Starting phenix.real_space_refine on Sat Mar 7 13:45:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jlw_22382/03_2026/7jlw_22382_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jlw_22382/03_2026/7jlw_22382.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7jlw_22382/03_2026/7jlw_22382_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jlw_22382/03_2026/7jlw_22382_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7jlw_22382/03_2026/7jlw_22382.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jlw_22382/03_2026/7jlw_22382.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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 24 5.49 5 S 120 5.16 5 C 14664 2.51 5 N 3132 2.21 5 O 3624 1.98 5 H 18720 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40284 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "B" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "C" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "D" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "E" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "F" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "G" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "H" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "I" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "J" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "K" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "L" Number of atoms: 3136 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 3136 Classifications: {'peptide': 193} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 185} Chain breaks: 1 Chain: "A" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-1': 9, 'MC3:plan-2': 8} Unresolved non-hydrogen planarities: 60 Chain: "B" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-1': 9, 'MC3:plan-2': 8} Unresolved non-hydrogen planarities: 60 Chain: "C" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-1': 9, 'MC3:plan-2': 8} Unresolved non-hydrogen planarities: 60 Chain: "D" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-1': 9, 'MC3:plan-2': 8} Unresolved non-hydrogen planarities: 60 Chain: "E" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-1': 9, 'MC3:plan-2': 8} Unresolved non-hydrogen planarities: 60 Chain: "F" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-1': 9, 'MC3:plan-2': 8} Unresolved non-hydrogen planarities: 60 Chain: "G" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-1': 9, 'MC3:plan-2': 8} Unresolved non-hydrogen planarities: 60 Chain: "H" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-1': 9, 'MC3:plan-2': 8} Unresolved non-hydrogen planarities: 60 Chain: "I" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-1': 9, 'MC3:plan-2': 8} Unresolved non-hydrogen planarities: 60 Chain: "J" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-1': 9, 'MC3:plan-2': 8} Unresolved non-hydrogen planarities: 60 Chain: "K" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-1': 9, 'MC3:plan-2': 8} Unresolved non-hydrogen planarities: 60 Chain: "L" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Unusual residues: {'MC3': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 269 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'MC3:plan-1': 9, 'MC3:plan-2': 8} Unresolved non-hydrogen planarities: 60 Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "B" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "C" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "D" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "E" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "F" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "G" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "H" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "I" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "J" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "K" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "L" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Time building chain proxies: 7.34, per 1000 atoms: 0.18 Number of scatterers: 40284 At special positions: 0 Unit cell: (96.701, 96.701, 161.601, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 120 16.00 P 24 15.00 O 3624 8.00 N 3132 7.00 C 14664 6.00 H 18720 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 195 " distance=2.04 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 190 " distance=2.95 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 201 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 195 " distance=2.04 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 190 " distance=2.95 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 201 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 195 " distance=2.04 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 190 " distance=2.94 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 201 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 195 " distance=2.04 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 190 " distance=2.95 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 201 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 195 " distance=2.04 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 190 " distance=2.94 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 201 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 195 " distance=2.04 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 190 " distance=2.94 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 201 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 195 " distance=2.04 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 190 " distance=2.94 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 201 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 195 " distance=2.04 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 190 " distance=2.95 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 201 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 195 " distance=2.04 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 190 " distance=2.94 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 201 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 195 " distance=2.04 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 190 " distance=2.95 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 201 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 195 " distance=2.04 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 190 " distance=2.95 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 201 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 195 " distance=2.04 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 190 " distance=2.94 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: 3.59 Conformation dependent library (CDL) restraints added in 1.1 seconds 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4344 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 12 sheets defined 78.2% alpha, 3.