 0.6802 (mt-10) REVERT: A 102 MET cc_start: 0.6189 (OUTLIER) cc_final: 0.5433 (mpt) REVERT: B 225 PHE cc_start: 0.8339 (t80) cc_final: 0.8116 (t80) REVERT: C 51 ASP cc_start: 0.8811 (m-30) cc_final: 0.8498 (m-30) REVERT: D 13 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.6680 (mt-10) REVERT: E 13 GLU cc_start: 0.7155 (OUTLIER) cc_final: 0.6793 (mt-10) REVERT: F 51 ASP cc_start: 0.8818 (m-30) cc_final: 0.8518 (m-30) REVERT: G 102 MET cc_start: 0.5988 (OUTLIER) cc_final: 0.5357 (mpt) REVERT: H 102 MET cc_start: 0.5883 (OUTLIER) cc_final: 0.5339 (mpt) REVERT: H 225 PHE cc_start: 0.8332 (t80) cc_final: 0.8118 (t80) REVERT: I 51 ASP cc_start: 0.8823 (m-30) cc_final: 0.8556 (m-30) REVERT: J 13 GLU cc_start: 0.7624 (tt0) cc_final: 0.7136 (mt-10) REVERT: J 102 MET cc_start: 0.6151 (OUTLIER) cc_final: 0.5469 (mpt) REVERT: K 13 GLU cc_start: 0.7606 (tt0) cc_final: 0.7046 (mt-10) REVERT: K 102 MET cc_start: 0.5971 (OUTLIER) cc_final: 0.5339 (mpt) REVERT: L 51 ASP cc_start: 0.8814 (m-30) cc_final: 0.8526 (m-30) outliers start: 21 outliers final: 12 residues processed: 341 average time/residue: 0.7294 time to fit residues: 286.3720 Evaluate side-chains 349 residues out of total 2148 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 329 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 102 MET Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 13 GLU Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 102 MET Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 102 MET Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 102 MET Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 102 MET Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 6 optimal weight: 0.9980 chunk 176 optimal weight: 2.9990 chunk 223 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 226 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 166 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.164565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.109312 restraints weight = 48590.427| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 1.12 r_work: 0.3108 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 2.58 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 21816 Z= 0.111 Angle : 0.498 5.366 28776 Z= 0.266 Chirality : 0.039 0.127 3048 Planarity : 0.005 0.074 3324 Dihedral : 6.844 58.676 4188 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 0.98 % Allowed : 10.75 % Favored : 88.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.25 (0.17), residues: 2304 helix: 3.05 (0.12), residues: 1740 sheet: -0.33 (0.34), residues: 132 loop : -1.06 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG I 183 TYR 0.013 0.002 TYR J 66 PHE 0.016 0.002 PHE J 212 TRP 0.005 0.001 TRP A 193 HIS 0.004 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00231 (21780) covalent geometry : angle 0.49592 (28704) SS BOND : bond 0.00261 ( 36) SS BOND : angle 0.96617 ( 72) hydrogen bonds : bond 0.03989 ( 1440) hydrogen bonds : angle 4.18742 ( 4248) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15100.06 seconds wall clock time: 254 minutes 56.37 seconds (15296.37 seconds total)