Starting phenix.real_space_refine on Thu Mar 5 05:04:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qet_13940/03_2026/7qet_13940.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qet_13940/03_2026/7qet_13940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qet_13940/03_2026/7qet_13940.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qet_13940/03_2026/7qet_13940.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qet_13940/03_2026/7qet_13940.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qet_13940/03_2026/7qet_13940.map" } resolution = 2.1 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= 0.001 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: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 12720 2.51 5 N 2952 2.21 5 O 3365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 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: 19205 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "B" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "C" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "D" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "E" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "F" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "G" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "H" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "I" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "J" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "K" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "L" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1527 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 181} Chain breaks: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "D" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "J" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "K" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 48 Unusual residues: {'LMT': 4, 'PTY': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 151 Unresolved non-hydrogen angles: 206 Unresolved non-hydrogen dihedrals: 256 Unresolved non-hydrogen chiralities: 41 Planarities with less than four sites: {'PTY:plan-1': 1, 'PTY:plan-2': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "E" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "G" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "J" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "L" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Time building chain proxies: 4.80, per 1000 atoms: 0.25 Number of scatterers: 19205 At special positions: 0 Unit cell: (99.45, 109.65, 155.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 3365 8.00 N 2952 7.00 C 12720 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 53 " - pdb=" SG CYS A 180 " distance=2.03 Simple disulfide: pdb=" SG CYS A 60 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 169 " distance=2.03 Simple disulfide: pdb=" SG CYS B 53 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 60 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 64 " - pdb=" SG CYS B 169 " distance=2.03 Simple disulfide: pdb=" SG CYS C 53 " - pdb=" SG CYS C 180 " distance=2.04 Simple disulfide: pdb=" SG CYS C 60 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 64 " - pdb=" SG CYS C 169 " distance=2.03 Simple disulfide: pdb=" SG CYS D 53 " - pdb=" SG CYS D 180 " distance=2.03 Simple disulfide: pdb=" SG CYS D 60 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 64 " - pdb=" SG CYS D 169 " distance=2.03 Simple disulfide: pdb=" SG CYS E 53 " - pdb=" SG CYS E 180 " distance=2.04 Simple disulfide: pdb=" SG CYS E 60 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 64 " - pdb=" SG CYS E 169 " distance=2.03 Simple disulfide: pdb=" SG CYS F 53 " - pdb=" SG CYS F 180 " distance=2.03 Simple disulfide: pdb=" SG CYS F 60 " - pdb=" SG CYS F 174 " distance=2.03 Simple disulfide: pdb=" SG CYS F 64 " - pdb=" SG CYS F 169 " distance=2.03 Simple disulfide: pdb=" SG CYS G 53 " - pdb=" SG CYS G 180 " distance=2.03 Simple disulfide: pdb=" SG CYS G 60 " - pdb=" SG CYS G 174 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 169 " distance=2.03 Simple disulfide: pdb=" SG CYS H 53 " - pdb=" SG CYS H 180 " distance=2.04 Simple disulfide: pdb=" SG CYS H 60 " - pdb=" SG CYS H 174 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 169 " distance=2.03 Simple disulfide: pdb=" SG CYS I 53 " - pdb=" SG CYS I 180 " distance=2.03 Simple disulfide: pdb=" SG CYS I 60 " - pdb=" SG CYS I 174 " distance=2.03 Simple disulfide: pdb=" SG CYS I 64 " - pdb=" SG CYS I 169 " distance=2.03 Simple disulfide: pdb=" SG CYS J 53 " - pdb=" SG CYS J 180 " distance=2.04 Simple disulfide: pdb=" SG CYS J 60 " - pdb=" SG CYS J 174 " distance=2.03 Simple disulfide: pdb=" SG CYS J 64 " - pdb=" SG CYS J 169 " distance=2.03 Simple disulfide: pdb=" SG CYS K 53 " - pdb=" SG CYS K 180 " distance=2.04 Simple disulfide: pdb=" SG CYS K 60 " - pdb=" SG CYS K 174 " distance=2.03 Simple disulfide: pdb=" SG CYS K 64 " - pdb=" SG CYS K 169 " distance=2.03 Simple disulfide: pdb=" SG CYS L 53 " - pdb=" SG CYS L 180 " distance=2.04 Simple disulfide: pdb=" SG CYS L 60 " - pdb=" SG CYS L 174 " distance=2.03 Simple disulfide: pdb=" SG CYS L 64 " - pdb=" SG CYS L 169 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 775.3 milliseconds 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4296 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 75.6% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 4 through 15 removed outlier: 4.147A pdb=" N THR A 8 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 39 removed outlier: 3.689A pdb=" N ILE A 23 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR A 26 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 43 Processing helix chain 'A' and resid 59 through 69 Processing helix chain 'A' and resid 72 through 102 Proline residue: A 87 - end of helix Processing helix chain 'A' and resid 130 through 159 Processing helix chain 'A' and resid 184 through 216 removed outlier: 3.590A pdb=" N ARG A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 15 Processing helix chain 'B' and resid 18 through 39 removed outlier: 