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 4 through 17 removed outlier: 4.031A pdb=" N GLU A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS A 17 " --> pdb=" O GLU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 33 removed outlier: 3.527A pdb=" N ARG A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 40 Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 106 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 151 through 181 removed outlier: 3.980A pdb=" N ARG A 156 " --> pdb=" O GLY A 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR A 157 " --> pdb=" O THR A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 236 Processing helix chain 'B' and resid 4 through 17 removed outlier: 4.032A pdb=" N GLU B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS B 17 " --> pdb=" O GLU B 13 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 33 removed outlier: 3.527A pdb=" N ARG B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 40 Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 106 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 151 through 181 removed outlier: 3.979A pdb=" N ARG B 156 " --> pdb=" O GLY B 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR B 157 " --> pdb=" O THR B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 236 Processing helix chain 'C' and resid 4 through 17 removed outlier: 4.032A pdb=" N GLU C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS C 17 " --> pdb=" O GLU C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 33 removed outlier: 3.527A pdb=" N ARG C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 106 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 151 through 181 removed outlier: 3.979A pdb=" N ARG C 156 " --> pdb=" O GLY C 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR C 157 " --> pdb=" O THR C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 205 through 236 Processing helix chain 'D' and resid 4 through 17 removed outlier: 4.031A pdb=" N GLU D 16 " --> pdb=" O GLU D 12 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS D 17 " --> pdb=" O GLU D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 33 removed outlier: 3.527A pdb=" N ARG D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 33 through 40 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 73 through 106 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 151 through 181 removed outlier: 3.980A pdb=" N ARG D 156 " --> pdb=" O GLY D 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR D 157 " --> pdb=" O THR D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 236 Processing helix chain 'E' and resid 4 through 17 removed outlier: 4.032A pdb=" N GLU E 16 " --> pdb=" O GLU E 12 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS E 17 " --> pdb=" O GLU E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 33 removed outlier: 3.527A pdb=" N ARG E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 33 through 40 Processing helix chain 'E' and resid 40 through 45 Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 73 through 106 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 151 through 181 removed outlier: 3.979A pdb=" N ARG E 156 " --> pdb=" O GLY E 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR E 157 " --> pdb=" O THR E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 236 Processing helix chain 'F' and resid 4 through 17 removed outlier: 4.032A pdb=" N GLU F 16 " --> pdb=" O GLU F 12 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS F 17 " --> pdb=" O GLU F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 33 removed outlier: 3.527A pdb=" N ARG F 33 " --> pdb=" O LEU F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 33 through 40 Processing helix chain 'F' and resid 40 through 45 Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 73 through 106 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 151 through 181 removed outlier: 3.979A pdb=" N ARG F 156 " --> pdb=" O GLY F 152 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR F 157 " --> pdb=" O THR F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 205 through 236 Processing helix chain 'G' and resid 4 through 17 removed outlier: 4.031A pdb=" N GLU G 16 " --> pdb=" O GLU G 12 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS G 17 " --> pdb=" O GLU G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 33 removed outlier: 3.527A pdb=" N ARG G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 33 through 40 Processing helix chain 'G' and resid 40 through 45 Processing helix chain 'G' and resid 60 through 70 Processing helix chain 'G' and resid 73 through 106 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 151 through 181 removed outlier: 3.979A pdb=" N ARG G 156 " --> pdb=" O GLY G 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR G 157 " --> pdb=" O THR G 153 " (cutoff:3.500A) Processing helix chain 'G' and resid 205 through 236 Processing helix chain 'H' and resid 4 through 17 removed outlier: 4.032A pdb=" N GLU H 16 " --> pdb=" O GLU H 12 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS H 17 " --> pdb=" O GLU H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 33 removed outlier: 3.527A pdb=" N ARG H 33 " --> pdb=" O LEU H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 40 Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 73 through 106 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 151 through 181 removed outlier: 3.980A pdb=" N ARG H 156 " --> pdb=" O GLY H 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR H 157 " --> pdb=" O THR H 153 " (cutoff:3.500A) Processing helix chain 'H' and resid 205 through 236 Processing helix chain 