Starting phenix.real_space_refine on Wed Mar 4 15:15:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fte_29424/03_2026/8fte_29424.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fte_29424/03_2026/8fte_29424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fte_29424/03_2026/8fte_29424.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fte_29424/03_2026/8fte_29424.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fte_29424/03_2026/8fte_29424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fte_29424/03_2026/8fte_29424.map" } resolution = 3.8 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= 1.000 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 22 5.16 5 C 8998 2.51 5 N 2618 2.21 5 O 2926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 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: 14564 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "C" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "E" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "G" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "H" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "I" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "J" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "K" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "L" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "M" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "N" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "O" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "P" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "Q" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "R" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "S" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "T" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "V" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Chain: "W" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 662 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 3.60, per 1000 atoms: 0.25 Number of scatterers: 14564 At special positions: 0 Unit cell: (176.8, 178.16, 44.88, 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 22 16.00 O 2926 8.00 N 2618 7.00 C 8998 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.34 Conformation dependent library (CDL) restraints added in 609.8 milliseconds 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3740 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 22 sheets defined 42.0% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA A 201 " --> pdb=" O LEU A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'B' and resid 126 through 146 Processing helix chain 'B' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA B 201 " --> pdb=" O LEU B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 208 No H-bonds generated for 'chain 'B' and resid 206 through 208' Processing helix chain 'C' and resid 126 through 146 Processing helix chain 'C' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA C 193 " --> pdb=" O GLY C 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA C 201 " --> pdb=" O LEU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'D' and resid 126 through 146 Processing helix chain 'D' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA D 193 " --> pdb=" O GLY D 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA D 201 " --> pdb=" O LEU D 197 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'E' and resid 126 through 146 Processing helix chain 'E' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA E 193 " --> pdb=" O GLY E 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA E 201 " --> pdb=" O LEU E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 208 No H-bonds generated for 'chain 'E' and resid 206 through 208' Processing helix chain 'F' and resid 126 through 146 Processing helix chain 'F' and resid 187 through 201 removed outlier: 3.581A pdb=" N ALA F 193 " --> pdb=" O GLY F 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA F 201 " --> pdb=" O LEU F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'G' and resid 126 through 146 Processing helix chain 'G' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA G 193 " --> pdb=" O GLY G 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA G 201 " --> pdb=" O LEU G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 208 No H-bonds generated for 'chain 'G' and resid 206 through 208' Processing helix chain 'H' and resid 126 through 146 Processing helix chain 'H' and resid 187 through 201 removed outlier: 3.581A pdb=" N ALA H 193 " --> pdb=" O GLY H 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA H 201 " --> pdb=" O LEU H 197 " (cutoff:3.500A) Processing helix chain 'H' and resid 206 through 208 No H-bonds generated for 'chain 'H' and resid 206 through 208' Processing helix chain 'I' and resid 126 through 146 Processing helix chain 'I' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA I 193 " --> pdb=" O GLY I 189 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA I 201 " --> pdb=" O LEU I 197 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 208 No H-bonds generated for 'chain 'I' and resid 206 through 208' Processing helix chain 'J' and resid 126 through 146 Processing helix chain 'J' and resid 187 through 201 removed outlier: 3.579A pdb=" N ALA J 193 " --> pdb=" O GLY J 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA J 201 " --> pdb=" O LEU J 197 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 208 No H-bonds generated for 'chain 'J' and resid 206 through 208' Processing helix chain 'K' and resid 126 through 146 Processing helix chain 'K' and resid 187 through 201 removed outlier: 3.579A pdb=" N ALA K 193 " --> pdb=" O GLY K 189 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA K 201 " --> pdb=" O LEU K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 208 No H-bonds generated for 'chain 'K' and resid 206 through 208' Processing helix chain 'L' and resid 126 through 146 Processing helix chain 'L' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA L 193 " --> pdb=" O GLY L 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA L 201 " --> pdb=" O LEU L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 208 No H-bonds generated for 'chain 'L' and resid 206 through 208' Processing helix