3.688A pdb=" N ILE B 23 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU B 25 " --> pdb=" O GLY B 21 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N THR B 26 " --> pdb=" O LYS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 43 Processing helix chain 'B' and resid 59 through 69 Processing helix chain 'B' and resid 72 through 102 Proline residue: B 87 - end of helix Processing helix chain 'B' and resid 130 through 159 Processing helix chain 'B' and resid 184 through 216 removed outlier: 3.591A pdb=" N ARG B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 15 Processing helix chain 'C' and resid 18 through 39 removed outlier: 3.689A pdb=" N ILE C 23 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU C 25 " --> pdb=" O GLY C 21 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR C 26 " --> pdb=" O LYS C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 43 Processing helix chain 'C' and resid 59 through 69 Processing helix chain 'C' and resid 72 through 102 Proline residue: C 87 - end of helix Processing helix chain 'C' and resid 130 through 159 Processing helix chain 'C' and resid 184 through 216 removed outlier: 3.591A pdb=" N ARG C 216 " --> pdb=" O TYR C 212 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 15 Processing helix chain 'D' and resid 18 through 39 removed outlier: 3.689A pdb=" N ILE D 23 " --> pdb=" O SER D 19 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU D 25 " --> pdb=" O GLY D 21 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR D 26 " --> pdb=" O LYS D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 43 Processing helix chain 'D' and resid 59 through 69 Processing helix chain 'D' and resid 72 through 102 Proline residue: D 87 - end of helix Processing helix chain 'D' and resid 130 through 159 Processing helix chain 'D' and resid 184 through 216 removed outlier: 3.591A pdb=" N ARG D 216 " --> pdb=" O TYR D 212 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 15 Processing helix chain 'E' and resid 18 through 39 removed outlier: 3.689A pdb=" N ILE E 23 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU E 25 " --> pdb=" O GLY E 21 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR E 26 " --> pdb=" O LYS E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 43 Processing helix chain 'E' and resid 59 through 69 Processing helix chain 'E' and resid 72 through 102 Proline residue: E 87 - end of helix Processing helix chain 'E' and resid 130 through 159 Processing helix chain 'E' and resid 184 through 216 removed outlier: 3.590A pdb=" N ARG E 216 " --> pdb=" O TYR E 212 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 15 Processing helix chain 'F' and resid 18 through 39 removed outlier: 3.689A pdb=" N ILE F 23 " --> pdb=" O SER F 19 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU F 25 " --> pdb=" O GLY F 21 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR F 26 " --> pdb=" O LYS F 22 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 43 Processing helix chain 'F' and resid 59 through 69 Processing helix chain 'F' and resid 72 through 102 Proline residue: F 87 - end of helix Processing helix chain 'F' and resid 130 through 159 Processing helix chain 'F' and resid 184 through 216 removed outlier: 3.591A pdb=" N ARG F 216 " --> pdb=" O TYR F 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 15 Processing helix chain 'G' and resid 18 through 39 removed outlier: 3.688A pdb=" N ILE G 23 " --> pdb=" O SER G 19 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU G 25 " --> pdb=" O GLY G 21 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 43 Processing helix chain 'G' and resid 59 through 69 Processing helix chain 'G' and resid 72 through 102 Proline residue: G 87 - end of helix Processing helix chain 'G' and resid 130 through 159 Processing helix chain 'G' and resid 184 through 216 removed outlier: 3.590A pdb=" N ARG G 216 " --> pdb=" O TYR G 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 15 Processing helix chain 'H' and resid 18 through 39 removed outlier: 3.688A pdb=" N ILE H 23 " --> pdb=" O SER H 19 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU H 25 " --> pdb=" O GLY H 21 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR H 26 " --> pdb=" O LYS H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 43 Processing helix chain 'H' and resid 59 through 69 Processing helix chain 'H' and resid 72 through 102 Proline residue: H 87 - end of helix Processing helix chain 'H' and resid 130 through 159 Processing helix chain 'H' and resid 184 through 216 removed outlier: 3.591A pdb=" N ARG H 216 " --> pdb=" O TYR H 212 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 15 Processing helix chain 'I' and resid 18 through 39 removed outlier: 3.689A pdb=" N ILE I 23 " --> pdb=" O SER I 19 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU I 25 " --> pdb=" O GLY I 21 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR I 26 " --> pdb=" O LYS I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 43 Processing helix chain 'I' and resid 59 through 69 Processing helix chain 'I' and resid 72 through 102 Proline residue: I 87 - end of helix Processing helix chain 'I' and resid 130 through 159 Processing helix chain 'I' and resid 184 through 216 removed outlier: 3.590A pdb=" N ARG I 216 " --> pdb=" O TYR I 212 " (cutoff:3.500A) Processing helix chain 'J' and resid 5 through 15 Processing helix chain 'J' and resid 18 through 39 removed outlier: 3.689A pdb=" N ILE J 23 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU J 25 " --> pdb=" O GLY J 21 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR J 26 " --> pdb=" O LYS J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 43 Processing helix chain 'J' and resid 59 through 69 Processing helix chain 'J' and resid 72 through 102 Proline residue: J 87 - end of helix Processing helix chain 'J' and resid 130 through 159 Processing helix chain 'J' and resid 184 through 216 removed outlier: 3.591A pdb=" N ARG J 216 " --> pdb=" O TYR J 212 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 18 through 39 removed outlier: 3.690A