'I' and resid 4 through 17 removed outlier: 4.032A pdb=" N GLU I 16 " --> pdb=" O GLU I 12 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS I 17 " --> pdb=" O GLU I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 33 removed outlier: 3.527A pdb=" N ARG I 33 " --> pdb=" O LEU I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 40 Processing helix chain 'I' and resid 40 through 45 Processing helix chain 'I' and resid 60 through 70 Processing helix chain 'I' and resid 73 through 106 Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 151 through 181 removed outlier: 3.979A pdb=" N ARG I 156 " --> pdb=" O GLY I 152 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N THR I 157 " --> pdb=" O THR I 153 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 236 Processing helix chain 'J' and resid 4 through 17 removed outlier: 4.031A pdb=" N GLU J 16 " --> pdb=" O GLU J 12 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS J 17 " --> pdb=" O GLU J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 33 removed outlier: 3.527A pdb=" N ARG J 33 " --> pdb=" O LEU J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 33 through 40 Processing helix chain 'J' and resid 40 through 45 Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 73 through 106 Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 151 through 181 removed outlier: 3.980A pdb=" N ARG J 156 " --> pdb=" O GLY J 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR J 157 " --> pdb=" O THR J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 205 through 236 Processing helix chain 'K' and resid 4 through 17 removed outlier: 4.031A pdb=" N GLU K 16 " --> pdb=" O GLU K 12 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS K 17 " --> pdb=" O GLU K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 33 removed outlier: 3.527A pdb=" N ARG K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 40 Processing helix chain 'K' and resid 40 through 45 Processing helix chain 'K' and resid 60 through 70 Processing helix chain 'K' and resid 73 through 106 Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 151 through 181 removed outlier: 3.979A pdb=" N ARG K 156 " --> pdb=" O GLY K 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR K 157 " --> pdb=" O THR K 153 " (cutoff:3.500A) Processing helix chain 'K' and resid 205 through 236 Processing helix chain 'L' and resid 4 through 17 removed outlier: 4.032A pdb=" N GLU L 16 " --> pdb=" O GLU L 12 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS L 17 " --> pdb=" O GLU L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 33 removed outlier: 3.527A pdb=" N ARG L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 33 through 40 Processing helix chain 'L' and resid 40 through 45 Processing helix chain 'L' and resid 60 through 70 Processing helix chain 'L' and resid 73 through 106 Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 151 through 181 removed outlier: 3.979A pdb=" N ARG L 156 " --> pdb=" O GLY L 152 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N THR L 157 " --> pdb=" O THR L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 205 through 236 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 1404 hydrogen bonds defined for protein. 4140 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: 8.90 Time building geometry restraints manager: 4.82 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: 18708 1.03 - 1.23: 327 1.23 - 1.43: 8409 1.43 - 1.63: 12840 1.63 - 1.82: 204 Bond restraints: 40488 Sorted by residual: bond pdb=" ND2 ASN E 63 " pdb="HD21 ASN E 63 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN B 63 " pdb="HD21 ASN B 63 " ideal model delta sigma weight residual 0.860 0.981 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" ND2 ASN J 63 " pdb="HD21 ASN J 63 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" ND2 ASN G 63 " pdb="HD21 ASN G 63 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" ND2 ASN A 63 " pdb="HD21 ASN A 63 " ideal model delta sigma weight residual 0.860 0.980 -0.120 2.00e-02 2.50e+03 3.61e+01 ... (remaining 40483 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 68449 2.86 - 5.72: 2345 5.72 - 8.59: 294 8.59 - 11.45: 84 11.45 - 14.31: 12 Bond angle restraints: 71184 Sorted by residual: angle pdb=" O3P MC3 B 506 " pdb=" P MC3 B 506 " pdb=" O4P MC3 B 506 " ideal model delta sigma weight residual 93.26 107.57 -14.31 3.00e+00 1.11e-01 2.27e+01 angle pdb=" O3P MC3 E 506 " pdb=" P MC3 E 506 " pdb=" O4P MC3 E 506 " ideal model delta sigma weight residual 93.26 107.57 -14.31 3.00e+00 1.11e-01 2.27e+01 angle pdb=" O3P MC3 G 501 " pdb=" P MC3 G 501 " pdb=" O4P MC3 G 501 " ideal model delta sigma weight residual 93.26 107.55 -14.29 3.00e+00 1.11e-01 2.27e+01 angle pdb=" O3P MC3 F 506 " pdb=" P MC3 F 506 " pdb=" O4P MC3 F 506 " ideal model delta sigma weight residual 93.26 107.55 -14.29 3.00e+00 1.11e-01 2.27e+01 angle pdb=" O3P MC3 I 506 " pdb=" P MC3 I 506 " pdb=" O4P MC3 I 506 " ideal model delta sigma weight residual 93.26 107.55 -14.29 3.00e+00 1.11e-01 2.27e+01 ... (remaining 71179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.51: 18990 27.51 - 55.01: 750 55.01 - 82.52: 192 82.52 - 110.03: 0 110.03 - 137.53: 24 Dihedral angle restraints: 19956 sinusoidal: 11352 harmonic: 8604 Sorted by residual: dihedral pdb=" N MC3 C 507 " pdb=" C4 MC3 C 507 " pdb=" C5 MC3 C 507 " pdb=" O4P MC3 C 507 " ideal model delta sinusoidal sigma weight residual -70.18 67.35 -137.53 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" N MC3 L 507 " pdb=" C4 MC3 L 507 " pdb=" C5 MC3 L 507 " pdb=" O4P MC3 L 507 " ideal model delta sinusoidal sigma weight residual -70.18 67.35 -137.53 1 3.00e+01 1.11e-03 1.85e+01 dihedral pdb=" N MC3 H 507 " pdb=" C4 MC3 H 507 " pdb=" C5 MC3 H 507 " pdb=" O4P MC3 H 507 " ideal model delta sinusoidal sigma weight residual -70.18 67.35 -137.53 1 3.00e+01 1.11e-03 1.85e+01 ... (remaining 19953 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.093: 2769 0.093 - 0.186: 201 0.186 - 0.279: 30 0.279 - 0.371: 12 0.371 - 0.464: 12 Chirality restraints: 3024 Sorted by residual: chirality pdb=" CA VAL E 198 " pdb=" N VAL E 198 " pdb=" C VAL E 198 " pdb=" CB VAL E 198 " both_signs ideal model delta sigma weight residual False 2.44 2.91 -0.46 2.00e-01 2.50e+01 5.39e+00 