chain 'M' and resid 126 through 146 Processing helix chain 'M' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA M 193 " --> pdb=" O GLY M 189 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA M 201 " --> pdb=" O LEU M 197 " (cutoff:3.500A) Processing helix chain 'M' and resid 206 through 208 No H-bonds generated for 'chain 'M' and resid 206 through 208' Processing helix chain 'N' and resid 126 through 146 Processing helix chain 'N' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA N 193 " --> pdb=" O GLY N 189 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA N 201 " --> pdb=" O LEU N 197 " (cutoff:3.500A) Processing helix chain 'N' and resid 206 through 208 No H-bonds generated for 'chain 'N' and resid 206 through 208' Processing helix chain 'O' and resid 126 through 146 Processing helix chain 'O' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA O 193 " --> pdb=" O GLY O 189 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA O 201 " --> pdb=" O LEU O 197 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 208 No H-bonds generated for 'chain 'O' and resid 206 through 208' Processing helix chain 'P' and resid 126 through 146 Processing helix chain 'P' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA P 193 " --> pdb=" O GLY P 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA P 201 " --> pdb=" O LEU P 197 " (cutoff:3.500A) Processing helix chain 'P' and resid 206 through 208 No H-bonds generated for 'chain 'P' and resid 206 through 208' Processing helix chain 'Q' and resid 126 through 146 Processing helix chain 'Q' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA Q 193 " --> pdb=" O GLY Q 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA Q 201 " --> pdb=" O LEU Q 197 " (cutoff:3.500A) Processing helix chain 'Q' and resid 206 through 208 No H-bonds generated for 'chain 'Q' and resid 206 through 208' Processing helix chain 'R' and resid 126 through 146 Processing helix chain 'R' and resid 187 through 201 removed outlier: 3.581A pdb=" N ALA R 193 " --> pdb=" O GLY R 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA R 201 " --> pdb=" O LEU R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 208 No H-bonds generated for 'chain 'R' and resid 206 through 208' Processing helix chain 'S' and resid 126 through 146 Processing helix chain 'S' and resid 187 through 201 removed outlier: 3.581A pdb=" N ALA S 193 " --> pdb=" O GLY S 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA S 201 " --> pdb=" O LEU S 197 " (cutoff:3.500A) Processing helix chain 'S' and resid 206 through 208 No H-bonds generated for 'chain 'S' and resid 206 through 208' Processing helix chain 'T' and resid 126 through 146 Processing helix chain 'T' and resid 187 through 201 removed outlier: 3.579A pdb=" N ALA T 193 " --> pdb=" O GLY T 189 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA T 201 " --> pdb=" O LEU T 197 " (cutoff:3.500A) Processing helix chain 'T' and resid 206 through 208 No H-bonds generated for 'chain 'T' and resid 206 through 208' Processing helix chain 'V' and resid 126 through 146 Processing helix chain 'V' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA V 193 " --> pdb=" O GLY V 189 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ALA V 201 " --> pdb=" O LEU V 197 " (cutoff:3.500A) Processing helix chain 'V' and resid 206 through 208 No H-bonds generated for 'chain 'V' and resid 206 through 208' Processing helix chain 'W' and resid 126 through 146 Processing helix chain 'W' and resid 187 through 201 removed outlier: 3.580A pdb=" N ALA W 193 " --> pdb=" O GLY W 189 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA W 201 " --> pdb=" O LEU W 197 " (cutoff:3.500A) Processing helix chain 'W' and resid 206 through 208 No H-bonds generated for 'chain 'W' and resid 206 through 208' Processing sheet with id=AA1, first strand: chain 'A' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER A 152 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR A 179 " --> pdb=" O SER A 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG A 154 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER A 173 " --> pdb=" O ALA A 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER B 152 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR B 179 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG B 154 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER B 173 " --> pdb=" O ALA B 158 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER C 152 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR C 179 " --> pdb=" O SER C 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG C 154 " --> pdb=" O THR C 177 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER C 173 " --> pdb=" O ALA C 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER D 152 " --> pdb=" O THR D 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR D 179 " --> pdb=" O SER D 152 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG D 154 " --> pdb=" O THR D 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER D 173 " --> pdb=" O ALA D 158 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER E 152 " --> pdb=" O THR E 179 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR E 179 " --> pdb=" O SER E 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG E 154 " --> pdb=" O THR E 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER E 173 " --> pdb=" O ALA E 158 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 150 through 158 removed outlier: 5.045A pdb=" N SER F 152 " --> pdb=" O THR F 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR F 179 " --> pdb=" O SER F 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG F 154 " --> pdb=" O THR F 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER F 173 " --> pdb=" O ALA F 158 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 150 through 158 removed outlier: 5.045A pdb=" N SER G 152 " --> pdb=" O THR G 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR G 179 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG G 154 " --> pdb=" O THR G 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER G 173 " --> pdb=" O ALA G 158 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 150 through 158 removed outlier: 5.045A pdb=" N SER H 152 " --> pdb=" O THR H 