pdb=" N ILE K 23 " --> pdb=" O SER K 19 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU K 25 " --> pdb=" O GLY K 21 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR K 26 " --> pdb=" O LYS K 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 43 Processing helix chain 'K' and resid 59 through 69 Processing helix chain 'K' and resid 72 through 102 Proline residue: K 87 - end of helix Processing helix chain 'K' and resid 130 through 159 Processing helix chain 'K' and resid 184 through 216 removed outlier: 3.591A pdb=" N ARG K 216 " --> pdb=" O TYR K 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 5 through 15 Processing helix chain 'L' and resid 18 through 39 removed outlier: 3.689A pdb=" N ILE L 23 " --> pdb=" O SER L 19 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU L 25 " --> pdb=" O GLY L 21 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N THR L 26 " --> pdb=" O LYS L 22 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 43 Processing helix chain 'L' and resid 59 through 69 Processing helix chain 'L' and resid 72 through 102 Proline residue: L 87 - end of helix Processing helix chain 'L' and resid 130 through 159 Processing helix chain 'L' and resid 184 through 216 removed outlier: 3.591A pdb=" N ARG L 216 " --> pdb=" O TYR L 212 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA2, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=AA5, first strand: chain 'E' and resid 52 through 53 Processing sheet with id=AA6, first strand: chain 'F' and resid 52 through 53 Processing sheet with id=AA7, first strand: chain 'G' and resid 52 through 53 Processing sheet with id=AA8, first strand: chain 'H' and resid 52 through 53 Processing sheet with id=AA9, first strand: chain 'I' and resid 52 through 53 Processing sheet with id=AB1, first strand: chain 'J' and resid 52 through 53 Processing sheet with id=AB2, first strand: chain 'K' and resid 52 through 53 Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 1368 hydrogen bonds defined for protein. 3996 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: 3.24 Time building geometry restraints manager: 2.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5424 1.34 - 1.46: 4495 1.46 - 1.58: 9197 1.58 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 19356 Sorted by residual: bond pdb=" C1 LMT H 303 " pdb=" C2 LMT H 303 " ideal model delta sigma weight residual 1.516 1.566 -0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C1 LMT L 301 " pdb=" C2 LMT L 301 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" C1 LMT A 303 " pdb=" C2 LMT A 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.09e+00 bond pdb=" C1 LMT I 303 " pdb=" C2 LMT I 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.08e+00 bond pdb=" C1 LMT E 303 " pdb=" C2 LMT E 303 " ideal model delta sigma weight residual 1.516 1.565 -0.049 2.00e-02 2.50e+03 6.06e+00 ... (remaining 19351 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 25259 1.58 - 3.15: 414 3.15 - 4.73: 81 4.73 - 6.31: 202 6.31 - 7.89: 132 Bond angle restraints: 26088 Sorted by residual: angle pdb=" C6 LMT E 303 " pdb=" C7 LMT E 303 " pdb=" C8 LMT E 303 " ideal model delta sigma weight residual 117.26 109.37 7.89 3.00e+00 1.11e-01 6.91e+00 angle pdb=" C6 LMT H 303 " pdb=" C7 LMT H 303 " pdb=" C8 LMT H 303 " ideal model delta sigma weight residual 117.26 109.38 7.88 3.00e+00 1.11e-01 6.90e+00 angle pdb=" C6 LMT A 303 " pdb=" C7 LMT A 303 " pdb=" C8 LMT A 303 " ideal model delta sigma weight residual 117.26 109.40 7.86 3.00e+00 1.11e-01 6.86e+00 angle pdb=" C6 LMT I 303 " pdb=" C7 LMT I 303 " pdb=" C8 LMT I 303 " ideal model delta sigma weight residual 117.26 109.41 7.85 3.00e+00 1.11e-01 6.85e+00 angle pdb=" C6 LMT C 305 " pdb=" C7 LMT C 305 " pdb=" C8 LMT C 305 " ideal model delta sigma weight residual 117.26 109.41 7.85 3.00e+00 1.11e-01 6.85e+00 ... (remaining 26083 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.01: 10251 16.01 - 32.02: 717 32.02 - 48.03: 228 48.03 - 64.04: 48 64.04 - 80.05: 24 Dihedral angle restraints: 11268 sinusoidal: 4632 harmonic: 6636 Sorted by residual: dihedral pdb=" CB GLU I 209 " pdb=" CG GLU I 209 " pdb=" CD GLU I 209 " pdb=" OE1 GLU I 209 " ideal model delta sinusoidal sigma weight residual 0.00 -80.05 80.05 1 3.00e+01 1.11e-03 8.82e+00 dihedral pdb=" CB GLU L 209 " pdb=" CG GLU L 209 " pdb=" CD GLU L 209 " pdb=" OE1 GLU L 209 " ideal model delta sinusoidal sigma weight residual 0.00 -80.04 80.04 1 3.00e+01 1.11e-03 8.82e+00 dihedral pdb=" CB GLU D 209 " pdb=" CG GLU D 209 " pdb=" CD GLU D 209 " pdb=" OE1 GLU D 209 " ideal model delta sinusoidal sigma weight residual 0.00 -80.03 80.03 1 3.00e+01 1.11e-03 8.82e+00 ... (remaining 11265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1450 0.025 - 0.049: 969 0.049 - 0.074: 328 0.074 - 0.098: 122 0.098 - 0.123: 71 Chirality restraints: 2940 Sorted by residual: chirality pdb=" CA PRO K 185 " pdb=" N PRO K 185 " pdb=" C PRO K 185 " pdb=" CB PRO K 185 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA PRO L 185 " pdb=" N PRO L 185 " pdb=" C PRO L 185 " pdb=" CB PRO L 185 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.76e-01 chirality pdb=" CA PRO A 185 " pdb=" N PRO A 185 " pdb=" C PRO A 185 " pdb=" CB PRO A 185 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 2937 not shown) Planarity restraints: 3084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 65 " 0.011 2.00e-02 2.50e+03 6.14e-03 7.54e-01 pdb=" CG TYR I 65 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR I 65 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR I 65 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR I 65 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR I 65 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR I 65 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR I 65 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 65 " 0.011 2.00e-02 2.50e+03 6.02e-03 7.25e-01 pdb=" CG TYR B 65 " -0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR B 65 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 65 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 