chirality pdb=" CA VAL B 198 " pdb=" N VAL B 198 " pdb=" C VAL B 198 " pdb=" CB VAL B 198 " both_signs ideal model delta sigma weight residual False 2.44 2.91 -0.46 2.00e-01 2.50e+01 5.39e+00 chirality pdb=" CA VAL F 198 " pdb=" N VAL F 198 " pdb=" C VAL F 198 " pdb=" CB VAL F 198 " both_signs ideal model delta sigma weight residual False 2.44 2.91 -0.46 2.00e-01 2.50e+01 5.38e+00 ... (remaining 3021 not shown) Planarity restraints: 5532 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 63 " -0.309 2.00e-02 2.50e+03 4.05e-01 2.46e+03 pdb=" CG ASN E 63 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN E 63 " 0.301 2.00e-02 2.50e+03 pdb=" ND2 ASN E 63 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN E 63 " -0.640 2.00e-02 2.50e+03 pdb="HD22 ASN E 63 " 0.623 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN G 63 " 0.309 2.00e-02 2.50e+03 4.05e-01 2.46e+03 pdb=" CG ASN G 63 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN G 63 " -0.301 2.00e-02 2.50e+03 pdb=" ND2 ASN G 63 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN G 63 " 0.640 2.00e-02 2.50e+03 pdb="HD22 ASN G 63 " -0.623 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 63 " 0.309 2.00e-02 2.50e+03 4.05e-01 2.46e+03 pdb=" CG ASN I 63 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN I 63 " -0.301 2.00e-02 2.50e+03 pdb=" ND2 ASN I 63 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN I 63 " 0.640 2.00e-02 2.50e+03 pdb="HD22 ASN I 63 " -0.623 2.00e-02 2.50e+03 ... (remaining 5529 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.33: 10864 2.33 - 2.90: 85832 2.90 - 3.47: 103460 3.47 - 4.03: 142109 4.03 - 4.60: 220362 Nonbonded interactions: 562627 Sorted by model distance: nonbonded pdb=" O ILE H 82 " pdb=" HG SER H 86 " model vdw 1.766 2.450 nonbonded pdb=" O ILE I 82 " pdb=" HG SER I 86 " model vdw 1.766 2.450 nonbonded pdb=" O ILE E 82 " pdb=" HG SER E 86 " model vdw 1.766 2.450 nonbonded pdb=" O ILE B 82 " pdb=" HG SER B 86 " model vdw 1.766 2.450 nonbonded pdb=" O ILE G 82 " pdb=" HG SER G 86 " model vdw 1.766 2.450 ... (remaining 562622 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 236 or (resid 501 and (name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)) or (resid 505 and (name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 8 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or r \ esid 506 or resid 508 or (resid 509 and (name C32 or name C33 or name C34 or nam \ e C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or \ name C42 or name C43 or name C44)) or resid 510 or (resid 511 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23 or name C24)))) selection = (chain 'B' and (resid 2 through 501 or resid 505 or (resid 506 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23 or name C24)) or (resid 508 and \ (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C \ 21 or name C22 or name C23 or name C24)) or resid 509 or (resid 510 and (name C1 \ 4 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or nam \ e C21 or name C22 or name C23 or name C24)) or resid 511)) selection = (chain 'C' and (resid 2 through 501 or resid 505 or (resid 506 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23 or name C24)) or (resid 508 and \ (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C \ 21 or name C22 or name C23 or name C24)) or resid 509 or (resid 510 and (name C1 \ 4 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or nam \ e C21 or name C22 or name C23 or name C24)) or resid 511)) selection = (chain 'D' and (resid 2 through 501 or resid 505 or (resid 506 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23 or name C24)) or (resid 508 and \ (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C \ 21 or name C22 or name C23 or name C24)) or resid 509 or (resid 510 and (name C1 \ 4 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or nam \ e C21 or name C22 or name C23 or name C24)) or resid 511)) selection = (chain 'E' and (resid 2 through 501 or resid 505 or (resid 506 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23 or name C24)) or (resid 508 and \ (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C \ 21 or name C22 or name C23 or name C24)) or resid 509 or (resid 510 and (name C1 \ 4 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or nam \ e C21 or name C22 or name C23 or name C24)) or resid 511)) selection = (chain 'F' and (resid 2 through 501 or resid 505 or (resid 506 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23 or name C24)) or (resid 508 and \ (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C \ 21 or name C22 or name C23 or name C24)) or resid 509 or (resid 510 and (name C1 \ 4 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or nam \ e C21 or name C22 or name C23 or name C24)) or resid 511)) selection = (chain 'G' and (resid 2 through 236 or (resid 501 and (name C12 or name C13 or n \ ame C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 \ or name C21 or name C22 or name C23 or name C24)) or (resid 505 and (name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name C1 \ 8 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24)) or r \ esid 506 or resid 508 or (resid 509 and (name C32 or name C33 or name C34 or nam \ e C35 or name C36 or name C37 or name C38 or name C39 or name C40 or name C41 or \ name C42 or name C43 or name C44)) or resid 510 or (resid 511 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23 or name C24)))) selection = (chain 'H' and (resid 2 through 501 or resid 505 or (resid 506 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23 or name C24)) or (resid 508 and \ (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C \ 21 or name C22 or name C23 or name C24)) or resid 509 or (resid 510 and (name C1 \ 4 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or nam \ e C21 or name C22 or name C23 or name C24)) or resid 511)) selection = (chain 'I' and (resid 2 through 501 or resid 505 or (resid 506 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23 or name C24)) or (resid 508 and \ (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C \ 21 or name C22 or name C23 or name C24)) or resid 509 or (resid 510 and (name C1 \ 4 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or nam \ e C21 or name C22 or name C23 or name C24)) or resid 