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR H 179 " --> pdb=" O SER H 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG H 154 " --> pdb=" O THR H 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER H 173 " --> pdb=" O ALA H 158 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 150 through 158 removed outlier: 5.045A pdb=" N SER I 152 " --> pdb=" O THR I 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR I 179 " --> pdb=" O SER I 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG I 154 " --> pdb=" O THR I 177 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER I 173 " --> pdb=" O ALA I 158 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER J 152 " --> pdb=" O THR J 179 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR J 179 " --> pdb=" O SER J 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG J 154 " --> pdb=" O THR J 177 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER J 173 " --> pdb=" O ALA J 158 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 150 through 158 removed outlier: 5.045A pdb=" N SER K 152 " --> pdb=" O THR K 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR K 179 " --> pdb=" O SER K 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG K 154 " --> pdb=" O THR K 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER K 173 " --> pdb=" O ALA K 158 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER L 152 " --> pdb=" O THR L 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR L 179 " --> pdb=" O SER L 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG L 154 " --> pdb=" O THR L 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER L 173 " --> pdb=" O ALA L 158 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER M 152 " --> pdb=" O THR M 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR M 179 " --> pdb=" O SER M 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG M 154 " --> pdb=" O THR M 177 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER M 173 " --> pdb=" O ALA M 158 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'N' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER N 152 " --> pdb=" O THR N 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR N 179 " --> pdb=" O SER N 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG N 154 " --> pdb=" O THR N 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER N 173 " --> pdb=" O ALA N 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'O' and resid 150 through 158 removed outlier: 5.045A pdb=" N SER O 152 " --> pdb=" O THR O 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR O 179 " --> pdb=" O SER O 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG O 154 " --> pdb=" O THR O 177 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER O 173 " --> pdb=" O ALA O 158 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'P' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER P 152 " --> pdb=" O THR P 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR P 179 " --> pdb=" O SER P 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG P 154 " --> pdb=" O THR P 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER P 173 " --> pdb=" O ALA P 158 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'Q' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER Q 152 " --> pdb=" O THR Q 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR Q 179 " --> pdb=" O SER Q 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG Q 154 " --> pdb=" O THR Q 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER Q 173 " --> pdb=" O ALA Q 158 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'R' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER R 152 " --> pdb=" O THR R 179 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR R 179 " --> pdb=" O SER R 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG R 154 " --> pdb=" O THR R 177 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER R 173 " --> pdb=" O ALA R 158 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'S' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER S 152 " --> pdb=" O THR S 179 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N THR S 179 " --> pdb=" O SER S 152 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG S 154 " --> pdb=" O THR S 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER S 173 " --> pdb=" O ALA S 158 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'T' and resid 150 through 158 removed outlier: 5.045A pdb=" N SER T 152 " --> pdb=" O THR T 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR T 179 " --> pdb=" O SER T 152 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG T 154 " --> pdb=" O THR T 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER T 173 " --> pdb=" O ALA T 158 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'V' and resid 150 through 158 removed outlier: 5.046A pdb=" N SER V 152 " --> pdb=" O THR V 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR V 179 " --> pdb=" O SER V 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG V 154 " --> pdb=" O THR V 177 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER V 173 " --> pdb=" O ALA V 158 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'W' and resid 150 through 158 removed outlier: 5.045A pdb=" N SER W 152 " --> pdb=" O THR W 179 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N THR W 179 " --> pdb=" O SER W 152 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG W 154 " --> pdb=" O THR W 177 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER W 173 " --> pdb=" O ALA W 158 " (cutoff:3.500A) 749 hydrogen bonds defined for protein. 