Starting phenix.real_space_refine on Sun Feb 8 10:41:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9za3_73965/02_2026/9za3_73965_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9za3_73965/02_2026/9za3_73965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9za3_73965/02_2026/9za3_73965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9za3_73965/02_2026/9za3_73965.map" model { file = "/net/cci-nas-00/data/ceres_data/9za3_73965/02_2026/9za3_73965_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9za3_73965/02_2026/9za3_73965_trim.cif" } resolution = 2.4 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= 0.002 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 S 102 5.16 5 C 14454 2.51 5 N 2844 2.21 5 O 3774 1.98 5 H 17412 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38598 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2971 Classifications: {'peptide': 183} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "B" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2971 Classifications: {'peptide': 183} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "C" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2971 Classifications: {'peptide': 183} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "D" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2971 Classifications: {'peptide': 183} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "E" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2971 Classifications: {'peptide': 183} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "F" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 2971 Classifications: {'peptide': 183} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 175} Chain breaks: 1 Chain: "G" Number of atoms: 2869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2869 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 177} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "H" Number of atoms: 2869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2869 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 177} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "I" Number of atoms: 2869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2869 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 177} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "J" Number of atoms: 2869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2869 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 177} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "K" Number of atoms: 2869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2869 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 177} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "L" Number of atoms: 2869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 2869 Classifications: {'peptide': 185} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 177} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TRP:plan': 1, 'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 4, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "A" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 199 Unusual residues: {'MC3': 19} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 675 Unresolved non-hydrogen angles: 846 Unresolved non-hydrogen dihedrals: 599 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'MC3:plan-1': 19, 'MC3:plan-2': 19} Unresolved non-hydrogen planarities: 147 Chain: "B" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 199 Unusual residues: {'MC3': 19} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 675 Unresolved non-hydrogen angles: 846 Unresolved non-hydrogen dihedrals: 599 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'MC3:plan-1': 19, 'MC3:plan-2': 19} Unresolved non-hydrogen planarities: 147 Chain: "C" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 199 Unusual residues: {'MC3': 19} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 675 Unresolved non-hydrogen angles: 846 Unresolved non-hydrogen dihedrals: 599 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'MC3:plan-1': 19, 'MC3:plan-2': 19} Unresolved non-hydrogen planarities: 147 Chain: "D" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 199 Unusual residues: {'MC3': 19} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 675 Unresolved non-hydrogen angles: 846 Unresolved non-hydrogen dihedrals: 599 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'MC3:plan-1': 19, 'MC3:plan-2': 19} Unresolved non-hydrogen planarities: 147 Chain: "E" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 199 Unusual residues: {'MC3': 19} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 675 Unresolved non-hydrogen angles: 846 Unresolved non-hydrogen dihedrals: 599 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'MC3:plan-1': 19, 'MC3:plan-2': 19} Unresolved non-hydrogen planarities: 147 Chain: "F" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 199 Unusual residues: {'MC3': 19} Classifications: {'undetermined': 19} Link IDs: {None: 18} Unresolved non-hydrogen bonds: 675 Unresolved non-hydrogen angles: 846 Unresolved non-hydrogen dihedrals: 599 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'MC3:plan-1': 19, 'MC3:plan-2': 19} Unresolved non-hydrogen planarities: 147 Chain: "G" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 276 Unusual residues: {'MC3': 23} Classifications: {'undetermined': 23} Link IDs: {None: 22} Unresolved non-hydrogen bonds: 782 Unresolved non-hydrogen angles: 977 Unresolved non-hydrogen dihedrals: 698 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'MC3:plan-1': 21, 'MC3:plan-2': 21} Unresolved non-hydrogen planarities: 160 Chain: "H" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 276 Unusual residues: {'MC3': 23} Classifications: {'undetermined': 23} Link IDs: {None: 22} Unresolved non-hydrogen bonds: 782 Unresolved non-hydrogen angles: 977 Unresolved non-hydrogen dihedrals: 698 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'MC3:plan-1': 21, 'MC3:plan-2': 21} Unresolved non-hydrogen planarities: 160 Chain: "I" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 276 Unusual residues: {'MC3': 23} Classifications: {'undetermined': 23} Link IDs: {None: 22} Unresolved non-hydrogen bonds: 782 Unresolved non-hydrogen angles: 977 Unresolved non-hydrogen dihedrals: 698 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'MC3:plan-1': 21, 'MC3:plan-2': 21} Unresolved non-hydrogen planarities: 160 Chain: "J" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 276 Unusual residues: {'MC3': 23} Classifications: {'undetermined': 23} Link IDs: {None: 22} Unresolved non-hydrogen bonds: 782 Unresolved non-hydrogen angles: 977 Unresolved non-hydrogen dihedrals: 698 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'MC3:plan-1': 21, 'MC3:plan-2': 21} Unresolved non-hydrogen planarities: 160 Chain: "K" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 276 Unusual residues: {'MC3': 23} Classifications: {'undetermined': 23} Link IDs: {None: 22} Unresolved non-hydrogen bonds: 782 Unresolved non-hydrogen angles: 977 Unresolved non-hydrogen dihedrals: 698 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'MC3:plan-1': 21, 'MC3:plan-2': 21} Unresolved non-hydrogen planarities: 160 Chain: "L" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 276 Unusual residues: {'MC3': 23} Classifications: {'undetermined': 23} Link IDs: {None: 22} Unresolved non-hydrogen bonds: 782 Unresolved non-hydrogen angles: 977 Unresolved non-hydrogen dihedrals: 698 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'MC3:plan-1': 21, 'MC3:plan-2': 21} Unresolved non-hydrogen planarities: 160 Chain: "A" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "B" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "C" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "D" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "E" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "F" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 63 Classifications: {'water': 63} Link IDs: {None: 62} Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "H" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "I" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "J" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "K" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Chain: "L" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 55 Classifications: {'water': 55} Link IDs: {None: 54} Time building chain proxies: 7.78, per 1000 atoms: 0.20 Number of scatterers: 38598 At special positions: 0 Unit cell: (102.75, 101.106, 151.