511)) selection = (chain 'J' and (resid 2 through 501 or resid 505 or (resid 506 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23 or name C24)) or (resid 508 and \ (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C \ 21 or name C22 or name C23 or name C24)) or resid 509 or (resid 510 and (name C1 \ 4 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or nam \ e C21 or name C22 or name C23 or name C24)) or resid 511)) selection = (chain 'K' and (resid 2 through 501 or resid 505 or (resid 506 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23 or name C24)) or (resid 508 and \ (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C \ 21 or name C22 or name C23 or name C24)) or resid 509 or (resid 510 and (name C1 \ 4 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or nam \ e C21 or name C22 or name C23 or name C24)) or resid 511)) selection = (chain 'L' and (resid 2 through 501 or resid 505 or (resid 506 and (name C12 or \ name C13 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 \ or name C20 or name C21 or name C22 or name C23 or name C24)) or (resid 508 and \ (name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C \ 21 or name C22 or name C23 or name C24)) or resid 509 or (resid 510 and (name C1 \ 4 or name C15 or name C16 or name C17 or name C18 or name C19 or name C20 or nam \ e C21 or name C22 or name C23 or name C24)) or resid 511)) } 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: 4.120 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: 0.220 Extract box with map and model: 0.620 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 35.860 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 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 : 0.024 0.915 21804 Z= 1.216 Angle : 1.508 28.264 28896 Z= 0.705 Chirality : 0.066 0.464 3024 Planarity : 0.005 0.020 3324 Dihedral : 14.502 137.533 8700 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.14 % Allowed : 4.55 % Favored : 94.32 % 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: 0.51 (0.16), residues: 2268 helix: 0.82 (0.12), residues: 1680 sheet: 1.12 (0.44), residues: 132 loop : -1.50 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 183 TYR 0.016 0.003 TYR G 66 PHE 0.029 0.003 PHE E 70 TRP 0.016 0.002 TRP I 193 HIS 0.007 0.001 HIS E 74 Details of bonding type rmsd covalent geometry : bond 0.01052 (21768) covalent geometry : angle 1.38768 (28824) SS BOND : bond 0.52773 ( 36) SS BOND : angle 11.89475 ( 72) hydrogen bonds : bond 0.11261 ( 1404) hydrogen bonds : angle 5.32134 ( 4140) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 284 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 177 TYR cc_start: 0.8278 (t80) cc_final: 0.8074 (t80) REVERT: E 177 TYR cc_start: 0.8264 (t80) cc_final: 0.8049 (t80) outliers start: 24 outliers final: 18 residues processed: 308 average time/residue: 1.0644 time to fit residues: 382.7169 Evaluate side-chains 255 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 237 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain A residue 163 ILE Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain G residue 163 ILE Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain H residue 163 ILE Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain J residue 163 ILE Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain K residue 163 ILE Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 0.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 227 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.0070 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 7.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 176 HIS F 176 HIS I 176 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.174224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.125123 restraints weight = 50949.434| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.19 r_work: 0.3095 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21804 Z= 0.141 Angle : 0.570 4.444 28896 Z= 0.306 Chirality : 0.041 0.124 3024 Planarity : 0.003 0.026 3324 Dihedral : 13.505 127.012 4452 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.37 % Allowed : 9.04 % Favored : 89.58 % 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: 1.96 (0.17), residues: 2268 helix: 1.95 (0.11), residues: 1692 sheet: 1.42 (0.48), residues: 132 loop : -1.33 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 33 TYR 0.012 0.002 TYR E 177 PHE 0.012 0.002 PHE C 202 TRP 0.005 0.001 TRP H 4 HIS 0.005 0.001 HIS F 176 Details of bonding type rmsd covalent geometry : bond 0.00302 (21768) covalent geometry : angle 0.56698 (28824) SS BOND : bond 0.00212 ( 36) SS BOND : angle 1.28398 ( 72) hydrogen bonds : bond 0.05602 ( 1404) hydrogen bonds : angle 4.67558 ( 4140) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 266 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 77 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8406 (tt) REVERT: F 77 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8428 (tt) outliers start: 29 outliers final: 15 residues processed: 292 average time/residue: 1.3997 time to fit residues: 460.8875 Evaluate side-chains 277 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 260 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 163 ILE Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 11 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 14 optimal weight: 2.9990 chunk 206 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 182 optimal weight: 7.9990 chunk 217 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 176 HIS H 176 HIS L 176 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.166231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.115233 restraints weight = 50693.660| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.21 r_work: 0.3141 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 21804 Z= 0.179 Angle : 0.557 4.308 28896 Z= 0.304 Chirality : 0.042 0.134 3024 Planarity : 0.004 0.034 3324 Dihedral : 13.837 123.938 4440 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.61 % Allowed : 8.43 % Favored : 89.96 % 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: 2.62 (0.17), residues: 2268 helix: 2.54 (0.12), residues: 1692 sheet: 0.65 (0.40), residues: 132 loop : -1.26 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 