2247 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: 2.17 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5038 1.34 - 1.46: 1946 1.46 - 1.57: 7734 1.57 - 1.69: 0 1.69 - 1.80: 44 Bond restraints: 14762 Sorted by residual: bond pdb=" N ASN C 209 " pdb=" CA ASN C 209 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.33e-02 5.65e+03 7.26e+00 bond pdb=" CA ASN C 209 " pdb=" C ASN C 209 " ideal model delta sigma weight residual 1.522 1.532 -0.011 1.31e-02 5.83e+03 6.77e-01 bond pdb=" C ASN C 209 " pdb=" O ASN C 209 " ideal model delta sigma weight residual 1.236 1.247 -0.011 1.39e-02 5.18e+03 6.50e-01 bond pdb=" C GLU P 181 " pdb=" N PRO P 182 " ideal model delta sigma weight residual 1.332 1.342 -0.010 1.30e-02 5.92e+03 6.01e-01 bond pdb=" C GLU O 181 " pdb=" N PRO O 182 " ideal model delta sigma weight residual 1.332 1.341 -0.010 1.30e-02 5.92e+03 5.77e-01 ... (remaining 14757 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 18188 0.91 - 1.81: 1518 1.81 - 2.72: 309 2.72 - 3.62: 115 3.62 - 4.53: 22 Bond angle restraints: 20152 Sorted by residual: angle pdb=" N ARG W 154 " pdb=" CA ARG W 154 " pdb=" C ARG W 154 " ideal model delta sigma weight residual 107.80 111.01 -3.21 1.73e+00 3.34e-01 3.44e+00 angle pdb=" N ARG M 154 " pdb=" CA ARG M 154 " pdb=" C ARG M 154 " ideal model delta sigma weight residual 107.80 110.99 -3.19 1.73e+00 3.34e-01 3.41e+00 angle pdb=" N ARG J 154 " pdb=" CA ARG J 154 " pdb=" C ARG J 154 " ideal model delta sigma weight residual 107.80 110.99 -3.19 1.73e+00 3.34e-01 3.41e+00 angle pdb=" N ARG K 154 " pdb=" CA ARG K 154 " pdb=" C ARG K 154 " ideal model delta sigma weight residual 107.80 110.99 -3.19 1.73e+00 3.34e-01 3.41e+00 angle pdb=" N ARG D 154 " pdb=" CA ARG D 154 " pdb=" C ARG D 154 " ideal model delta sigma weight residual 107.80 110.99 -3.19 1.73e+00 3.34e-01 3.40e+00 ... (remaining 20147 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.58: 7943 11.58 - 23.15: 638 23.15 - 34.73: 205 34.73 - 46.30: 80 46.30 - 57.88: 88 Dihedral angle restraints: 8954 sinusoidal: 3190 harmonic: 5764 Sorted by residual: dihedral pdb=" CA GLN W 190 " pdb=" C GLN W 190 " pdb=" N ILE W 191 " pdb=" CA ILE W 191 " ideal model delta harmonic sigma weight residual 180.00 165.02 14.98 0 5.00e+00 4.00e-02 8.97e+00 dihedral pdb=" CA GLN N 190 " pdb=" C GLN N 190 " pdb=" N ILE N 191 " pdb=" CA ILE N 191 " ideal model delta harmonic sigma weight residual 180.00 165.03 14.97 0 5.00e+00 4.00e-02 8.97e+00 dihedral pdb=" CA GLN B 190 " pdb=" C GLN B 190 " pdb=" N ILE B 191 " pdb=" CA ILE B 191 " ideal model delta harmonic sigma weight residual 180.00 165.03 14.97 0 5.00e+00 4.00e-02 8.97e+00 ... (remaining 8951 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1344 0.024 - 0.047: 621 0.047 - 0.071: 325 0.071 - 0.095: 195 0.095 - 0.118: 45 Chirality restraints: 2530 Sorted by residual: chirality pdb=" CA VAL D 213 " pdb=" N VAL D 213 " pdb=" C VAL D 213 " pdb=" CB VAL D 213 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.51e-01 chirality pdb=" CA VAL P 213 " pdb=" N VAL P 213 " pdb=" C VAL P 213 " pdb=" CB VAL P 213 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.48e-01 chirality pdb=" CA VAL H 213 " pdb=" N VAL H 213 " pdb=" C VAL H 213 " pdb=" CB VAL H 213 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.47e-01 ... (remaining 2527 not shown) Planarity restraints: 2640 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER J 171 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO J 172 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO J 172 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO J 172 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER N 171 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO N 172 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO N 172 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO N 172 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 171 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO D 172 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 172 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO D 172 " -0.016 5.00e-02 4.00e+02 ... (remaining 2637 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1559 2.74 - 3.28: 14713 3.28 - 3.82: 22183 3.82 - 4.36: 24609 4.36 - 4.90: 40535 Nonbonded interactions: 103599 Sorted by model distance: nonbonded pdb=" NH1 ARG D 154 " pdb=" NH2 ARG E 142 " model vdw 2.203 3.200 nonbonded pdb=" NH1 ARG H 154 " pdb=" NH2 ARG I 142 " model vdw 2.208 3.200 nonbonded pdb=" NH1 ARG M 154 " pdb=" NH2 ARG N 142 " model vdw 2.220 3.200 nonbonded pdb=" NH1 ARG T 154 " pdb=" NH2 ARG V 142 " model vdw 2.220 3.200 nonbonded pdb=" NH1 ARG V 154 " pdb=" NH2 ARG W 142 " model vdw 2.221 3.200 ... (remaining 103594 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.600 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: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.370 Find NCS groups from input model: 0.130 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4932 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14762 Z= 0.156 Angle : 0.627 4.530 20152 Z= 0.375 Chirality : 0.039 0.118 2530 Planarity : 0.004 0.029 2640 Dihedral : 12.353 57.877 5214 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.56 % Allowed : 13.89 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.20), residues: 1958 helix: 1.95 (0.19), residues: 770 sheet: -1.10 (0.26), residues: 440 loop : -1.24 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 184 TYR 0.004 0.001 TYR C 132 PHE 0.001 0.001 PHE K 126 HIS 0.002 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00279 (14762) covalent geometry : angle 0.62702 (20152) hydrogen bonds : bond 0.17722 ( 749) hydrogen bonds : angle 7.28947 ( 2247) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 511 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 423 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 176 VAL cc_start: 0.7465 (t) cc_final: 0.7175 (m) REVERT: D 160 PRO cc_start: 0.5619 (Cg_exo) cc_final: 0.5316 (Cg_endo) REVERT: F 220 LEU cc_start: 0.7565 (mt) cc_final: 0.5266 (tt) REVERT: I 220 LEU cc_start: 0.6616 (mt) cc_final: 0.6400 (mt) REVERT: J 177 THR cc_start: 0.6018 (p) cc_final: 0.5793 (p) REVERT: K 159 MET cc_start: 0.6754 (mmt) cc_final: 0.5976 (mmp) REVERT: M 159 MET cc_start: 0.6271 (mmt) cc_final: 0.5475 (mmm) REVERT: N 159 MET cc_start: 0.6330 (mmt) cc_final: 0.5561 (mmm) REVERT: O 159 MET cc_start: 0.5642 (mmt) cc_final: 0.5002 (mmp) REVERT: O 180 LEU cc_start: 0.5527 (tp) cc_final: 0.4936 (mp) REVERT: P 159 MET cc_start: 0.4903 (mmt) cc_final: 0.4686 (mmm) REVERT: Q 147 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6380 (tm) REVERT: T 129 GLN cc_start: 0.5664 (mm-40) cc_final: 0.4996 (mm110) REVERT: V 129 GLN cc_start: 0.6458 (mm-40) cc_final: 0.5916 (mp10) outliers start: 88 outliers final: 21 residues processed: 463 average time/residue: 0.1413 time to fit