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 12 15.00 O 3774 8.00 N 2844 7.00 C 14454 6.00 H 17412 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 189 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 178 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 189 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 178 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 189 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 178 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 189 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 183 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 178 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 189 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 183 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 178 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 189 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 183 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 178 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 189 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 183 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 178 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 189 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 183 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 178 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 189 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 183 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 178 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 189 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 183 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 178 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 189 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 183 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 178 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 189 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 183 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 178 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 1.1 seconds 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4152 Finding SS restraints... Secondary structure from input PDB file: 102 helices and 12 sheets defined 78.0% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.92 Creating SS restraints... Processing helix chain 'A' and resid 4 through 17 removed outlier: 3.578A pdb=" N HIS A 17 " --> pdb=" O ASN A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 33 Processing helix chain 'A' and resid 33 through 40 Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 100 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 141 through 169 Processing helix chain 'A' and resid 193 through 223 Processing helix chain 'B' and resid 4 through 17 removed outlier: 3.579A pdb=" N HIS B 17 " --> pdb=" O ASN B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 33 Processing helix chain 'B' and resid 33 through 40 Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 100 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 141 through 169 Processing helix chain 'B' and resid 193 through 223 Processing helix chain 'C' and resid 4 through 17 removed outlier: 3.578A pdb=" N HIS C 17 " --> pdb=" O ASN C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 33 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 100 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 141 through 169 Processing helix chain 'C' and resid 193 through 223 Processing helix chain 'D' and resid 4 through 17 removed outlier: 3.577A pdb=" N HIS D 17 " --> pdb=" O ASN D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 33 Processing helix chain 'D' and resid 33 through 40 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 73 through 100 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 141 through 169 Processing helix chain 'D' and resid 193 through 223 Processing helix chain 'E' and resid 4 through 17 removed outlier: 3.578A pdb=" N HIS E 17 " --> pdb=" O ASN E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 33 Processing helix chain 'E' and resid 33 through 40 Processing helix chain 'E' and resid 40 through 45 Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 73 through 100 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 141 through 169 Processing helix chain 'E' and resid 193 through 223 Processing helix chain 'F' and resid 4 through 17 removed outlier: 3.577A pdb=" N HIS F 17 " --> pdb=" O ASN F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 33 Processing helix chain 'F' and resid 33 through 40 Processing helix chain 'F' and resid 40 through 45 Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 73 through 100 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 141 through 169 Processing helix chain 'F' and resid 193 through 223 Processing helix chain 'G' and resid 5 through 17 removed outlier: 3.502A pdb=" N ARG G 9 " --> pdb=" O SER G 5 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS G 17 " --> pdb=" O ASN G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 32 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 104 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 140 through 168 Processing helix chain 'G' and resid 193 through 221 Processing helix chain 'H' and resid 5 through 17 removed outlier: 3.501A pdb=" N ARG H 9 " --> pdb=" O SER H 5 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS H 17 " --> pdb=" O ASN H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 32 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 104 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 140 through 168 Processing helix chain 'H' and resid 193 through 221 Processing helix chain 'I' and resid 5 through 17 removed outlier: 3.501A pdb=" N ARG I 9 " --> pdb=" O SER I 5 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS I 17 " --> pdb=" O ASN I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 32 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 104 Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 140 through 168 Processing helix chain 'I' and resid 193 through 221 Processing helix chain 'J' and resid 5 through 17 removed outlier: 3.501A pdb=" N ARG J 9 " --> pdb=" O SER J 5 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS J 17 " --> pdb=" O ASN J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 32 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 104 Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 