33 TYR 0.012 0.002 TYR I 66 PHE 0.020 0.002 PHE B 202 TRP 0.008 0.001 TRP L 45 HIS 0.007 0.001 HIS L 176 Details of bonding type rmsd covalent geometry : bond 0.00428 (21768) covalent geometry : angle 0.55414 (28824) SS BOND : bond 0.00301 ( 36) SS BOND : angle 1.26066 ( 72) hydrogen bonds : bond 0.05346 ( 1404) hydrogen bonds : angle 4.46129 ( 4140) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: H 37 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8457 (mt) REVERT: H 42 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8039 (mt-10) REVERT: K 37 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8447 (mt) REVERT: K 42 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8064 (mt-10) outliers start: 34 outliers final: 17 residues processed: 237 average time/residue: 1.5747 time to fit residues: 415.7056 Evaluate side-chains 227 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain C residue 231 MET Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain G residue 231 MET Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 18 SER Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 93 optimal weight: 3.9990 chunk 86 optimal weight: 0.0020 chunk 153 optimal weight: 0.8980 chunk 191 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 218 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 104 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 overall best weight: 0.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 176 HIS K 176 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.170548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.121180 restraints weight = 50874.897| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 1.18 r_work: 0.3140 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.43 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 21804 Z= 0.108 Angle : 0.458 3.909 28896 Z= 0.247 Chirality : 0.039 0.122 3024 Planarity : 0.003 0.052 3324 Dihedral : 12.859 114.923 4440 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.89 % Allowed : 8.95 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.01 (0.17), residues: 2268 helix: 2.88 (0.12), residues: 1692 sheet: 0.54 (0.40), residues: 132 loop : -1.28 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 23 TYR 0.011 0.001 TYR I 66 PHE 0.012 0.001 PHE F 202 TRP 0.007 0.001 TRP B 4 HIS 0.004 0.001 HIS E 176 Details of bonding type rmsd covalent geometry : bond 0.00225 (21768) covalent geometry : angle 0.45710 (28824) SS BOND : bond 0.00150 ( 36) SS BOND : angle 0.81766 ( 72) hydrogen bonds : bond 0.04348 ( 1404) hydrogen bonds : angle 4.24202 ( 4140) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 0.799 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ARG cc_start: 0.8722 (mtt180) cc_final: 0.8506 (mtt180) REVERT: B 42 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7985 (mt-10) REVERT: D 77 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8473 (tt) REVERT: G 33 ARG cc_start: 0.8716 (mtt180) cc_final: 0.8503 (mtt180) REVERT: H 37 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8328 (mt) REVERT: H 42 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7996 (mt-10) REVERT: J 33 ARG cc_start: 0.8719 (mtt180) cc_final: 0.8502 (mtt180) REVERT: J 77 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8483 (tt) REVERT: K 37 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8325 (mt) REVERT: K 42 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7957 (mt-10) outliers start: 40 outliers final: 13 residues processed: 231 average time/residue: 1.5955 time to fit residues: 409.7356 Evaluate side-chains 217 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain E residue 231 MET Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 28 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 chunk 143 optimal weight: 9.9990 chunk 198 optimal weight: 3.9990 chunk 52 optimal weight: 0.5980 chunk 101 optimal weight: 1.9990 chunk 147 optimal weight: 0.5980 chunk 86 optimal weight: 8.9990 chunk 92 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.169484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.119932 restraints weight = 50803.051| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.18 r_work: 0.3024 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2891 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21804 Z= 0.119 Angle : 0.471 4.078 28896 Z= 0.253 Chirality : 0.039 0.122 3024 Planarity : 0.003 0.026 3324 Dihedral : 12.697 109.889 4440 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 1.47 % Allowed : 9.61 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.24 (0.17), residues: 2268 helix: 3.07 (0.12), residues: 1692 sheet: 0.40 (0.39), residues: 132 loop : -1.21 (0.25), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 23 TYR 0.010 0.001 TYR I 66 PHE 0.016 0.002 PHE F 202 TRP 0.006 0.001 TRP A 45 HIS 0.004 0.001 HIS D 161 Details of bonding type rmsd covalent geometry : bond 0.00265 (21768) covalent geometry : angle 0.46949 (28824) SS BOND : bond 0.00188 ( 36) SS BOND : angle 0.90568 ( 72) hydrogen bonds : bond 0.04170 ( 1404) hydrogen bonds : angle 4.09105 ( 4140) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 216 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 77 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8453 (tt) REVERT: K 37 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8339 (mt) outliers start: 31 outliers final: 13 residues processed: 236 average time/residue: 1.5781 time to fit residues: 416.2754 Evaluate side-chains 218 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 203 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 37 LEU Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 104 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 213 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 187 optimal weight: 2.9990 chunk 201 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.162644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.109314 restraints weight = 49552.973| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.23 r_work: 0.2957 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 21804 Z= 0.194 Angle : 0.535 4.335 28896 Z= 0.290 Chirality : 0.041 0.129 3024 Planarity : 0.004 0.036 3324 Dihedral : 13.409 112.847 4440 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.89 % Allowed : 9.42 % Favored : 88.68 % 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: 2.85 (0.17), residues: 2268 helix: 2.82 (0.12), residues: 1692 sheet: -0.15 (0.32), residues: 204 loop : -1.57 (0.24), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 23 TYR 0.015 0.002 TYR B 66 PHE 0.020 0.002 PHE B 212 TRP 0.010 0.002 TRP L 193 HIS 0.004 0.001 HIS A 161 Details of bonding type rmsd covalent geometry : bond 0.00462 (21768) covalent geometry : angle 0.53255 (28824) SS BOND : bond 0.00354 ( 36) SS BOND : angle 1.11534 ( 72) hydrogen bonds : bond 0.04770 ( 1404) hydrogen bonds : angle 4.20119 ( 4140) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 203 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8499 (tt) REVERT: B 68 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8142 (tp30) REVERT: D 77 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8474 (tt) REVERT: E 42 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: G 77 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8512 (tt) REVERT: J 77 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8507 (tt) REVERT: K 68 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8126 (tp30) outliers start: 40 outliers final: 13 residues processed: 235 average time/residue: 1.3789 time to fit residues: 366.4276 Evaluate side-chains 222 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 120 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 192 optimal weight: 3.9990 chunk 193 optimal weight: 0.4980 chunk 12 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.166751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.116502 restraints weight = 50871.672| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.18 r_work: 0.3130 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 21804 Z= 0.149 Angle : 0.498 4.047 28896 Z= 0.269 Chirality : 0.039 0.119 3024 Planarity : 0.003 0.026 3324 Dihedral : 12.975 108.559 4440 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.52 % Allowed : 9.85 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.04 (0.17), residues: 2268 helix: 2.88 (0.12), residues: 1692 sheet: 0.31 (0.39), residues: 132 loop : -1.08 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 23 TYR 0.014 0.002 TYR I 66 PHE 0.017 0.002 PHE I 202 TRP 0.007 0.001 TRP C 193 HIS 0.005 0.001 HIS K 98 Details of bonding type rmsd covalent geometry : bond 0.00336 (21768) covalent geometry : angle 0.49654 (28824) SS BOND : bond 0.00260 ( 36) SS BOND : angle 0.99672 ( 72) hydrogen bonds : bond 0.04329 ( 1404) hydrogen bonds : angle 4.13047 ( 4140) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 203 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8525 (tt) REVERT: B 42 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: B 68 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.7982 (tp30) REVERT: D 77 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8493 (tt) REVERT: E 42 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8034 (mt-10) REVERT: E 68 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8006 (tp30) REVERT: G 77 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8537 (tt) REVERT: H 68 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.7959 (tp30) REVERT: J 77 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8532 (tt) REVERT: K 42 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.7985 (mt-10) REVERT: K 68 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.7988 (tp30) outliers start: 32 outliers final: 13 residues processed: 229 average time/residue: 1.3963 time to fit residues: 361.9494 Evaluate side-chains 217 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 chunk 127 optimal weight: 3.9990 chunk 219 optimal weight: 9.9990 chunk 155 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 158 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.3922 r_free = 0.3922 target = 0.168980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.119344 restraints weight = 50980.910| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.17 r_work: 0.3013 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 21804 Z= 0.108 Angle : 0.460 3.939 28896 Z= 0.246 Chirality : 0.038 0.124 3024 Planarity : 0.003 0.022 3324 Dihedral : 12.287 98.801 4440 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.28 % Allowed : 9.99 % Favored : 88.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.33 (0.17), residues: 2268 helix: 3.14 (0.12), residues: 1692 sheet: 0.24 (0.39), residues: 132 loop : -1.15 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 23 TYR 0.011 0.001 TYR G 66 PHE 0.013 0.001 PHE C 202 TRP 0.006 0.001 TRP E 4 HIS 0.009 0.001 HIS B 98 Details of bonding type rmsd covalent geometry : bond 0.00237 (21768) covalent geometry : angle 0.45837 (28824) SS BOND : bond 0.00184 ( 36) SS BOND : angle 0.79529 ( 72) hydrogen bonds : bond 0.03843 ( 1404) hydrogen bonds : angle 4.04360 ( 4140) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 201 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8459 (tt) REVERT: B 42 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7976 (mt-10) REVERT: D 77 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8453 (tt) REVERT: E 42 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: G 77 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8474 (tt) REVERT: H 68 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.7963 (tp30) REVERT: J 77 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8486 (tt) REVERT: K 42 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7911 (mt-10) outliers start: 27 outliers final: 13 residues processed: 224 average time/residue: 1.3539 time to fit residues: 341.6662 Evaluate side-chains 215 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 77 LEU Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 77 LEU Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 113 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 202 optimal weight: 3.9990 chunk 160 optimal weight: 3.9990 chunk 186 optimal weight: 1.9990 chunk 187 optimal weight: 0.6980 chunk 134 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.165437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.114490 restraints weight = 51219.338| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 1.19 