65 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 65 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 65 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 65 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 65 " -0.011 2.00e-02 2.50e+03 6.00e-03 7.20e-01 pdb=" CG TYR G 65 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR G 65 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR G 65 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR G 65 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR G 65 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR G 65 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR G 65 " -0.003 2.00e-02 2.50e+03 ... (remaining 3081 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 372 2.69 - 3.24: 18626 3.24 - 3.80: 30224 3.80 - 4.35: 40250 4.35 - 4.90: 65857 Nonbonded interactions: 155329 Sorted by model distance: nonbonded pdb=" O ILE H 71 " pdb=" OH TYR H 158 " model vdw 2.140 3.040 nonbonded pdb=" O ILE I 71 " pdb=" OH TYR I 158 " model vdw 2.140 3.040 nonbonded pdb=" O ILE J 71 " pdb=" OH TYR J 158 " model vdw 2.140 3.040 nonbonded pdb=" O ILE G 71 " pdb=" OH TYR G 158 " model vdw 2.140 3.040 nonbonded pdb=" O ILE D 71 " pdb=" OH TYR D 158 " model vdw 2.140 3.040 ... (remaining 155324 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: 0.02 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'B' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'C' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'D' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'E' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'F' and (resid 4 through 217 or (resid 301 and (name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 )) or resid 303 through 304)) selection = (chain 'G' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'H' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'I' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'J' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'K' and (resid 4 through 301 or resid 303 through 304)) selection = (chain 'L' and (resid 4 through 217 or (resid 301 and (name C2 or name C3 or nam \ e C4 or name C5 or name C6 or name C7 or name C8 )) or resid 303 through 304)) } 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: 7.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 17.690 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8805 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 : 0.006 0.050 19392 Z= 0.268 Angle : 0.878 7.887 26160 Z= 0.367 Chirality : 0.039 0.123 2940 Planarity : 0.003 0.021 3084 Dihedral : 13.419 80.046 6864 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.38 % Allowed : 6.55 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 1.49 (0.17), residues: 2208 helix: 1.53 (0.12), residues: 1524 sheet: 2.44 (0.43), residues: 132 loop : -0.86 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 165 TYR 0.011 0.002 TYR I 65 PHE 0.014 0.002 PHE K 51 TRP 0.005 0.001 TRP A 24 HIS 0.002 0.001 HIS E 73 Details of bonding type rmsd covalent geometry : bond 0.00576 (19356) covalent geometry : angle 0.87667 (26088) SS BOND : bond 0.00323 ( 36) SS BOND : angle 1.27880 ( 72) hydrogen bonds : bond 0.22548 ( 1368) hydrogen bonds : angle 6.23361 ( 3996) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 302 time to evaluate : 0.545 Fit side-chains REVERT: B 94 HIS cc_start: 0.7281 (t-90) cc_final: 0.6977 (t-90) REVERT: C 94 HIS cc_start: 0.7221 (t-90) cc_final: 0.6972 (t-90) REVERT: D 32 ARG cc_start: 0.8939 (mtm180) cc_final: 0.8714 (mtm180) REVERT: F 94 HIS cc_start: 0.7203 (t-90) cc_final: 0.6912 (t-90) REVERT: I 94 HIS cc_start: 0.7248 (t-90) cc_final: 0.6996 (t-90) REVERT: J 94 HIS cc_start: 0.7177 (t-90) cc_final: 0.6902 (t-90) outliers start: 48 outliers final: 13 residues processed: 335 average time/residue: 0.5522 time to fit residues: 209.9366 Evaluate side-chains 273 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 260 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 38 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.7980 chunk 212 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 57 GLN E 57 GLN G 57 GLN J 57 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.136735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.081979 restraints weight = 25956.850| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.88 r_work: 0.2904 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2787 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9005 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 19392 Z= 0.156 Angle : 0.577 5.715 26160 Z= 0.323 Chirality : 0.042 0.144 2940 Planarity : 0.004 0.020 3084 Dihedral : 9.465 58.363 2810 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.84 % Allowed : 11.16 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.06 (0.17), residues: 2208 helix: 3.05 (0.12), residues: 1512 sheet: 2.64 (0.43), residues: 132 loop : -1.20 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 98 TYR 0.014 0.002 TYR J 65 PHE 0.016 0.002 PHE H 31 TRP 0.008 0.001 TRP C 134 HIS 0.002 0.001 HIS J 73 Details of bonding type rmsd covalent geometry : bond 0.00330 (19356) covalent geometry : angle 0.57526 (26088) SS BOND : bond 0.00247 ( 36) SS BOND : angle 1.08273 ( 72) hydrogen bonds : bond 0.06592 ( 1368) hydrogen bonds : angle 3.99372 ( 3996) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 281 time to evaluate : 0.753 Fit side-chains REVERT: A 94 HIS cc_start: 0.7163 (t-90) cc_final: 0.6926 (t-90) REVERT: B 94 HIS cc_start: 0.7021 (t-90) cc_final: 0.6661 (t-90) REVERT: B 159 ASP cc_start: 0.8714 (t0) cc_final: 0.8348 (p0) REVERT: E 94 HIS cc_start: 0.7145 (t-90) cc_final: 0.6708 (t-90) REVERT: F 5 THR cc_start: 0.3338 (OUTLIER) cc_final: 0.3130 (p) REVERT: F 94 HIS cc_start: 0.7028 (t-90) cc_final: 0.6675 (t-90) REVERT: G 94 HIS cc_start: 0.6978 (t-90) cc_final: 0.6638 (t-90) REVERT: G 159 ASP cc_start: 0.8651 (t0) cc_final: 0.8176 (p0) REVERT: H 94 HIS cc_start: 0.7055 (t-90) cc_final: 0.6668 (t-90) REVERT: I 159 ASP cc_start: 0.8727 (t0) cc_final: 0.8382 (p0) REVERT: J 5 THR cc_start: 0.3243 (OUTLIER) cc_final: 0.3031 (p) REVERT: J 94 HIS cc_start: 0.6965 (t-90) cc_final: 0.6639 (t-90) REVERT: K 94 HIS cc_start: 0.7070 (t-90) cc_final: 0.6767 (t-90) REVERT: L 94 HIS cc_start: 0.7068 (t-90) cc_final: 0.6650 (t-90) outliers start: 37 outliers final: 18 residues processed: 304 average time/residue: 0.5359 time to fit residues: 185.8438 Evaluate side-chains 276 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 256 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 209 GLU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 38 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 93 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 8 optimal weight: 0.0770 chunk 119 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 95 optimal weight: 0.1980 chunk 23 optimal weight: 3.