residues: 91.0403 Evaluate side-chains 252 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain C residue 144 ILE Chi-restraints excluded: chain D residue 144 ILE Chi-restraints excluded: chain F residue 144 ILE Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain O residue 136 LEU Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain P residue 136 LEU Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain Q residue 147 LEU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain W residue 147 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 98 optimal weight: 0.0030 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.4980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 0.9980 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN A 156 HIS A 222 GLN B 156 HIS B 222 GLN C 156 HIS C 209 ASN C 222 GLN D 156 HIS D 222 GLN E 156 HIS E 222 GLN F 156 HIS F 222 GLN G 156 HIS G 222 GLN H 222 GLN I 222 GLN J 222 GLN K 222 GLN M 222 GLN N 222 GLN O 222 GLN P 156 HIS P 222 GLN Q 156 HIS Q 222 GLN R 156 HIS R 222 GLN S 156 HIS S 222 GLN T 156 HIS T 222 GLN V 156 HIS V 222 GLN W 222 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5378 r_free = 0.5378 target = 0.249349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.5097 r_free = 0.5097 target = 0.212512 restraints weight = 16345.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5163 r_free = 0.5163 target = 0.220908 restraints weight = 8689.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5209 r_free = 0.5209 target = 0.226989 restraints weight = 5396.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.5241 r_free = 0.5241 target = 0.231326 restraints weight = 3728.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5263 r_free = 0.5263 target = 0.234409 restraints weight = 2775.903| |-----------------------------------------------------------------------------| r_work (final): 0.5297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5125 moved from start: 0.3767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14762 Z= 0.124 Angle : 0.619 10.028 20152 Z= 0.286 Chirality : 0.041 0.160 2530 Planarity : 0.004 0.040 2640 Dihedral : 6.305 59.995 2156 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 7.13 % Allowed : 12.82 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.21), residues: 1958 helix: 2.21 (0.19), residues: 770 sheet: -0.56 (0.27), residues: 440 loop : -0.69 (0.26), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 154 TYR 0.008 0.001 TYR B 132 PHE 0.020 0.001 PHE V 126 HIS 0.007 0.002 HIS W 156 Details of bonding type rmsd covalent geometry : bond 0.00269 (14762) covalent geometry : angle 0.61860 (20152) hydrogen bonds : bond 0.02738 ( 749) hydrogen bonds : angle 5.07823 ( 2247) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 296 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 220 LEU cc_start: 0.6722 (mt) cc_final: 0.6421 (mt) REVERT: J 142 ARG cc_start: 0.8633 (mmp80) cc_final: 0.8414 (mmp80) REVERT: K 142 ARG cc_start: 0.8439 (mmp80) cc_final: 0.7061 (ttp80) REVERT: K 159 MET cc_start: 0.6405 (mmt) cc_final: 0.6136 (mmp) REVERT: M 159 MET cc_start: 0.6521 (mmt) cc_final: 0.5809 (mmm) REVERT: N 142 ARG cc_start: 0.7810 (tpp-160) cc_final: 0.7445 (tpp-160) REVERT: N 150 VAL cc_start: 0.5087 (OUTLIER) cc_final: 0.4606 (m) REVERT: N 159 MET cc_start: 0.6731 (mmt) cc_final: 0.5847 (mmm) REVERT: O 159 MET cc_start: 0.6447 (mmt) cc_final: 0.5629 (mmp) REVERT: O 180 LEU cc_start: 0.5142 (tp) cc_final: 0.4666 (mp) REVERT: O 184 ARG cc_start: 0.4406 (mmm160) cc_final: 0.4187 (mmm160) REVERT: P 129 GLN cc_start: 0.6311 (tm-30) cc_final: 0.6021 (tm-30) REVERT: P 159 MET cc_start: 0.5523 (mmt) cc_final: 0.5115 (mmm) REVERT: P 180 LEU cc_start: 0.5360 (tp) cc_final: 0.5037 (mp) REVERT: Q 180 LEU cc_start: 0.5307 (tp) cc_final: 0.4759 (mp) REVERT: S 154 ARG cc_start: 0.5741 (mpp-170) cc_final: 0.5034 (mpp-170) REVERT: V 147 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7237 (tm) outliers start: 113 outliers final: 53 residues processed: 370 average time/residue: 0.1190 time to fit residues: 63.5642 Evaluate side-chains 300 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 245 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 GLN Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 155 VAL Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain P residue 146 THR Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain T residue 220 LEU Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 197 LEU Chi-restraints excluded: chain V residue 220 LEU Chi-restraints excluded: chain W residue 147 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 122 optimal weight: 0.6980 chunk 158 optimal weight: 0.8980 chunk 176 optimal weight: 0.9980 chunk 194 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 187 optimal weight: 3.9990 chunk 180 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS F 209 ASN G 209 ASN H 156 HIS H 209 ASN I 156 HIS I 209 ASN J 156 HIS J 209 ASN K 125 GLN K 156 HIS K 209 ASN L 156 HIS L 209 ASN M 156 HIS M 209 ASN N 156 HIS N 196 HIS T 196 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5327 r_free = 0.5327 target = 0.241799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5032 r_free = 0.5032 target = 0.205285 restraints weight = 16709.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.5096 r_free = 0.5096 target = 0.213031 restraints weight = 9074.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5141 r_free = 0.5141 target = 0.218726 restraints weight = 5731.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.5174 r_free = 0.5174 target = 0.222817 restraints weight = 4019.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.5197 r_free = 0.5197 target = 0.225768 restraints weight = 3034.440| |-----------------------------------------------------------------------------| r_work (final): 0.5193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5440 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14762 Z= 0.163 Angle : 0.707 11.828 20152 Z= 0.335 Chirality : 0.043 0.212 2530 Planarity : 0.005 0.052 2640 Dihedral : 6.034 57.273 2134 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 7.45 % Allowed : 14.02 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.21), residues: 1958 helix: 2.09 (0.19), residues: 748 sheet: -0.67 (0.26), residues: 440 loop : -1.03 (0.26), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 154 TYR 0.016 0.001 TYR A 132 PHE 0.011 0.001 PHE A 126 HIS 0.010 0.002 HIS P 196 Details of bonding type rmsd covalent geometry : bond 0.00361 (14762) covalent geometry : angle 0.70731 (20152) hydrogen bonds : bond 0.03245 ( 749) hydrogen bonds : angle 4.99913 ( 2247) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 260 time to evaluate : 0.