140 through 168 Processing helix chain 'J' and resid 193 through 221 Processing helix chain 'K' and resid 5 through 17 removed outlier: 3.502A pdb=" N ARG K 9 " --> pdb=" O SER K 5 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N HIS K 17 " --> pdb=" O ASN K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 32 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 104 Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 140 through 168 Processing helix chain 'K' and resid 193 through 221 Processing helix chain 'L' and resid 5 through 17 removed outlier: 3.502A pdb=" N ARG L 9 " --> pdb=" O SER L 5 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS L 17 " --> pdb=" O ASN L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 32 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 104 Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 140 through 168 Processing helix chain 'L' and resid 193 through 221 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.582A pdb=" N THR A 53 " --> pdb=" O PHE A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.583A pdb=" N THR B 53 " --> pdb=" O PHE B 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.582A pdb=" N THR C 53 " --> pdb=" O PHE C 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.583A pdb=" N THR D 53 " --> pdb=" O PHE D 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.583A pdb=" N THR E 53 " --> pdb=" O PHE E 190 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.582A pdb=" N THR F 53 " --> pdb=" O PHE F 190 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.525A pdb=" N THR G 53 " --> pdb=" O PHE G 190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.525A pdb=" N THR H 53 " --> pdb=" O PHE H 190 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 53 through 54 removed outlier: 3.525A pdb=" N THR I 53 " --> pdb=" O PHE I 190 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.525A pdb=" N THR J 53 " --> pdb=" O PHE J 190 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.525A pdb=" N THR K 53 " --> pdb=" O PHE K 190 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.525A pdb=" N THR L 53 " --> pdb=" O PHE L 190 " (cutoff:3.500A) 1326 hydrogen bonds defined for protein. 3942 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: 8.76 Time building geometry restraints manager: 4.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17388 1.03 - 1.23: 54 1.23 - 1.42: 7871 1.42 - 1.62: 12691 1.62 - 1.81: 132 Bond restraints: 38136 Sorted by residual: bond pdb=" NE2 HIS E 17 " pdb=" HE2 HIS E 17 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" NE2 HIS D 17 " pdb=" HE2 HIS D 17 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.66e+01 bond pdb=" ND1 HIS B 221 " pdb=" HD1 HIS B 221 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" ND1 HIS E 221 " pdb=" HD1 HIS E 221 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" ND1 HIS E 74 " pdb=" HD1 HIS E 74 " ideal model delta sigma weight residual 0.860 1.010 -0.150 2.00e-02 2.50e+03 5.65e+01 ... (remaining 38131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 63912 1.84 - 3.69: 1556 3.69 - 5.53: 1060 5.53 - 7.37: 6 7.37 - 9.22: 6 Bond angle restraints: 66540 Sorted by residual: angle pdb=" N GLU D 12 " pdb=" CA GLU D 12 " pdb=" C GLU D 12 " ideal model delta sigma weight residual 111.36 107.94 3.42 1.09e+00 8.42e-01 9.87e+00 angle pdb=" N GLU B 12 " pdb=" CA GLU B 12 " pdb=" C GLU B 12 " ideal model delta sigma weight residual 111.36 107.98 3.38 1.09e+00 8.42e-01 9.64e+00 angle pdb=" N GLU A 12 " pdb=" CA GLU A 12 " pdb=" C GLU A 12 " ideal model delta sigma weight residual 111.36 107.98 3.38 1.09e+00 8.42e-01 9.63e+00 angle pdb=" N GLU F 12 " pdb=" CA GLU F 12 " pdb=" C GLU F 12 " ideal model delta sigma weight residual 111.36 107.98 3.38 1.09e+00 8.42e-01 9.59e+00 angle pdb=" N GLU C 12 " pdb=" CA GLU C 12 " pdb=" C GLU C 12 " ideal model delta sigma weight residual 111.36 107.98 3.38 1.09e+00 8.42e-01 9.59e+00 ... (remaining 66535 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 17339 17.87 - 35.74: 1070 35.74 - 53.61: 387 53.61 - 71.48: 116 71.48 - 89.35: 36 Dihedral angle restraints: 18948 sinusoidal: 10698 harmonic: 8250 Sorted by residual: dihedral pdb=" CB GLU K 157 " pdb=" CG GLU K 157 " pdb=" CD GLU K 157 " pdb=" OE1 GLU K 157 " ideal model delta sinusoidal sigma weight residual 0.00 -89.13 89.13 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU I 157 " pdb=" CG GLU I 157 " pdb=" CD GLU I 157 " pdb=" OE1 GLU I 157 " ideal model delta sinusoidal sigma weight residual 0.00 -89.12 89.12 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLU H 157 " pdb=" CG GLU H 157 " pdb=" CD GLU H 157 " pdb=" OE1 GLU H 157 " ideal model delta sinusoidal sigma weight residual 0.00 -89.09 89.09 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 18945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2107 0.033 - 0.065: 480 0.065 - 0.098: 247 0.098 - 0.131: 34 0.131 - 0.163: 6 Chirality restraints: 2874 Sorted by residual: chirality pdb=" CA HIS C 95 " pdb=" N HIS C 95 " pdb=" C HIS C 95 " pdb=" CB HIS C 95 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CA HIS D 95 " pdb=" N HIS D 95 " pdb=" C HIS D 95 " pdb=" CB HIS D 95 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CA HIS F 95 " pdb=" N HIS F 95 " pdb=" C HIS F 95 " pdb=" CB HIS F 95 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 2871 not shown) Planarity restraints: 5172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 173 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.53e+00 pdb=" N PRO D 174 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 174 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 174 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS E 173 " -0.020 5.00e-02 4.00e+02 3.09e-02 1.52e+00 pdb=" N PRO E 174 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO E 174 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO E 174 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 173 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.52e+00 pdb=" N PRO A 174 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 174 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 174 " -0.017 5.00e-02 4.00e+02 ... (remaining 5169 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.34: 10346 2.34 - 2.91: 80783 2.91 - 3.47: 97865 3.47 - 4.04: 138955 4.04 - 4.60: 209079 Nonbonded interactions: 537028 Sorted by model distance: nonbonded pdb=" HE3 TRP B 4 " pdb="HD21 LEU B 7 " model vdw 1.777 2.270 nonbonded pdb=" HE3 TRP A 4 " pdb="HD21 LEU A 7 " model vdw 1.777 2.270 nonbonded pdb=" HE3 TRP C 4 " pdb="HD21 LEU C 7 " model vdw 1.778 2.270 nonbonded pdb=" HE3 TRP F 4 " pdb="HD21 LEU F 7 " model vdw 1.778 2.270 nonbonded pdb=" HE3 TRP E 4 " pdb="HD21 LEU E 7 " model vdw 1.778 2.270 ... (remaining 537023 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 4 and (name N or name CA or name C or name O or name CB o \ r name HA )) or (resid 5 through 7 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 8 or (resid 9 through 16 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 17 thr \ ough 222)) selection = (chain 'B' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name HA )) or (resid 5 through 7 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 8 or (resid 9 through 16 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 17 thr \ ough 222)) selection = (chain 'C' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name HA )) or (resid 5 through 7 