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.138499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.083836 restraints weight = 26329.398| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 1.89 r_work: 0.2940 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8976 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19392 Z= 0.127 Angle : 0.513 6.376 26160 Z= 0.285 Chirality : 0.040 0.152 2940 Planarity : 0.003 0.024 3084 Dihedral : 8.219 57.694 2809 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.82 % Allowed : 11.46 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.36 (0.17), residues: 2208 helix: 3.32 (0.12), residues: 1524 sheet: 2.64 (0.42), residues: 132 loop : -1.32 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 32 TYR 0.010 0.002 TYR D 158 PHE 0.018 0.001 PHE A 31 TRP 0.008 0.001 TRP J 134 HIS 0.001 0.000 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00272 (19356) covalent geometry : angle 0.51151 (26088) SS BOND : bond 0.00231 ( 36) SS BOND : angle 0.90352 ( 72) hydrogen bonds : bond 0.05297 ( 1368) hydrogen bonds : angle 3.65702 ( 3996) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 265 time to evaluate : 0.723 Fit side-chains REVERT: B 159 ASP cc_start: 0.8701 (t0) cc_final: 0.8358 (p0) REVERT: C 94 HIS cc_start: 0.6939 (t-90) cc_final: 0.6697 (t-90) REVERT: D 94 HIS cc_start: 0.7040 (t-90) cc_final: 0.6809 (t-90) REVERT: E 94 HIS cc_start: 0.7030 (t-90) cc_final: 0.6636 (t-90) REVERT: F 94 HIS cc_start: 0.6985 (t-90) cc_final: 0.6537 (t-90) REVERT: G 94 HIS cc_start: 0.7051 (t-90) cc_final: 0.6767 (t-90) REVERT: G 159 ASP cc_start: 0.8666 (t0) cc_final: 0.8289 (p0) REVERT: H 94 HIS cc_start: 0.7029 (t-90) cc_final: 0.6712 (t-90) REVERT: I 159 ASP cc_start: 0.8684 (t0) cc_final: 0.8362 (p0) REVERT: J 94 HIS cc_start: 0.6890 (t-90) cc_final: 0.6647 (t-90) REVERT: K 94 HIS cc_start: 0.7047 (t-90) cc_final: 0.6813 (t-90) REVERT: L 94 HIS cc_start: 0.7028 (t-90) cc_final: 0.6699 (t-90) outliers start: 77 outliers final: 27 residues processed: 322 average time/residue: 0.5217 time to fit residues: 193.5886 Evaluate side-chains 282 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 255 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 39 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 180 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 chunk 101 optimal weight: 0.9990 chunk 195 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 190 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.137407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.082275 restraints weight = 26297.782| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.88 r_work: 0.2907 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9000 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19392 Z= 0.149 Angle : 0.551 7.610 26160 Z= 0.297 Chirality : 0.042 0.180 2940 Planarity : 0.003 0.019 3084 Dihedral : 7.908 55.443 2809 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.78 % Allowed : 14.43 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.48 (0.17), residues: 2208 helix: 3.34 (0.12), residues: 1536 sheet: 2.67 (0.45), residues: 132 loop : -1.16 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 98 TYR 0.014 0.002 TYR G 65 PHE 0.022 0.002 PHE E 31 TRP 0.006 0.001 TRP F 172 HIS 0.003 0.001 HIS J 73 Details of bonding type rmsd covalent geometry : bond 0.00340 (19356) covalent geometry : angle 0.54912 (26088) SS BOND : bond 0.00289 ( 36) SS BOND : angle 1.06069 ( 72) hydrogen bonds : bond 0.05367 ( 1368) hydrogen bonds : angle 3.67922 ( 3996) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 262 time to evaluate : 0.577 Fit side-chains REVERT: B 159 ASP cc_start: 0.8708 (t0) cc_final: 0.8364 (p0) REVERT: C 94 HIS cc_start: 0.6997 (t-90) cc_final: 0.6731 (t-90) REVERT: D 94 HIS cc_start: 0.7015 (t-90) cc_final: 0.6815 (t-90) REVERT: E 94 HIS cc_start: 0.7027 (t-90) cc_final: 0.6702 (t-90) REVERT: F 94 HIS cc_start: 0.6782 (t-90) cc_final: 0.6473 (t-90) REVERT: G 94 HIS cc_start: 0.7009 (t-90) cc_final: 0.6734 (t-90) REVERT: G 159 ASP cc_start: 0.8719 (t0) cc_final: 0.8327 (p0) REVERT: H 94 HIS cc_start: 0.7012 (t-90) cc_final: 0.6709 (t-90) REVERT: I 159 ASP cc_start: 0.8720 (t0) cc_final: 0.8383 (p0) REVERT: J 89 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8625 (tt) REVERT: J 94 HIS cc_start: 0.6927 (t-90) cc_final: 0.6659 (t-90) REVERT: K 94 HIS cc_start: 0.7042 (t-90) cc_final: 0.6827 (t-90) REVERT: L 94 HIS cc_start: 0.7037 (t-90) cc_final: 0.6733 (t-90) outliers start: 56 outliers final: 33 residues processed: 303 average time/residue: 0.5060 time to fit residues: 175.2075 Evaluate side-chains 294 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 260 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 86 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 146 optimal weight: 0.8980 chunk 99 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 215 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 210 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 174 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.137826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.082906 restraints weight = 26167.930| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 1.87 r_work: 0.2919 