r_work: 0.3131 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21804 Z= 0.158 Angle : 0.504 4.521 28896 Z= 0.270 Chirality : 0.040 0.121 3024 Planarity : 0.003 0.028 3324 Dihedral : 12.466 98.987 4440 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 1.47 % Allowed : 9.75 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.14 (0.17), residues: 2268 helix: 2.97 (0.12), residues: 1692 sheet: 0.24 (0.38), residues: 132 loop : -1.08 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 23 TYR 0.014 0.002 TYR F 66 PHE 0.018 0.002 PHE B 202 TRP 0.008 0.001 TRP L 193 HIS 0.005 0.001 HIS H 98 Details of bonding type rmsd covalent geometry : bond 0.00364 (21768) covalent geometry : angle 0.50190 (28824) SS BOND : bond 0.00276 ( 36) SS BOND : angle 0.96598 ( 72) hydrogen bonds : bond 0.04232 ( 1404) hydrogen bonds : angle 4.09133 ( 4140) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8502 (tt) REVERT: B 42 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8016 (mt-10) REVERT: B 68 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.7908 (tp30) REVERT: D 77 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8488 (tt) REVERT: E 42 GLU cc_start: 0.8352 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: E 68 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.7974 (tp30) REVERT: H 68 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.7987 (tp30) REVERT: K 42 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: K 68 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.7919 (tp30) outliers start: 31 outliers final: 13 residues processed: 221 average time/residue: 1.1765 time to fit residues: 296.3441 Evaluate side-chains 217 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 195 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 68 GLU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 68 GLU Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 172 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 153 optimal weight: 6.9990 chunk 117 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3905 r_free = 0.3905 target = 0.167444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.117213 restraints weight = 50953.920| |-----------------------------------------------------------------------------| r_work (start): 0.3150 rms_B_bonded: 1.18 r_work: 0.2985 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 21804 Z= 0.138 Angle : 0.485 5.175 28896 Z= 0.261 Chirality : 0.039 0.121 3024 Planarity : 0.003 0.025 3324 Dihedral : 12.116 98.065 4440 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.18 % Allowed : 10.04 % Favored : 88.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.17 (0.17), residues: 2268 helix: 2.99 (0.12), residues: 1692 sheet: 0.30 (0.39), residues: 132 loop : -1.11 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 23 TYR 0.013 0.002 TYR L 66 PHE 0.017 0.002 PHE F 202 TRP 0.007 0.001 TRP C 193 HIS 0.012 0.001 HIS H 98 Details of bonding type rmsd covalent geometry : bond 0.00311 (21768) covalent geometry : angle 0.48336 (28824) SS BOND : bond 0.00234 ( 36) SS BOND : angle 0.91767 ( 72) hydrogen bonds : bond 0.04027 ( 1404) hydrogen bonds : angle 4.06206 ( 4140) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7969 (tp30) REVERT: A 77 LEU cc_start: 0.8749 (OUTLIER) cc_final: 0.8485 (tt) REVERT: B 42 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7997 (mt-10) REVERT: B 102 MET cc_start: 0.6083 (mmp) cc_final: 0.5873 (mmm) REVERT: D 77 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8465 (tt) REVERT: E 68 GLU cc_start: 0.8752 (OUTLIER) cc_final: 0.8017 (tp30) REVERT: G 68 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7987 (tp30) REVERT: H 68 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7982 (tp30) REVERT: K 42 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7976 (mt-10) outliers start: 25 outliers final: 13 residues processed: 221 average time/residue: 0.9914 time to fit residues: 249.5097 Evaluate side-chains 216 residues out of total 2112 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 161 HIS Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain B residue 161 HIS Chi-restraints excluded: chain C residue 161 HIS Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain E residue 68 GLU Chi-restraints excluded: chain E residue 161 HIS Chi-restraints excluded: chain F residue 161 HIS Chi-restraints excluded: chain G residue 68 GLU Chi-restraints excluded: chain G residue 161 HIS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 161 HIS Chi-restraints excluded: chain I residue 18 SER Chi-restraints excluded: chain I residue 161 HIS Chi-restraints excluded: chain J residue 161 HIS Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 161 HIS Chi-restraints excluded: chain L residue 161 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 187 optimal weight: 0.0670 chunk 150 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 125 optimal weight: 6.9990 chunk 77 optimal weight: 7.9990 chunk 156 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 84 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 98 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.168135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.118121 restraints weight = 51403.000| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 1.18 r_work: 0.2999 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 21804 Z= 0.117 Angle : 0.466 5.776 28896 Z= 0.250 Chirality : 0.039 0.123 3024 Planarity : 0.003 0.046 3324 Dihedral : 11.746 96.562 4440 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.23 % Allowed : 10.23 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.31 (0.17), residues: 2268 helix: 3.11 (0.12), residues: 1692 sheet: 0.29 (0.39), residues: 132 loop : -1.13 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 23 TYR 0.012 0.002 TYR A 66 PHE 0.015 0.002 PHE F 202 TRP 0.005 0.001 TRP C 193 HIS 0.008 0.001 HIS A 98 Details of bonding type rmsd covalent geometry : bond 0.00260 (21768) covalent geometry : angle 0.46491 (28824) SS BOND : bond 0.00187 ( 36) SS BOND : angle 0.83234 ( 72) hydrogen bonds : bond 0.03804 ( 1404) hydrogen bonds : angle 4.01037 ( 4140) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12858.46 seconds wall clock time: 217 minutes 33.30 seconds (13053.30 seconds total)