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 8 or (resid 9 through 16 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 17 thr \ ough 222)) selection = (chain 'D' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name HA )) or (resid 5 through 7 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 8 or (resid 9 through 16 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 17 thr \ ough 222)) selection = (chain 'E' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name HA )) or (resid 5 through 7 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 8 or (resid 9 through 16 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 17 thr \ ough 222)) selection = (chain 'F' and ((resid 4 and (name N or name CA or name C or name O or name CB o \ r name HA )) or (resid 5 through 7 and (name N or name CA or name C or name O or \ name CB or name H or name HA )) or resid 8 or (resid 9 through 16 and (name N o \ r name CA or name C or name O or name CB or name H or name HA )) or resid 17 thr \ ough 222)) selection = (chain 'G' and (resid 4 through 100 or resid 140 through 222)) selection = (chain 'H' and (resid 4 through 100 or resid 140 through 222)) selection = (chain 'I' and (resid 4 through 100 or resid 140 through 222)) selection = (chain 'J' and (resid 4 through 100 or resid 140 through 222)) selection = (chain 'K' and (resid 4 through 100 or resid 140 through 222)) selection = (chain 'L' and (resid 4 through 100 or resid 140 through 222)) } 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: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.280 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.110 Process input model: 35.800 Find NCS groups from input model: 0.960 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 20760 Z= 0.175 Angle : 1.124 9.217 27216 Z= 0.426 Chirality : 0.036 0.163 2874 Planarity : 0.003 0.031 3072 Dihedral : 13.389 89.348 8214 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 2.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 0.64 % Allowed : 11.02 % Favored : 88.34 % 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: 0.86 (0.17), residues: 2160 helix: 1.13 (0.12), residues: 1638 sheet: 0.09 (0.38), residues: 168 loop : -1.62 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 9 TYR 0.008 0.001 TYR B 220 PHE 0.013 0.001 PHE B 190 TRP 0.005 0.001 TRP B 25 HIS 0.002 0.000 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00351 (20724) covalent geometry : angle 1.12521 (27144) SS BOND : bond 0.00114 ( 36) SS BOND : angle 0.73957 ( 72) hydrogen bonds : bond 0.15067 ( 1326) hydrogen bonds : angle 6.63808 ( 3942) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Evaluate side-chains 201 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 189 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.7622 (m-30) cc_final: 0.7310 (m-30) REVERT: A 173 LYS cc_start: 0.6924 (mttt) cc_final: 0.6325 (mmpt) REVERT: B 47 ASP cc_start: 0.6417 (p0) cc_final: 0.6146 (p0) REVERT: B 173 LYS cc_start: 0.6964 (mttt) cc_final: 0.6153 (mmpt) REVERT: C 51 ASP cc_start: 0.7563 (m-30) cc_final: 0.7243 (m-30) REVERT: C 172 LEU cc_start: 0.6641 (mt) cc_final: 0.6440 (tp) REVERT: C 173 LYS cc_start: 0.7056 (mttt) cc_final: 0.6206 (mmmt) REVERT: D 47 ASP cc_start: 0.6632 (p0) cc_final: 0.6382 (p0) REVERT: D 51 ASP cc_start: 0.7640 (m-30) cc_final: 0.7252 (m-30) REVERT: D 173 LYS cc_start: 0.6946 (mttt) cc_final: 0.6347 (mmpt) REVERT: E 47 ASP cc_start: 0.6424 (p0) cc_final: 0.6107 (p0) REVERT: E 51 ASP cc_start: 0.7453 (m-30) cc_final: 0.7064 (m-30) REVERT: E 173 LYS cc_start: 0.6956 (mttt) cc_final: 0.6157 (mmpt) REVERT: F 51 ASP cc_start: 0.7565 (m-30) cc_final: 0.7249 (m-30) REVERT: F 173 LYS cc_start: 0.7034 (mttt) cc_final: 0.6203 (mmmt) REVERT: G 47 ASP cc_start: 0.7163 (p0) cc_final: 0.6770 (p0) REVERT: H 149 ASN cc_start: 0.7027 (OUTLIER) cc_final: 0.6426 (t0) REVERT: H 204 MET cc_start: 0.8783 (mmt) cc_final: 0.8070 (mmm) REVERT: I 151 ILE cc_start: 0.8368 (mm) cc_final: 0.7989 (mt) REVERT: J 47 ASP cc_start: 0.7113 (p0) cc_final: 0.6715 (p0) REVERT: K 204 MET cc_start: 0.8876 (mmt) cc_final: 0.8272 (mmt) REVERT: L 23 LYS cc_start: 0.7758 (mttt) cc_final: 0.7495 (mttm) REVERT: L 151 ILE cc_start: 0.8400 (mm) cc_final: 0.8028 (mt) outliers start: 12 outliers final: 11 residues processed: 201 average time/residue: 1.1568 time to fit residues: 268.7298 Evaluate side-chains 182 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 170 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 149 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 ASN B 13 ASN C 13 ASN D 13 ASN E 13 ASN F 13 ASN I 49 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.211867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.133331 restraints weight = 40189.057| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.40 r_work: 0.3108 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 20760 Z= 0.162 Angle : 0.551 4.804 27216 Z= 0.285 Chirality : 0.039 0.131 2874 Planarity : 0.004 0.027 3072 Dihedral : 7.948 81.035 4428 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 1.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.44 % Allowed : 10.54 % Favored : 88.02 % 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: 2.26 (0.17), residues: 2160 helix: 2.30 (0.12), residues: 1650 sheet: -0.47 (0.32), residues: 204 loop : -1.68 (0.30), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 33 TYR 0.020 0.002 TYR B 66 PHE 0.024 0.002 PHE A 190 TRP 0.008 0.001 TRP E 181 HIS 0.005 0.001 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00329 (20724) covalent geometry : angle 0.54901 (27144) SS BOND : bond 0.00125 ( 36) SS BOND : angle 1.02516 ( 72) hydrogen bonds : bond 0.04503 ( 1326) hydrogen bonds : angle 4.52275 ( 3942) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Evaluate side-chains 241 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 214 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.8781 (m-30) cc_final: 0.8567 (m-30) REVERT: A 173 LYS cc_start: 0.8403 (mttt) cc_final: 0.8124 (mmpt) REVERT: B 47 ASP cc_start: 0.8280 (p0) cc_final: 0.8047 (p0) REVERT: B 155 LEU cc_start: 0.7363 (mt) cc_final: 0.7150 (mm) REVERT: B 164 GLN cc_start: 0.6303 (tt0) cc_final: 0.6064 (mt0) REVERT: C 173 LYS cc_start: 0.8389 (mttt) cc_final: 0.7982 (mmpt) REVERT: D 51 ASP cc_start: 0.8811 (m-30) cc_final: 0.8584 (m-30) REVERT: D 173 LYS cc_start: 0.8440 (mttt) cc_final: 0.8160 (mmpt) REVERT: E 155 LEU cc_start: 0.7404 (mt) cc_final: 0.7188 (mm) REVERT: E 164 GLN cc_start: 0.6245 (tt0) cc_final: 0.6028 (mt0) REVERT: E 173 LYS cc_start: 0.8455 (mttt) cc_final: 0.8039 (mmpt) REVERT: F 173 LYS cc_start: 0.8413 (mttt) cc_final: 0.8012 (mmpt) REVERT: G 47 ASP cc_start: 0.7696 (p0) cc_final: 0.7490 (p0) REVERT: G 149 ASN cc_start: 0.7065 (OUTLIER) cc_final: 0.6612 (t0) REVERT: H 149 ASN cc_start: 0.7098 (OUTLIER) cc_final: 0.6653 (t0) REVERT: H 204 MET cc_start: 0.8921 (mmt) cc_final: 0.8438 (mmt) REVERT: I 23 LYS cc_start: 0.7322 (mttt) cc_final: 0.7094 (mttm) REVERT: I 47 ASP cc_start: 0.7718 (p0) cc_final: 0.7299 (p0) REVERT: I 149 ASN cc_start: 0.7066 (OUTLIER) cc_final: 0.6579 (t0) REVERT: I 151 ILE cc_start: 0.8185 (mm) cc_final: 0.7808 (mt) REVERT: J 47 ASP cc_start: 0.7659 (p0) cc_final: 0.7452 (p0) REVERT: J 149 ASN cc_start: 0.7092 (OUTLIER) cc_final: 0.6621 (t0) REVERT: K 149 ASN cc_start: 0.6984 (OUTLIER) cc_final: 0.6561 (t0) REVERT: K 204 MET cc_start: 0.8986 (mmt) cc_final: 0.8486 (mmt) REVERT: L 23 LYS cc_start: 0.7250 (mttt) cc_final: 