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19392 Z= 0.139 Angle : 0.529 6.617 26160 Z= 0.287 Chirality : 0.041 0.175 2940 Planarity : 0.003 0.032 3084 Dihedral : 7.633 54.652 2809 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.73 % Allowed : 15.28 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.54 (0.17), residues: 2208 helix: 3.40 (0.12), residues: 1536 sheet: 2.59 (0.44), residues: 132 loop : -1.16 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 98 TYR 0.011 0.002 TYR I 158 PHE 0.018 0.001 PHE B 31 TRP 0.005 0.001 TRP J 172 HIS 0.002 0.001 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00315 (19356) covalent geometry : angle 0.52758 (26088) SS BOND : bond 0.00257 ( 36) SS BOND : angle 0.96302 ( 72) hydrogen bonds : bond 0.05076 ( 1368) hydrogen bonds : angle 3.60665 ( 3996) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 264 time to evaluate : 0.527 Fit side-chains REVERT: B 159 ASP cc_start: 0.8694 (t0) cc_final: 0.8359 (p0) REVERT: C 94 HIS cc_start: 0.6965 (t-90) cc_final: 0.6712 (t-90) REVERT: E 94 HIS cc_start: 0.6986 (t-90) cc_final: 0.6675 (t-90) REVERT: F 94 HIS cc_start: 0.6796 (t-90) cc_final: 0.6501 (t-90) REVERT: G 94 HIS cc_start: 0.6996 (t-90) cc_final: 0.6723 (t-90) REVERT: G 159 ASP cc_start: 0.8714 (t0) cc_final: 0.8328 (p0) REVERT: H 94 HIS cc_start: 0.6998 (t-90) cc_final: 0.6718 (t-90) REVERT: I 159 ASP cc_start: 0.8703 (t0) cc_final: 0.8397 (p0) REVERT: J 94 HIS cc_start: 0.6871 (t-90) cc_final: 0.6596 (t-90) REVERT: L 94 HIS cc_start: 0.7045 (t-90) cc_final: 0.6763 (t-90) outliers start: 55 outliers final: 42 residues processed: 300 average time/residue: 0.5272 time to fit residues: 180.8092 Evaluate side-chains 294 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 252 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 194 PHE Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 86 THR Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 50 ASP Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 147 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 1 optimal weight: 8.9990 chunk 161 optimal weight: 0.9990 chunk 168 optimal weight: 0.0970 chunk 116 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 68 optimal weight: 0.7980 chunk 5 optimal weight: 0.0980 chunk 144 optimal weight: 0.5980 chunk 165 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 184 optimal weight: 0.0030 overall best weight: 0.2988 ------------------------------------------------------------------------------- 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 = 0.4029 r_free = 0.4029 target = 0.139742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.085565 restraints weight = 26278.815| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.87 r_work: 0.2974 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19392 Z= 0.112 Angle : 0.497 6.789 26160 Z= 0.267 Chirality : 0.039 0.168 2940 Planarity : 0.003 0.029 3084 Dihedral : 6.884 55.346 2808 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.88 % Allowed : 15.62 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.82 (0.18), residues: 2208 helix: 3.65 (0.12), residues: 1548 sheet: 2.61 (0.42), residues: 132 loop : -1.28 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 98 TYR 0.008 0.001 TYR E 158 PHE 0.019 0.001 PHE E 31 TRP 0.006 0.001 TRP F 133 HIS 0.002 0.000 HIS J 73 Details of bonding type rmsd covalent geometry : bond 0.00229 (19356) covalent geometry : angle 0.49578 (26088) SS BOND : bond 0.00158 ( 36) SS BOND : angle 0.75700 ( 72) hydrogen bonds : bond 0.04210 ( 1368) hydrogen bonds : angle 3.44578 ( 3996) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 284 time to evaluate : 0.586 Fit side-chains REVERT: B 159 ASP cc_start: 0.8652 (t0) cc_final: 0.8353 (p0) REVERT: C 94 HIS cc_start: 0.6950 (t-90) cc_final: 0.6707 (t-90) REVERT: E 94 HIS cc_start: 0.6961 (t-90) cc_final: 0.6749 (t-90) REVERT: E 159 ASP cc_start: 0.8705 (t0) cc_final: 0.8376 (p0) REVERT: F 89 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8659 (tt) REVERT: F 94 HIS cc_start: 0.6787 (t-90) cc_final: 0.6531 (t-90) REVERT: G 94 HIS cc_start: 0.6926 (t-90) cc_final: 0.6667 (t-90) REVERT: G 159 ASP cc_start: 0.8706 (t0) cc_final: 0.8351 (p0) REVERT: H 94 HIS cc_start: 0.7004 (t-90) cc_final: 0.6738 (t-90) REVERT: I 159 ASP cc_start: 0.8650 (t0) cc_final: 0.8363 (p0) REVERT: J 89 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8710 (tt) REVERT: J 94 HIS cc_start: 0.6882 (t-90) cc_final: 0.6459 (t-90) REVERT: L 94 HIS cc_start: 0.7026 (t-90) cc_final: 0.6691 (t-90) outliers start: 58 outliers final: 28 residues processed: 322 average time/residue: 0.5256 time to fit residues: 194.3489 Evaluate side-chains 295 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 265 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain F residue 154 PHE Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 147 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 144 optimal weight: 0.3980 chunk 61 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 115 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 85 optimal weight: 0.0980 chunk 73 optimal weight: 0.4980 chunk 133 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.138913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.084118 restraints weight = 26422.672| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.88 r_work: 0.2949 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19392 Z= 0.123 Angle : 0.527 6.475 26160 Z= 0.285 Chirality : 0.040 0.171 2940 Planarity : 0.003 0.039 3084 Dihedral : 6.620 54.736 2800 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.98 % Allowed : 15.67 % Favored : 81.