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASN cc_start: 0.5935 (OUTLIER) cc_final: 0.4487 (t0) REVERT: B 159 MET cc_start: 0.6612 (mmm) cc_final: 0.6390 (mmm) REVERT: B 160 PRO cc_start: 0.6165 (Cg_endo) cc_final: 0.5580 (Cg_exo) REVERT: B 209 ASN cc_start: 0.5805 (OUTLIER) cc_final: 0.4664 (t0) REVERT: F 209 ASN cc_start: 0.5586 (OUTLIER) cc_final: 0.4676 (t0) REVERT: G 142 ARG cc_start: 0.8476 (mmp80) cc_final: 0.7080 (ttp-170) REVERT: G 177 THR cc_start: 0.7526 (p) cc_final: 0.7138 (p) REVERT: G 209 ASN cc_start: 0.6274 (OUTLIER) cc_final: 0.4889 (t0) REVERT: G 213 VAL cc_start: 0.5504 (p) cc_final: 0.5281 (t) REVERT: H 209 ASN cc_start: 0.5397 (OUTLIER) cc_final: 0.4473 (t0) REVERT: J 154 ARG cc_start: 0.6149 (mtm-85) cc_final: 0.5203 (mtm-85) REVERT: K 142 ARG cc_start: 0.8363 (mmp80) cc_final: 0.6902 (ttp80) REVERT: K 209 ASN cc_start: 0.5516 (OUTLIER) cc_final: 0.4523 (t0) REVERT: M 159 MET cc_start: 0.7037 (mmt) cc_final: 0.6125 (mmm) REVERT: N 159 MET cc_start: 0.7273 (mmt) cc_final: 0.6369 (mmm) REVERT: O 159 MET cc_start: 0.6979 (mmt) cc_final: 0.5949 (mmp) REVERT: O 180 LEU cc_start: 0.4883 (tp) cc_final: 0.4555 (mp) REVERT: O 184 ARG cc_start: 0.4947 (mmm160) cc_final: 0.4572 (mmm160) REVERT: P 129 GLN cc_start: 0.6547 (tm-30) cc_final: 0.6346 (tm-30) REVERT: P 142 ARG cc_start: 0.7772 (tpp-160) cc_final: 0.7435 (tpp80) REVERT: P 159 MET cc_start: 0.6963 (mmt) cc_final: 0.6097 (mmm) REVERT: Q 159 MET cc_start: 0.6065 (mmp) cc_final: 0.4804 (mmt) REVERT: Q 180 LEU cc_start: 0.5360 (tp) cc_final: 0.4925 (mp) REVERT: R 159 MET cc_start: 0.7325 (mmm) cc_final: 0.7041 (mmm) REVERT: S 159 MET cc_start: 0.7257 (mmm) cc_final: 0.6816 (mmp) REVERT: V 154 ARG cc_start: 0.5023 (mpp-170) cc_final: 0.3990 (mtm-85) REVERT: W 142 ARG cc_start: 0.7861 (tpp-160) cc_final: 0.7434 (tpp80) outliers start: 118 outliers final: 77 residues processed: 348 average time/residue: 0.1218 time to fit residues: 62.1609 Evaluate side-chains 314 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 231 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 171 SER Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 209 ASN Chi-restraints excluded: chain H residue 155 VAL Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 209 ASN Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 202 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 209 ASN Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 146 THR Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 147 LEU Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain T residue 220 LEU Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 197 LEU Chi-restraints excluded: chain V residue 220 LEU Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 197 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 80 optimal weight: 3.9990 chunk 191 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 150 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 185 optimal weight: 0.0040 chunk 110 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 209 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5701 r_free = 0.5701 target = 0.305438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5643 r_free = 0.5643 target = 0.294044 restraints weight = 18488.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.5661 r_free = 0.5661 target = 0.296285 restraints weight = 13284.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5677 r_free = 0.5677 target = 0.297918 restraints weight = 10073.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.5683 r_free = 0.5683 target = 0.298908 restraints weight = 7921.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.5695 r_free = 0.5695 target = 0.299912 restraints weight = 6475.921| |-----------------------------------------------------------------------------| r_work (final): 0.5680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5673 moved from start: 0.6042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14762 Z= 0.126 Angle : 0.633 11.497 20152 Z= 0.290 Chirality : 0.042 0.242 2530 Planarity : 0.004 0.036 2640 Dihedral : 5.793 58.700 2134 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 6.38 % Allowed : 16.35 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.21), residues: 1958 helix: 2.23 (0.19), residues: 748 sheet: -0.21 (0.27), residues: 440 loop : -0.98 (0.26), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG W 184 TYR 0.011 0.001 TYR B 132 PHE 0.005 0.001 PHE V 126 HIS 0.005 0.001 HIS R 196 Details of bonding type rmsd covalent geometry : bond 0.00290 (14762) covalent geometry : angle 0.63258 (20152) hydrogen bonds : bond 0.02785 ( 749) hydrogen bonds : angle 4.65660 ( 2247) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 242 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7057 (tm) REVERT: B 160 PRO cc_start: 0.8011 (Cg_endo) cc_final: 0.7399 (Cg_exo) REVERT: D 159 MET cc_start: 0.7452 (tpp) cc_final: 0.6586 (mmm) REVERT: F 147 LEU cc_start: 0.6620 (OUTLIER) cc_final: 0.6373 (tt) REVERT: F 209 ASN cc_start: 0.6264 (OUTLIER) cc_final: 0.5623 (t0) REVERT: G 142 ARG cc_start: 0.7099 (mmp80) cc_final: 0.6275 (ttp-170) REVERT: H 140 LEU cc_start: 0.7239 (OUTLIER) cc_final: 0.6898 (tt) REVERT: H 159 MET cc_start: 0.7072 (mmm) cc_final: 0.6036 (mmm) REVERT: H 209 ASN cc_start: 0.6218 (OUTLIER) cc_final: 0.5717 (t0) REVERT: I 140 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7086 (tt) REVERT: J 209 ASN cc_start: 0.5698 (OUTLIER) cc_final: 0.5364 (t0) REVERT: K 142 ARG cc_start: 0.6331 (mmp80) cc_final: 0.5993 (ttp80) REVERT: K 159 MET cc_start: 0.6128 (mmt) cc_final: 0.5332 (mmp) REVERT: K 209 ASN cc_start: 0.5736 (OUTLIER) cc_final: 0.4996 (t0) REVERT: M 159 MET cc_start: 0.6351 (mmt) cc_final: 0.5491 (mmm) REVERT: N 159 MET cc_start: 0.6289 (mmt) cc_final: 