0.7037 (mttm) REVERT: L 47 ASP cc_start: 0.7754 (p0) cc_final: 0.7524 (p0) REVERT: L 149 ASN cc_start: 0.7005 (OUTLIER) cc_final: 0.6556 (t0) REVERT: L 151 ILE cc_start: 0.8202 (mm) cc_final: 0.7839 (mt) outliers start: 27 outliers final: 9 residues processed: 234 average time/residue: 1.1406 time to fit residues: 307.1323 Evaluate side-chains 218 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 149 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 78 optimal weight: 0.9990 chunk 80 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 172 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 114 optimal weight: 0.0770 chunk 151 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 62 optimal weight: 0.2980 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 164 GLN F 58 GLN F 164 GLN G 49 GLN G 58 GLN H 49 GLN J 49 GLN K 49 GLN L 49 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.209873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.132896 restraints weight = 40367.188| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.40 r_work: 0.3062 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 20760 Z= 0.117 Angle : 0.489 5.200 27216 Z= 0.249 Chirality : 0.037 0.126 2874 Planarity : 0.003 0.038 3072 Dihedral : 7.517 72.779 4428 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.91 % Allowed : 11.40 % Favored : 87.70 % 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: 2.90 (0.18), residues: 2160 helix: 2.81 (0.12), residues: 1650 sheet: -0.44 (0.33), residues: 168 loop : -1.54 (0.29), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 33 TYR 0.014 0.001 TYR E 66 PHE 0.020 0.002 PHE H 190 TRP 0.006 0.001 TRP F 181 HIS 0.004 0.000 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00255 (20724) covalent geometry : angle 0.48697 (27144) SS BOND : bond 0.00158 ( 36) SS BOND : angle 0.89998 ( 72) hydrogen bonds : bond 0.04090 ( 1326) hydrogen bonds : angle 4.40207 ( 3942) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Evaluate side-chains 238 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 221 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.8790 (m-30) cc_final: 0.8589 (m-30) REVERT: A 173 LYS cc_start: 0.8468 (mttt) cc_final: 0.8150 (mmpt) REVERT: B 47 ASP cc_start: 0.8290 (p0) cc_final: 0.8078 (p0) REVERT: B 155 LEU cc_start: 0.7639 (mt) cc_final: 0.7438 (mm) REVERT: B 173 LYS cc_start: 0.8494 (mtpt) cc_final: 0.8007 (mmpt) REVERT: C 47 ASP cc_start: 0.8505 (p0) cc_final: 0.8263 (p0) REVERT: C 51 ASP cc_start: 0.8799 (m-30) cc_final: 0.8593 (m-30) REVERT: C 155 LEU cc_start: 0.7529 (mt) cc_final: 0.7306 (mm) REVERT: C 173 LYS cc_start: 0.8403 (mttt) cc_final: 0.8000 (mmpt) REVERT: D 51 ASP cc_start: 0.8862 (m-30) cc_final: 0.8648 (m-30) REVERT: D 155 LEU cc_start: 0.7577 (mt) cc_final: 0.7377 (mm) REVERT: D 173 LYS cc_start: 0.8461 (mttt) cc_final: 0.8162 (mmpt) REVERT: E 155 LEU cc_start: 0.7614 (mt) cc_final: 0.7410 (mm) REVERT: E 164 GLN cc_start: 0.6306 (tt0) cc_final: 0.5963 (mt0) REVERT: E 173 LYS cc_start: 0.8438 (mttt) cc_final: 0.8016 (mmpt) REVERT: F 47 ASP cc_start: 0.8435 (p0) cc_final: 0.8193 (p0) REVERT: F 51 ASP cc_start: 0.8816 (m-30) cc_final: 0.8610 (m-30) REVERT: F 155 LEU cc_start: 0.7500 (mt) cc_final: 0.7276 (mm) REVERT: F 173 LYS cc_start: 0.8412 (mttt) cc_final: 0.8064 (mmpt) REVERT: G 47 ASP cc_start: 0.7840 (p0) cc_final: 0.7614 (p0) REVERT: G 149 ASN cc_start: 0.7137 (OUTLIER) cc_final: 0.6582 (t0) REVERT: H 47 ASP cc_start: 0.8089 (p0) cc_final: 0.7879 (p0) REVERT: H 149 ASN cc_start: 0.7117 (OUTLIER) cc_final: 0.6591 (t0) REVERT: H 151 ILE cc_start: 0.8217 (mm) cc_final: 0.7824 (mt) REVERT: H 204 MET cc_start: 0.9014 (mmt) cc_final: 0.8652 (mmt) REVERT: I 23 LYS cc_start: 0.7353 (mttt) cc_final: 0.7135 (mttm) REVERT: I 47 ASP cc_start: 0.7859 (p0) cc_final: 0.7648 (p0) REVERT: I 149 ASN cc_start: 0.7021 (OUTLIER) cc_final: 0.6462 (t0) REVERT: I 151 ILE cc_start: 0.8176 (mm) cc_final: 0.7838 (mt) REVERT: J 47 ASP cc_start: 0.7807 (p0) cc_final: 0.7573 (p0) REVERT: J 149 ASN cc_start: 0.7144 (OUTLIER) cc_final: 0.6584 (t0) REVERT: K 149 ASN cc_start: 0.7024 (OUTLIER) cc_final: 0.6529 (t0) REVERT: K 151 ILE cc_start: 0.8280 (mm) cc_final: 0.7895 (mt) REVERT: K 204 MET cc_start: 0.9030 (mmt) cc_final: 0.8681 (mmt) REVERT: L 23 LYS cc_start: 0.7328 (mttt) cc_final: 0.7109 (mttm) REVERT: L 47 ASP cc_start: 0.7860 (p0) cc_final: 0.7657 (p0) REVERT: L 149 ASN cc_start: 0.6990 (OUTLIER) cc_final: 0.6460 (t0) REVERT: L 151 ILE cc_start: 0.8205 (mm) cc_final: 0.7854 (mt) outliers start: 17 outliers final: 7 residues processed: 233 average time/residue: 1.0329 time to fit residues: 281.3410 Evaluate side-chains 227 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 214 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain H residue 155 LEU Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 149 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 62 optimal weight: 0.7980 chunk 185 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 159 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 196 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.4267 r_free = 0.4267 target = 0.205892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.129961 restraints weight = 40481.556| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 1.42 r_work: 0.3012 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 3.49 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20760 Z= 0.144 Angle : 0.517 5.231 27216 Z= 0.266 Chirality : 0.038 0.127 2874 Planarity : 0.003 0.027 3072 Dihedral : 7.590 64.412 4428 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.08 % Allowed : 10.44 % Favored : 87.49 % 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: 2.80 (0.18), residues: 2160 helix: 2.75 (0.12), residues: 1650 sheet: -0.70 (0.32), residues: 168 loop : -1.51 (0.29), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 33 TYR 0.018 0.002 TYR B 66 PHE 0.022 0.002 PHE H 190 TRP 0.009 0.001 TRP C 181 HIS 0.003 0.001 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00322 (20724) covalent geometry : angle 0.51497 (27144) SS BOND : bond 0.00210 ( 36) SS BOND : angle 1.02226 ( 72) hydrogen bonds : bond 0.03690 ( 1326) hydrogen bonds : angle 4.31692 ( 3942) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Evaluate side-chains 263 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 224 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8540 (mttt) cc_final: 0.8227 (mmpt) REVERT: B 173 LYS cc_start: 0.8540 (mtpt) cc_final: 0.8131 (mmpt) REVERT: C 155 LEU cc_start: 0.7696 (mt) cc_final: 0.7494 (mm) REVERT: C 173 LYS cc_start: 0.8477 (mttt) cc_final: 0.8107 (mmpt) REVERT: D 155 LEU cc_start: 0.7794 (mt) cc_final: 0.7589 (mm) REVERT: D 173 LYS cc_start: 0.8544 (mttt) cc_final: 0.8220 (mmpt) REVERT: E 173 LYS cc_start: 0.8480 (mttt) cc_final: 0.8122 (mmpt) REVERT: F 47 ASP cc_start: 0.8503 (p0) cc_final: 0.8291 (p0) REVERT: F 155 LEU cc_start: 0.7676 (mt) cc_final: 0.7472 (mm) REVERT: F 173 LYS cc_start: 0.8478 (mttt) cc_final: 0.8135 (mmpt) REVERT: G 149 ASN cc_start: 0.7203 (OUTLIER) cc_final: 0.6616 (t0) REVERT: H 149 ASN cc_start: 0.7208 (OUTLIER) cc_final: 0.6640 (t0) REVERT: H 151 ILE cc_start: 0.8227 (mm) cc_final: 0.7850 (mt) REVERT: H 204 MET cc_start: 0.9063 (mmt) cc_final: 0.8779 (mmt) REVERT: I 23 LYS cc_start: 0.7426 (mttt) cc_final: 0.7189 (mttm) REVERT: I 149 ASN cc_start: 0.7090 (OUTLIER) cc_final: 0.6507 (t0) REVERT: I 151 ILE cc_start: 0.8231 (mm) cc_final: 0.7882 (mt) REVERT: J 47 ASP cc_start: 0.7977 (p0) cc_final: 0.7775 (p0) REVERT: J 149 ASN cc_start: 0.7206 (OUTLIER) cc_final: 0.6585 (t0) REVERT: K 43 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7267 (pm20) REVERT: K 149 ASN cc_start: 0.7091 (OUTLIER) cc_final: 0.6535 (t0) REVERT: K 151 ILE cc_start: 0.8317 (mm) cc_final: 0.7947 (mt) REVERT: K 204 MET cc_start: 0.9066 (mmt) cc_final: 0.8784 (mmt) REVERT: L 23 LYS cc_start: 0.7408 (mttt) cc_final: 0.7170 (mttm) REVERT: L 149 ASN cc_start: 0.7061 (OUTLIER) cc_final: 0.6513 (t0) REVERT: L 151 ILE cc_start: 0.8231 (mm) cc_final: 0.7899 (mt) outliers start: 39 outliers final: 12 residues processed: 254 average time/residue: 1.0119 time to fit residues: 301.8199 Evaluate side-chains 239 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 220 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 149 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 170 optimal weight: 3.9990 chunk 215 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 58 GLN K 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.205572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.126799 restraints weight = 40151.130| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.55 r_work: 0.2948 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 20760 Z= 0.208 Angle : 0.585 6.107 27216 Z= 0.302 Chirality : 0.040 0.135 2874 Planarity : 0.004 0.031 3072 Dihedral : 8.586 56.897 4428 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.50 % Allowed : 10.54 % Favored : 86.95 % 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: 2.32 (0.18), residues: 2160 helix: 2.43 (0.13), residues: 1650 sheet: -0.93 (0.31), residues: 204 loop : -1.84 (0.30), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 180 TYR 0.023 0.003 TYR B 66 PHE 0.027 0.003 PHE K 190 TRP 0.013 0.002 TRP C 181 HIS 0.005 0.001 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00479 (20724) covalent geometry : angle 0.58255 (27144) SS BOND : bond 0.00364 ( 36) SS BOND : angle 1.24347 ( 72) hydrogen bonds : bond 0.04093 ( 1326) hydrogen bonds : angle 4.49471 ( 3942) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Evaluate side-chains 287 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 240 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8651 (m-30) REVERT: A 173 LYS cc_start: 0.8440 (mttt) cc_final: 0.8076 (mmpt) REVERT: B 173 LYS cc_start: 0.8491 (mtpt) cc_final: 0.8037 (mmpt) REVERT: C 155 LEU cc_start: 0.7896 (mt) cc_final: 0.7695 (mm) REVERT: C 173 LYS cc_start: 0.8456 (mttt) cc_final: 0.7998 (mmpt) REVERT: D 51 ASP cc_start: 0.8995 (OUTLIER) cc_final: 0.8667 (m-30) REVERT: D 173 LYS cc_start: 0.8440 (mttt) cc_final: 0.8076 (mmpt) REVERT: E 156 PHE cc_start: 0.8042 (m-10) cc_final: 0.7769 (m-80) REVERT: E 173 LYS cc_start: 0.8441 (mttt) cc_final: 0.8082 (mmpt) REVERT: F 155 LEU cc_start: 0.7884 (mt) cc_final: 0.7681 (mm) REVERT: F 173 LYS cc_start: 0.8446 (mttt) cc_final: 0.8037 (mmpt) REVERT: G 149 ASN cc_start: 0.7294 (OUTLIER) cc_final: 0.6719 (t0) REVERT: H 43 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7183 (pm20) REVERT: H 149 ASN cc_start: 0.7241 (OUTLIER) cc_final: 0.6633 (t0) REVERT: H 151 ILE cc_start: 0.8170 (mm) cc_final: 0.7781 (mt) REVERT: H 204 MET cc_start: 0.9051 (mmt) cc_final: 0.8764 (mmt) REVERT: I 149 ASN cc_start: 0.7226 (OUTLIER) cc_final: 0.7000 (t0) REVERT: I 151 ILE cc_start: 0.8149 (mm) cc_final: 0.7800 (mt) REVERT: J 149 ASN cc_start: 0.7294 (OUTLIER) cc_final: 0.6666 (t0) REVERT: K 43 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.7193 (pm20) REVERT: K 149 ASN cc_start: 0.7240 (OUTLIER) cc_final: 0.6625 (t0) REVERT: K 151 ILE cc_start: 0.8154 (mm) cc_final: 0.7774 (mt) REVERT: K 204 MET cc_start: 0.9059 (mmt) cc_final: 0.8773 (mmt) REVERT: L 149 ASN cc_start: 0.7195 (OUTLIER) cc_final: 0.6984 (t0) REVERT: L 151 ILE cc_start: 0.8182 (mm) cc_final: 0.7853 (mt) outliers start: 47 outliers final: 17 residues processed: 275 average time/residue: 0.9674 time to fit residues: 312.1154 Evaluate side-chains 263 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 236 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 43 GLU Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 149 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 47 optimal weight: 4.9990 chunk 105 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 63 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 191 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.207112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.130112 restraints weight = 40450.919| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.47 r_work: 0.3001 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 20760 Z= 0.130 Angle : 0.504 5.632 27216 Z= 0.259 Chirality : 0.037 0.121 2874 Planarity : 0.003 0.029 3072 Dihedral : 7.666 49.356 4428 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.13 % Allowed : 11.13 % Favored : 86.74 % 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: 2.65 (0.18), residues: 2160 helix: 2.68 (0.13), residues: 1650 sheet: -1.08 (0.29), residues: 168 loop : -1.58 (0.29), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 33 TYR 0.017 0.002 TYR B 66 PHE 0.021 0.002 PHE I 190 TRP 0.008 0.001 TRP C 181 HIS 0.003 0.000 HIS H 74 Details of bonding type rmsd covalent geometry : bond 0.00288 (20724) covalent geometry : angle 0.50149 (27144) SS BOND : bond 0.00217 ( 36) SS BOND : angle 1.02304 ( 72) hydrogen bonds : bond 0.03382 ( 1326) hydrogen bonds : angle 4.30012 ( 3942) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Evaluate side-chains 277 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 237 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.8921 (m-30) cc_final: 0.8688 (m-30) REVERT: A 173 LYS cc_start: 0.8479 (mttt) cc_final: 0.8137 (mmpt) REVERT: B 173 LYS cc_start: 0.8486 (mtpt) cc_final: 0.8024 (mmpt) REVERT: C 173 LYS cc_start: 0.8469 (mttt) cc_final: 0.8054 (mmpt) REVERT: D 51 ASP cc_start: 0.8981 (OUTLIER) cc_final: 0.8737 (m-30) REVERT: D 173 LYS cc_start: 0.8464 (mttt) cc_final: 0.8121 (mmpt) REVERT: E 156 PHE cc_start: 0.8041 (m-10) cc_final: 0.7766 (m-80) REVERT: E 173 LYS cc_start: 0.8427 (mttt) cc_final: 0.8057 (mmpt) REVERT: F 173 LYS cc_start: 0.8468 (mttt) cc_final: 0.8064 (mmpt) REVERT: G 149 ASN cc_start: 0.7229 (OUTLIER) cc_final: 0.6549 (t0) REVERT: H 43 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7185 (pm20) REVERT: H 149 ASN cc_start: 0.7279 (OUTLIER) cc_final: 0.6449 (t0) REVERT: H 151 ILE cc_start: 0.8135 (mm) cc_final: 0.7758 (mt) REVERT: I 149 ASN cc_start: 0.7161 (OUTLIER) cc_final: 0.6521 (t0) REVERT: I 151 ILE cc_start: 0.8122 (mm) cc_final: 0.7778 (mt) REVERT: J 149 ASN cc_start: 0.7213 (OUTLIER) cc_final: 0.6499 (t0) REVERT: K 149 ASN cc_start: 0.7204 (OUTLIER) cc_final: 0.6399 (t0) REVERT: K 151 ILE cc_start: 0.8157 (mm) cc_final: 0.7783 (mt) REVERT: L 149 ASN cc_start: 0.7125 (OUTLIER) cc_final: 0.6504 (t0) REVERT: L 151 ILE cc_start: 0.8091 (mm) cc_final: 0.7762 (mt) outliers start: 40 outliers final: 27 residues processed: 266 average time/residue: 1.0462 time to fit residues: 326.5219 Evaluate side-chains 271 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 236 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 155 LEU Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain K residue 155 LEU Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 149 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 124 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 135 