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.83 (0.18), residues: 2208 helix: 3.65 (0.12), residues: 1548 sheet: 2.53 (0.43), residues: 132 loop : -1.21 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 98 TYR 0.011 0.001 TYR B 158 PHE 0.025 0.001 PHE K 31 TRP 0.005 0.001 TRP I 133 HIS 0.002 0.000 HIS J 73 Details of bonding type rmsd covalent geometry : bond 0.00269 (19356) covalent geometry : angle 0.52590 (26088) SS BOND : bond 0.00194 ( 36) SS BOND : angle 0.82116 ( 72) hydrogen bonds : bond 0.04419 ( 1368) hydrogen bonds : angle 3.42100 ( 3996) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 272 time to evaluate : 0.701 Fit side-chains REVERT: B 159 ASP cc_start: 0.8677 (t0) cc_final: 0.8346 (p0) REVERT: C 94 HIS cc_start: 0.6945 (t-90) cc_final: 0.6696 (t-90) REVERT: E 94 HIS cc_start: 0.6962 (t-90) cc_final: 0.6761 (t-90) REVERT: E 159 ASP cc_start: 0.8714 (t0) cc_final: 0.8355 (p0) REVERT: F 94 HIS cc_start: 0.6812 (t-90) cc_final: 0.6582 (t-90) REVERT: G 94 HIS cc_start: 0.6932 (t-90) cc_final: 0.6670 (t-90) REVERT: G 159 ASP cc_start: 0.8719 (t0) cc_final: 0.8355 (p0) REVERT: H 94 HIS cc_start: 0.6977 (t-90) cc_final: 0.6700 (t-90) REVERT: I 159 ASP cc_start: 0.8702 (t0) cc_final: 0.8368 (p0) REVERT: J 89 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8701 (tt) REVERT: J 94 HIS cc_start: 0.6817 (t-90) cc_final: 0.6490 (t-90) REVERT: L 94 HIS cc_start: 0.7028 (t-90) cc_final: 0.6783 (t-90) outliers start: 60 outliers final: 43 residues processed: 312 average time/residue: 0.5334 time to fit residues: 190.5643 Evaluate side-chains 312 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 268 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 38 VAL Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 93 MET Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain J residue 154 PHE Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain K residue 215 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 147 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 96 optimal weight: 0.8980 chunk 169 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 119 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 141 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 75 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.138055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.083221 restraints weight = 26335.254| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.85 r_work: 0.2926 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8977 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19392 Z= 0.136 Angle : 0.552 6.470 26160 Z= 0.301 Chirality : 0.041 0.172 2940 Planarity : 0.003 0.039 3084 Dihedral : 6.698 53.358 2799 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.68 % Allowed : 15.87 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.78 (0.17), residues: 2208 helix: 3.58 (0.12), residues: 1548 sheet: 2.55 (0.44), residues: 132 loop : -1.14 (0.25), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG L 98 TYR 0.012 0.001 TYR B 65 PHE 0.026 0.002 PHE E 31 TRP 0.005 0.001 TRP C 172 HIS 0.002 0.001 HIS J 73 Details of bonding type rmsd covalent geometry : bond 0.00309 (19356) covalent geometry : angle 0.55055 (26088) SS BOND : bond 0.00239 ( 36) SS BOND : angle 0.93266 ( 72) hydrogen bonds : bond 0.04702 ( 1368) hydrogen bonds : angle 3.44028 ( 3996) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 265 time to evaluate : 0.757 Fit side-chains REVERT: B 159 ASP cc_start: 0.8682 (t0) cc_final: 0.8359 (p0) REVERT: C 94 HIS cc_start: 0.6917 (t-90) cc_final: 0.6663 (t-90) REVERT: E 94 HIS cc_start: 0.6986 (t-90) cc_final: 0.6782 (t-90) REVERT: E 159 ASP cc_start: 0.8721 (t0) cc_final: 0.8381 (p0) REVERT: F 7 GLN cc_start: 0.5386 (OUTLIER) cc_final: 0.5048 (pp30) REVERT: F 94 HIS cc_start: 0.6815 (t-90) cc_final: 0.6597 (t-90) REVERT: G 94 HIS cc_start: 0.6853 (t-90) cc_final: 0.6581 (t-90) REVERT: G 159 ASP cc_start: 0.8734 (t0) cc_final: 0.8373 (p0) REVERT: H 94 HIS cc_start: 0.6985 (t-90) cc_final: 0.6707 (t-90) REVERT: I 159 ASP cc_start: 0.8696 (t0) cc_final: 0.8363 (p0) REVERT: J 94 HIS cc_start: 0.6829 (t-90) cc_final: 0.6541 (t-90) REVERT: K 159 ASP cc_start: 0.8291 (p0) cc_final: 0.8062 (p0) REVERT: L 94 HIS cc_start: 0.6955 (t-90) cc_final: 0.6683 (t-90) outliers start: 54 outliers final: 40 residues processed: 300 average time/residue: 0.5277 time to fit residues: 180.5192 Evaluate side-chains 304 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 263 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 7 GLN Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 147 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 192 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 114 optimal weight: 0.5980 chunk 152 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 138 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 168 optimal weight: 0.0870 chunk 37 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.138623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.083826 restraints weight = 26178.216| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.85 r_work: 0.2938 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19392 Z= 0.129 Angle : 0.539 6.453 26160 Z= 0.293 Chirality : 0.041 0.170 2940 Planarity : 0.003 0.045 3084 Dihedral : 6.573 52.708 2798 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.53 % Allowed : 15.67 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.80 (0.17), residues: 2208 helix: 3.60 (0.12), residues: 1548 sheet: 2.49 (0.43), residues: 132 loop : -1.16 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 98 TYR 0.011 0.001 TYR B 158 PHE 0.022 0.001 PHE E 31 TRP 0.005 0.001 TRP F 133 HIS 0.002 0.001 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00288 (19356) covalent geometry : angle 0.53769 (26088) SS BOND : bond 0.00211 ( 36) SS BOND : angle 0.86009 ( 72) hydrogen bonds : bond 0.04530 ( 1368) hydrogen bonds : angle 3.41376 ( 3996) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 265 time to evaluate : 0.769 Fit side-chains REVERT: B 159 ASP cc_start: 0.8682 (t0) cc_final: 0.8371 (p0) REVERT: C 94 HIS cc_start: 0.6918 (t-90) cc_final: 0.6661 (t-90) REVERT: E 159 ASP cc_start: 0.8705 (t0) cc_final: 0.8379 (p0) REVERT: F 7 GLN cc_start: 0.5370 (OUTLIER) cc_final: 0.5029 (pp30) REVERT: F 94 HIS cc_start: 0.6808 (t-90) cc_final: 0.6600 (t-90) REVERT: G 94 HIS cc_start: 0.6853 (t-90) cc_final: 0.6581 (t-90) REVERT: G 159 ASP cc_start: 0.8722 (t0) cc_final: 0.8384 (p0) REVERT: H 94 HIS cc_start: 0.6985 (t-90) cc_final: 0.6709 (t-90) REVERT: I 159 ASP cc_start: 0.8696 (t0) cc_final: 0.8387 (p0) REVERT: J 94 HIS cc_start: 0.6825 (t-90) cc_final: 0.6545 (t-90) REVERT: L 7 GLN cc_start: 0.5680 (OUTLIER) cc_final: 0.5010 (tm-30) REVERT: L 159 ASP cc_start: 0.8722 (t0) cc_final: 0.8382 (p0) outliers start: 51 outliers final: 39 residues processed: 296 average time/residue: 0.5651 time to fit residues: 190.2066 Evaluate side-chains 304 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 263 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 7 GLN Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 5 THR Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 147 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 64 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 204 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 127 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4014 r_free = 0.4014 target = 0.138569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.083567 restraints weight = 26279.201| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.86 r_work: 0.2935 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19392 Z= 0.137 Angle : 0.549 6.501 26160 Z= 0.299 Chirality : 0.041 0.173 2940 Planarity : 0.003 0.048 3084 Dihedral : 6.736 58.528 2797 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 2.18 % Allowed : 15.97 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.73 (0.17), residues: 2208 helix: 3.55 (0.12), residues: 1548 sheet: 2.52 (0.44), residues: 132 loop : -1.17 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 98 TYR 0.012 0.001 TYR B 158 PHE 0.024 0.002 PHE A 31 TRP 0.005 0.001 TRP J 172 HIS 0.002 0.001 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00315 (19356) covalent geometry : angle 0.54773 (26088) SS BOND : bond 0.00243 ( 36) SS BOND : angle 0.92357 ( 72) hydrogen bonds : bond 0.04701 ( 1368) hydrogen bonds : angle 3.44427 ( 3996) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4416 Ramachandran restraints generated. 2208 Oldfield, 0 Emsley, 2208 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 265 time to evaluate : 0.788 Fit side-chains REVERT: B 159 ASP cc_start: 0.8712 (t0) cc_final: 0.8385 (p0) REVERT: C 94 HIS cc_start: 0.6926 (t-90) cc_final: 0.6661 (t-90) REVERT: E 159 ASP cc_start: 0.8729 (t0) cc_final: 0.8424 (p0) REVERT: F 7 GLN cc_start: 0.5332 (OUTLIER) cc_final: 0.4988 (pp30) REVERT: F 94 HIS cc_start: 0.6799 (t-90) cc_final: 0.6593 (t-90) REVERT: G 94 HIS cc_start: 0.6841 (t-90) cc_final: 0.6584 (t-90) REVERT: G 159 ASP cc_start: 0.8731 (t0) cc_final: 0.8389 (p0) REVERT: H 94 HIS cc_start: 0.6994 (t-90) cc_final: 0.6720 (t-90) REVERT: I 159 ASP cc_start: 0.8726 (t0) cc_final: 0.8398 (p0) REVERT: I 194 PHE cc_start: 0.8823 (t80) cc_final: 0.8449 (t80) REVERT: J 94 HIS cc_start: 0.6785 (t-90) cc_final: 0.6540 (t-90) REVERT: L 7 GLN cc_start: 0.5748 (OUTLIER) cc_final: 0.5081 (tm-30) REVERT: L 159 ASP cc_start: 0.8724 (t0) cc_final: 0.8418 (p0) outliers start: 44 outliers final: 38 residues processed: 290 average time/residue: 0.5580 time to fit residues: 183.5332 Evaluate side-chains 302 residues out of total 2016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 262 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 147 GLU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 147 GLU Chi-restraints excluded: chain C residue 147 GLU Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 85 SER Chi-restraints excluded: chain D residue 210 LEU Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 38 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 7 GLN Chi-restraints excluded: chain F residue 38 VAL Chi-restraints excluded: chain F residue 147 GLU Chi-restraints excluded: chain G residue 38 VAL Chi-restraints excluded: chain G residue 147 GLU Chi-restraints excluded: chain H residue 5 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 210 LEU Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 38 VAL Chi-restraints excluded: chain I residue 85 SER Chi-restraints excluded: chain I residue 147 GLU Chi-restraints excluded: chain J residue 5 THR Chi-restraints excluded: chain J residue 38 VAL Chi-restraints excluded: chain J residue 147 GLU Chi-restraints excluded: chain K residue 5 THR Chi-restraints excluded: chain K residue 38 VAL Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 210 LEU Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 7 GLN Chi-restraints excluded: chain L residue 38 VAL Chi-restraints excluded: chain L residue 147 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 38 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 12 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 205 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 0 optimal weight: 30.0000 chunk 71 optimal weight: 0.6980 chunk 130 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.137778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.082580 restraints weight = 26285.218| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.85 r_work: 0.2914 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8996 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 19392 Z= 0.159 Angle : 0.568 7.220 26160 Z= 0.310 Chirality : 0.042 0.176 2940 Planarity : 0.004 0.048 3084 Dihedral : 6.993 59.736 2797 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.28 % Allowed : 15.92 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 16.67 % 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: 3.61 (0.17), residues: 2208 helix: 3.44 (0.12), residues: 1548 sheet: 2.51 (0.45), residues: 132 loop : -1.13 (0.24), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 98 TYR 0.014 0.002 TYR E 65 PHE 0.028 0.002 PHE L 31 TRP 0.006 0.001 TRP G 172 HIS 0.003 0.001 HIS G 73 Details of bonding type rmsd covalent geometry : bond 0.00376 (19356) covalent geometry : angle 0.56642 (26088) SS BOND : bond 0.00311 ( 36) SS BOND : angle 1.08430 ( 72) hydrogen bonds : bond 0.05059 ( 1368) hydrogen bonds : angle 3.52695 ( 3996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10256.40 seconds wall clock time: 174 minutes 26.23 seconds (10466.23 seconds total)