0.5622 (mmm) REVERT: O 159 MET cc_start: 0.6550 (mmt) cc_final: 0.5476 (mmp) REVERT: P 159 MET cc_start: 0.6047 (mmt) cc_final: 0.5467 (mmm) REVERT: P 209 ASN cc_start: 0.6682 (OUTLIER) cc_final: 0.6346 (t0) REVERT: Q 159 MET cc_start: 0.5486 (mmp) cc_final: 0.4796 (mmt) REVERT: R 159 MET cc_start: 0.7276 (mmm) cc_final: 0.7000 (mmm) REVERT: S 159 MET cc_start: 0.6710 (mmm) cc_final: 0.6472 (mmp) REVERT: V 147 LEU cc_start: 0.7207 (OUTLIER) cc_final: 0.6894 (tm) REVERT: W 209 ASN cc_start: 0.6309 (OUTLIER) cc_final: 0.5784 (t0) outliers start: 101 outliers final: 72 residues processed: 316 average time/residue: 0.1153 time to fit residues: 54.4506 Evaluate side-chains 299 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 216 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 209 ASN Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 209 ASN Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 143 THR Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 209 ASN Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain O residue 125 GLN Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain P residue 209 ASN Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain T residue 220 LEU Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 197 LEU Chi-restraints excluded: chain V residue 220 LEU Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 197 LEU Chi-restraints excluded: chain W residue 209 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 148 optimal weight: 0.9980 chunk 18 optimal weight: 0.2980 chunk 175 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 chunk 46 optimal weight: 0.1980 chunk 37 optimal weight: 0.7980 chunk 192 optimal weight: 4.9990 chunk 90 optimal weight: 0.2980 chunk 107 optimal weight: 1.9990 chunk 161 optimal weight: 6.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5334 r_free = 0.5334 target = 0.242139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.5032 r_free = 0.5032 target = 0.204653 restraints weight = 16711.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.5096 r_free = 0.5096 target = 0.212426 restraints weight = 8971.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5142 r_free = 0.5142 target = 0.218258 restraints weight = 5658.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.5175 r_free = 0.5175 target = 0.222478 restraints weight = 3975.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.5198 r_free = 0.5198 target = 0.225490 restraints weight = 2998.057| |-----------------------------------------------------------------------------| r_work (final): 0.5194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5442 moved from start: 0.6514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14762 Z= 0.111 Angle : 0.633 11.682 20152 Z= 0.284 Chirality : 0.041 0.233 2530 Planarity : 0.004 0.031 2640 Dihedral : 5.525 59.277 2132 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 6.94 % Allowed : 17.23 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.04 (0.21), residues: 1958 helix: 2.39 (0.19), residues: 748 sheet: 0.26 (0.28), residues: 440 loop : -0.76 (0.26), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 184 TYR 0.010 0.001 TYR T 132 PHE 0.004 0.001 PHE Q 126 HIS 0.004 0.001 HIS R 196 Details of bonding type rmsd covalent geometry : bond 0.00254 (14762) covalent geometry : angle 0.63259 (20152) hydrogen bonds : bond 0.02645 ( 749) hydrogen bonds : angle 4.44447 ( 2247) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 242 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASN cc_start: 0.5858 (OUTLIER) cc_final: 0.4450 (t0) REVERT: D 159 MET cc_start: 0.7553 (tpp) cc_final: 0.7189 (mmm) REVERT: E 159 MET cc_start: 0.7710 (mmm) cc_final: 0.7287 (mmm) REVERT: G 142 ARG cc_start: 0.8463 (mmp80) cc_final: 0.7079 (ttp-170) REVERT: H 140 LEU cc_start: 0.6289 (OUTLIER) cc_final: 0.6025 (tt) REVERT: I 140 LEU cc_start: 0.6629 (OUTLIER) cc_final: 0.6342 (tt) REVERT: I 209 ASN cc_start: 0.5613 (OUTLIER) cc_final: 0.4759 (t0) REVERT: K 140 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6746 (mm) REVERT: K 142 ARG cc_start: 0.8359 (mmp80) cc_final: 0.7065 (ttp80) REVERT: K 159 MET cc_start: 0.7123 (mmt) cc_final: 0.6115 (mmp) REVERT: M 159 MET cc_start: 0.7111 (mmt) cc_final: 0.6221 (mmm) REVERT: N 159 MET cc_start: 0.7517 (mmt) cc_final: 0.6631 (mmm) REVERT: O 159 MET cc_start: 0.7236 (mmt) cc_final: 0.6220 (mmp) REVERT: P 142 ARG cc_start: 0.7557 (tpp-160) cc_final: 0.7231 (tpp80) REVERT: P 159 MET cc_start: 0.7276 (mmt) cc_final: 0.6462 (mmm) REVERT: P 209 ASN cc_start: 0.6066 (OUTLIER) cc_final: 0.5546 (t0) REVERT: Q 159 MET cc_start: 0.6558 (mmp) cc_final: 0.5864 (mmm) REVERT: R 159 MET cc_start: 0.7593 (mmm) cc_final: 0.7237 (mmm) REVERT: R 209 ASN cc_start: 0.5894 (OUTLIER) cc_final: 0.5295 (m-40) REVERT: S 159 MET cc_start: 0.7121 (mmm) cc_final: 0.6888 (mmp) REVERT: W 159 MET cc_start: 0.7375 (tpp) cc_final: 0.6891 (mmm) REVERT: W 209 ASN cc_start: 0.6049 (OUTLIER) cc_final: 0.5244 (t0) outliers start: 110 outliers final: 80 residues processed: 321 average time/residue: 0.1015 time to fit residues: 49.5146 Evaluate side-chains 311 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 223 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 209 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 209 ASN Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 209 ASN Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 125 GLN Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain T residue 220 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 197 LEU Chi-restraints excluded: chain V residue 209 ASN Chi-restraints excluded: chain V residue 220 LEU Chi-restraints excluded: chain W residue 136 LEU Chi-restraints excluded: chain W residue 146 THR Chi-restraints excluded: chain W residue 155 VAL Chi-restraints excluded: chain W residue 197 LEU Chi-restraints excluded: chain W residue 209 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 123 optimal weight: 0.7980 chunk 92 optimal weight: 0.1980 chunk 149 optimal weight: 0.8980 chunk 37 optimal weight: 0.8980 chunk 143 optimal weight: 0.0370 chunk 111 optimal weight: 0.9990 chunk 165 optimal weight: 6.9990 chunk 13 optimal weight: 0.1980 chunk 132 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 181 optimal weight: 0.6980 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 125 GLN G 209 ASN J 222 GLN K 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5718 r_free = 0.5718 target = 0.308075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5665 r_free = 0.5665 target = 0.297318 restraints weight = 18339.