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 98 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.209937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.136301 restraints weight = 41133.318| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 1.26 r_work: 0.2957 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 20760 Z= 0.182 Angle : 0.559 6.040 27216 Z= 0.288 Chirality : 0.039 0.138 2874 Planarity : 0.004 0.030 3072 Dihedral : 8.174 48.552 4428 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.08 % Allowed : 11.45 % Favored : 86.47 % 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: 2.45 (0.18), residues: 2160 helix: 2.53 (0.13), residues: 1650 sheet: -1.11 (0.29), residues: 168 loop : -1.61 (0.28), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG K 180 TYR 0.022 0.003 TYR E 66 PHE 0.027 0.002 PHE I 190 TRP 0.012 0.002 TRP F 181 HIS 0.005 0.001 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00420 (20724) covalent geometry : angle 0.55640 (27144) SS BOND : bond 0.00315 ( 36) SS BOND : angle 1.15949 ( 72) hydrogen bonds : bond 0.03702 ( 1326) hydrogen bonds : angle 4.39306 ( 3942) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Evaluate side-chains 278 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 239 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.8980 (OUTLIER) cc_final: 0.8664 (m-30) REVERT: A 173 LYS cc_start: 0.8482 (mttt) cc_final: 0.8201 (mmpt) REVERT: B 173 LYS cc_start: 0.8520 (mtpt) cc_final: 0.8153 (mmpt) REVERT: C 173 LYS cc_start: 0.8496 (mttt) cc_final: 0.8158 (mmpt) REVERT: D 51 ASP cc_start: 0.9013 (OUTLIER) cc_final: 0.8706 (m-30) REVERT: D 173 LYS cc_start: 0.8477 (mttt) cc_final: 0.8194 (mmpt) REVERT: E 156 PHE cc_start: 0.8185 (m-80) cc_final: 0.7878 (m-10) REVERT: E 173 LYS cc_start: 0.8496 (mttt) cc_final: 0.8191 (mmpt) REVERT: F 173 LYS cc_start: 0.8508 (mttt) cc_final: 0.8170 (mmpt) REVERT: G 149 ASN cc_start: 0.7432 (OUTLIER) cc_final: 0.6716 (t0) REVERT: H 43 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7309 (pm20) REVERT: H 149 ASN cc_start: 0.7351 (OUTLIER) cc_final: 0.6544 (t0) REVERT: H 151 ILE cc_start: 0.8190 (mm) cc_final: 0.7816 (mt) REVERT: I 149 ASN cc_start: 0.7371 (OUTLIER) cc_final: 0.6753 (t0) REVERT: I 151 ILE cc_start: 0.8236 (mm) cc_final: 0.7901 (mt) REVERT: J 149 ASN cc_start: 0.7421 (OUTLIER) cc_final: 0.6687 (t0) REVERT: K 149 ASN cc_start: 0.7323 (OUTLIER) cc_final: 0.6531 (t0) REVERT: K 151 ILE cc_start: 0.8205 (mm) cc_final: 0.7833 (mt) REVERT: L 149 ASN cc_start: 0.7306 (OUTLIER) cc_final: 0.6913 (t0) REVERT: L 151 ILE cc_start: 0.8209 (mm) cc_final: 0.7890 (mt) outliers start: 39 outliers final: 19 residues processed: 268 average time/residue: 0.6673 time to fit residues: 210.9667 Evaluate side-chains 266 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 238 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 149 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 172 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 109 optimal weight: 7.9990 chunk 21 optimal weight: 2.9990 chunk 72 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 81 GLN E 81 GLN H 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.202753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.127037 restraints weight = 40385.584| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.42 r_work: 0.2906 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20760 Z= 0.234 Angle : 0.608 6.466 27216 Z= 0.316 Chirality : 0.042 0.151 2874 Planarity : 0.004 0.036 3072 Dihedral : 9.025 52.798 4428 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.02 % Allowed : 12.03 % Favored : 85.94 % 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: 2.10 (0.18), residues: 2160 helix: 2.28 (0.13), residues: 1650 sheet: -1.08 (0.30), residues: 204 loop : -1.86 (0.29), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 180 TYR 0.026 0.003 TYR E 66 PHE 0.030 0.003 PHE I 190 TRP 0.015 0.002 TRP F 181 HIS 0.005 0.001 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00538 (20724) covalent geometry : angle 0.60516 (27144) SS BOND : bond 0.00426 ( 36) SS BOND : angle 1.37419 ( 72) hydrogen bonds : bond 0.03973 ( 1326) hydrogen bonds : angle 4.48343 ( 3942) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Evaluate side-chains 282 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 244 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.8989 (OUTLIER) cc_final: 0.8680 (m-30) REVERT: A 173 LYS cc_start: 0.8481 (mttt) cc_final: 0.8119 (mmpt) REVERT: A 213 LEU cc_start: 0.7312 (tp) cc_final: 0.7070 (tm) REVERT: B 173 LYS cc_start: 0.8466 (mtpt) cc_final: 0.8057 (mmpt) REVERT: C 156 PHE cc_start: 0.8098 (m-10) cc_final: 0.7753 (m-10) REVERT: C 173 LYS cc_start: 0.8449 (mttt) cc_final: 0.8128 (mmpt) REVERT: D 51 ASP cc_start: 0.9011 (OUTLIER) cc_final: 0.8701 (m-30) REVERT: D 173 LYS cc_start: 0.8476 (mttt) cc_final: 0.8105 (mmpt) REVERT: E 156 PHE cc_start: 0.8202 (m-80) cc_final: 0.7841 (m-10) REVERT: E 173 LYS cc_start: 0.8490 (mttt) cc_final: 0.8121 (mmpt) REVERT: F 156 PHE cc_start: 0.8093 (m-10) cc_final: 0.7755 (m-10) REVERT: F 173 LYS cc_start: 0.8459 (mttt) cc_final: 0.8134 (mmpt) REVERT: G 149 ASN cc_start: 0.7544 (OUTLIER) cc_final: 0.6792 (t0) REVERT: H 43 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.7307 (pm20) REVERT: H 149 ASN cc_start: 0.7338 (OUTLIER) cc_final: 0.6520 (t0) REVERT: H 151 ILE cc_start: 0.8102 (mm) cc_final: 0.7717 (mt) REVERT: I 149 ASN cc_start: 0.7488 (OUTLIER) cc_final: 0.7070 (t0) REVERT: I 151 ILE cc_start: 0.8133 (mm) cc_final: 0.7792 (mt) REVERT: J 149 ASN cc_start: 0.7544 (OUTLIER) cc_final: 0.6769 (t0) REVERT: K 149 ASN cc_start: 0.7344 (OUTLIER) cc_final: 0.6535 (t0) REVERT: K 151 ILE cc_start: 0.8114 (mm) cc_final: 0.7730 (mt) REVERT: L 149 ASN cc_start: 0.7471 (OUTLIER) cc_final: 0.7064 (t0) REVERT: L 151 ILE cc_start: 0.8132 (mm) cc_final: 0.7804 (mt) outliers start: 38 outliers final: 17 residues processed: 275 average time/residue: 0.6164 time to fit residues: 200.8984 Evaluate side-chains 268 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 242 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 149 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 82 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 116 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 137 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 114 optimal weight: 0.5980 chunk 173 optimal weight: 0.9990 chunk 58 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN D 81 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.208826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.135182 restraints weight = 41621.926| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.66 r_work: 0.2970 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.3316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 20760 Z= 0.113 Angle : 0.498 5.699 27216 Z= 0.255 Chirality : 0.037 0.116 2874 Planarity : 0.003 0.029 3072 Dihedral : 7.826 49.917 4428 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.17 % Allowed : 13.21 % Favored : 85.62 % 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: 2.64 (0.18), residues: 2160 helix: 2.68 (0.13), residues: 1650 sheet: -1.12 (0.30), residues: 168 loop : -1.60 (0.28), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 33 TYR 0.014 0.002 TYR J 66 PHE 0.019 0.001 PHE I 190 TRP 0.006 0.001 TRP F 181 HIS 0.003 0.000 HIS K 74 Details of bonding type rmsd covalent geometry : bond 0.00244 (20724) covalent geometry : angle 0.49594 (27144) SS BOND : bond 0.00158 ( 36) SS BOND : angle 1.01028 ( 72) hydrogen bonds : bond 0.03185 ( 1326) hydrogen bonds : angle 4.28170 ( 3942) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Evaluate side-chains 269 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 247 time to evaluate : 0.595 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 51 ASP cc_start: 0.8899 (m-30) cc_final: 0.8689 (m-30) REVERT: A 173 LYS cc_start: 0.8457 (mttt) cc_final: 0.8118 (mmpt) REVERT: B 173 LYS cc_start: 0.8419 (mtpt) cc_final: 0.7970 (mmpt) REVERT: C 156 PHE cc_start: 0.8067 (m-10) cc_final: 0.7716 (m-10) REVERT: C 173 LYS cc_start: 0.8410 (mttt) cc_final: 0.8025 (mmpt) REVERT: D 51 ASP cc_start: 0.8923 (OUTLIER) cc_final: 0.8714 (m-30) REVERT: D 173 LYS cc_start: 0.8460 (mttt) cc_final: 0.8109 (mmpt) REVERT: E 156 PHE cc_start: 0.8139 (m-80) cc_final: 0.7837 (m-10) REVERT: E 173 LYS cc_start: 0.8439 (mttt) cc_final: 0.8073 (mmpt) REVERT: F 156 PHE cc_start: 0.8037 (m-10) cc_final: 0.7700 (m-10) REVERT: F 173 LYS cc_start: 0.8408 (mttt) cc_final: 0.8021 (mmpt) REVERT: G 149 ASN cc_start: 0.7475 (OUTLIER) cc_final: 0.6587 (t0) REVERT: H 43 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7152 (pm20) REVERT: H 149 ASN cc_start: 0.7345 (OUTLIER) cc_final: 0.6374 (t0) REVERT: H 151 ILE cc_start: 0.8088 (mm) cc_final: 0.7710 (mt) REVERT: I 149 ASN cc_start: 0.7375 (OUTLIER) cc_final: 0.6539 (t0) REVERT: I 151 ILE cc_start: 0.8126 (mm) cc_final: 0.7787 (mt) REVERT: J 149 ASN cc_start: 0.7473 (OUTLIER) cc_final: 0.6557 (t0) REVERT: K 149 ASN cc_start: 0.7314 (OUTLIER) cc_final: 0.6351 (t0) REVERT: K 151 ILE cc_start: 0.8107 (mm) cc_final: 0.7714 (mt) REVERT: L 149 ASN cc_start: 0.7342 (OUTLIER) cc_final: 0.6526 (t0) REVERT: L 151 ILE cc_start: 0.8116 (mm) cc_final: 0.7784 (mt) outliers start: 22 outliers final: 14 residues processed: 265 average time/residue: 0.6299 time to fit residues: 197.3352 Evaluate side-chains 265 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 243 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 149 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 82 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 chunk 187 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 37 optimal weight: 9.9990 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 205 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN B 81 GLN D 81 GLN E 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.204450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.128328 restraints weight = 40878.858| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.35 r_work: 0.2975 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20760 Z= 0.143 Angle : 0.524 5.897 27216 Z= 0.268 Chirality : 0.038 0.124 2874 Planarity : 0.004 0.029 3072 Dihedral : 7.752 52.974 4428 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.76 % Allowed : 12.73 % Favored : 85.52 % 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: 2.65 (0.18), residues: 2160 helix: 2.69 (0.13), residues: 1650 sheet: -1.18 (0.29), residues: 168 loop : -1.58 (0.28), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 33 TYR 0.018 0.002 TYR E 66 PHE 0.024 0.002 PHE L 190 TRP 0.009 0.001 TRP C 181 HIS 0.004 0.000 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00325 (20724) covalent geometry : angle 0.52212 (27144) SS BOND : bond 0.00237 ( 36) SS BOND : angle 1.08138 ( 72) hydrogen bonds : bond 0.03330 ( 1326) hydrogen bonds : angle 4.29527 ( 3942) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4320 Ramachandran restraints generated. 2160 Oldfield, 0 Emsley, 2160 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Residue SER 5 is missing expected H atoms. Skipping. Residue LEU 7 is missing expected H atoms. Skipping. Residue LEU 10 is missing expected H atoms. Skipping. Residue LEU 11 is missing expected H atoms. Skipping. Residue ALA 14 is missing expected H atoms. Skipping. Evaluate side-chains 274 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 241 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 LYS cc_start: 0.8503 (mttt) cc_final: 0.8176 (mmpt) REVERT: B 173 LYS cc_start: 0.8456 (mtpt) cc_final: 0.8059 (mmpt) REVERT: C 156 PHE cc_start: 0.8121 (m-10) cc_final: 0.7782 (m-10) REVERT: C 173 LYS cc_start: 0.8508 (mttt) cc_final: 0.8081 (mmpt) REVERT: D 51 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8621 (m-30) REVERT: D 173 LYS cc_start: 0.8502 (mttt) cc_final: 0.8170 (mmpt) REVERT: E 156 PHE cc_start: 0.8219 (m-80) cc_final: 0.7927 (m-10) REVERT: E 173 LYS cc_start: 0.8496 (mttt) cc_final: 0.8173 (mmpt) REVERT: F 156 PHE cc_start: 0.8116 (m-10) cc_final: 0.7784 (m-10) REVERT: F 173 LYS cc_start: 0.8503 (mttt) cc_final: 0.8078 (mmpt) REVERT: G 149 ASN cc_start: 0.7518 (OUTLIER) cc_final: 0.6594 (t0) REVERT: H 43 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7288 (pm20) REVERT: H 149 ASN cc_start: 0.7424 (OUTLIER) cc_final: 0.6417 (t0) REVERT: H 151 ILE cc_start: 0.8151 (mm) cc_final: 0.7777 (mt) REVERT: I 149 ASN cc_start: 0.7431 (OUTLIER) cc_final: 0.6562 (t0) REVERT: I 151 ILE cc_start: 0.8200 (mm) cc_final: 0.7871 (mt) REVERT: J 149 ASN cc_start: 0.7517 (OUTLIER) cc_final: 0.6577 (t0) REVERT: K 149 ASN cc_start: 0.7397 (OUTLIER) cc_final: 0.6395 (t0) REVERT: K 151 ILE cc_start: 0.8177 (mm) cc_final: 0.7790 (mt) REVERT: L 149 ASN cc_start: 0.7417 (OUTLIER) cc_final: 0.6563 (t0) REVERT: L 151 ILE cc_start: 0.8182 (mm) cc_final: 0.7855 (mt) outliers start: 33 outliers final: 14 residues processed: 267 average time/residue: 0.6198 time to fit residues: 195.9095 Evaluate side-chains 262 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 240 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain B residue 149 ASN Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 29 LEU Chi-restraints excluded: chain H residue 43 GLU Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 26 LEU Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 149 ASN Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 149 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 38 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 68 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 191 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 GLN B 81 GLN D 81 GLN E 81 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.210721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.139199 restraints weight = 41534.014| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.15 r_work: 0.2997 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 20760 Z= 0.119 Angle : 0.499 6.273 27216 Z= 0.255 Chirality : 0.037 0.118 2874 Planarity : 0.003 0.033 3072 Dihedral : 7.297 57.530 4428 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.12 % Allowed : 13.42 % Favored : 85.46 % 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: 2.83 (0.18), residues: 2160 helix: 2.83 (0.13), residues: 1650 sheet: -1.16 (0.29), residues: 168 loop : -1.59 (0.28), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 68 TYR 0.015 0.002 TYR B 66 PHE 0.022 0.001 PHE I 190 TRP 0.007 0.001 TRP C 181 HIS 0.003 0.000 HIS K 74 Details of bonding type rmsd covalent geometry : bond 0.00264 (20724) covalent geometry : angle 0.49724 (27144) SS BOND : bond 0.00165 ( 36) SS BOND : angle 0.99600 ( 72) hydrogen bonds : bond 0.03088 ( 1326) hydrogen bonds : angle 4.22041 ( 3942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12574.51 seconds wall clock time: 212 minutes 59.02 seconds (12779.02 seconds total)