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5678 r_free = 0.5678 target = 0.299421 restraints weight = 12968.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.5698 r_free = 0.5698 target = 0.301102 restraints weight = 9703.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.5704 r_free = 0.5704 target = 0.302073 restraints weight = 7543.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.5716 r_free = 0.5716 target = 0.303065 restraints weight = 6104.795| |-----------------------------------------------------------------------------| r_work (final): 0.5698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5679 moved from start: 0.6811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14762 Z= 0.099 Angle : 0.634 11.758 20152 Z= 0.276 Chirality : 0.041 0.206 2530 Planarity : 0.004 0.023 2640 Dihedral : 4.928 58.401 2124 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 6.76 % Allowed : 18.43 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.35 (0.22), residues: 1958 helix: 2.45 (0.19), residues: 748 sheet: 0.71 (0.29), residues: 440 loop : -0.57 (0.27), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 184 TYR 0.006 0.001 TYR B 132 PHE 0.007 0.001 PHE D 126 HIS 0.003 0.001 HIS R 196 Details of bonding type rmsd covalent geometry : bond 0.00227 (14762) covalent geometry : angle 0.63388 (20152) hydrogen bonds : bond 0.02505 ( 749) hydrogen bonds : angle 4.31906 ( 2247) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 237 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 159 MET cc_start: 0.7331 (mmm) cc_final: 0.6933 (mmm) REVERT: F 147 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6421 (tt) REVERT: F 191 ILE cc_start: 0.4948 (OUTLIER) cc_final: 0.4415 (mt) REVERT: F 209 ASN cc_start: 0.6366 (OUTLIER) cc_final: 0.5558 (t0) REVERT: G 142 ARG cc_start: 0.6990 (mmp80) cc_final: 0.6234 (ttp-170) REVERT: G 146 THR cc_start: 0.5603 (t) cc_final: 0.5393 (t) REVERT: H 140 LEU cc_start: 0.6902 (OUTLIER) cc_final: 0.6595 (tt) REVERT: H 159 MET cc_start: 0.7221 (mmm) cc_final: 0.6178 (mmm) REVERT: I 140 LEU cc_start: 0.7331 (OUTLIER) cc_final: 0.7070 (tt) REVERT: J 222 GLN cc_start: 0.7421 (mp-120) cc_final: 0.7042 (mp10) REVERT: K 140 LEU cc_start: 0.7934 (OUTLIER) cc_final: 0.7615 (mm) REVERT: K 146 THR cc_start: 0.5262 (m) cc_final: 0.4999 (m) REVERT: K 159 MET cc_start: 0.6020 (mmt) cc_final: 0.5500 (mmp) REVERT: M 159 MET cc_start: 0.6374 (mmt) cc_final: 0.5565 (mmm) REVERT: N 159 MET cc_start: 0.6380 (mmt) cc_final: 0.5729 (mmm) REVERT: O 159 MET cc_start: 0.6698 (mmt) cc_final: 0.5609 (mmp) REVERT: P 159 MET cc_start: 0.6240 (mmt) cc_final: 0.5584 (mmm) REVERT: Q 129 GLN cc_start: 0.6587 (tp-100) cc_final: 0.6374 (mm110) REVERT: Q 159 MET cc_start: 0.5593 (mmp) cc_final: 0.5138 (mmm) REVERT: W 159 MET cc_start: 0.7152 (tpp) cc_final: 0.6593 (mmm) REVERT: W 209 ASN cc_start: 0.6193 (OUTLIER) cc_final: 0.5766 (t0) outliers start: 107 outliers final: 80 residues processed: 310 average time/residue: 0.1046 time to fit residues: 48.9863 Evaluate side-chains 312 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 225 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 147 LEU Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 209 ASN Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain O residue 125 GLN Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 125 GLN Chi-restraints excluded: chain S residue 143 THR Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain T residue 220 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 197 LEU Chi-restraints excluded: chain V residue 220 LEU Chi-restraints excluded: chain W residue 136 LEU Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 197 LEU Chi-restraints excluded: chain W residue 209 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 131 optimal weight: 0.8980 chunk 159 optimal weight: 1.9990 chunk 196 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 38 optimal weight: 0.0770 chunk 163 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 150 optimal weight: 0.8980 chunk 16 optimal weight: 0.4980 chunk 114 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 125 GLN K 222 GLN P 209 ASN S 209 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5318 r_free = 0.5318 target = 0.240861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.203728 restraints weight = 16478.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5083 r_free = 0.5083 target = 0.211449 restraints weight = 8898.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.5129 r_free = 0.5129 target = 0.217245 restraints weight = 5621.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5160 r_free = 0.5160 target = 0.221293 restraints weight = 3945.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5180 r_free = 0.5180 target = 0.224019 restraints weight = 2999.304| |-----------------------------------------------------------------------------| r_work (final): 0.5178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5470 moved from start: 0.7018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14762 Z= 0.111 Angle : 0.652 11.547 20152 Z= 0.284 Chirality : 0.041 0.278 2530 Planarity : 0.004 0.033 2640 Dihedral : 4.977 58.438 2124 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 6.57 % Allowed : 19.00 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.35 (0.22), residues: 1958 helix: 2.45 (0.19), residues: 748 sheet: 0.82 (0.29), residues: 440 loop : -0.63 (0.26), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 184 TYR 0.011 0.001 TYR T 132 PHE 0.006 0.001 PHE K 126 HIS 0.004 0.001 HIS R 196 Details of bonding type rmsd covalent geometry : bond 0.00258 (14762) covalent geometry : angle 0.65177 (20152) hydrogen bonds : bond 0.02562 ( 749) hydrogen bonds : angle 4.34566 ( 2247) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 224 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASN cc_start: 0.5972 (OUTLIER) cc_final: 0.4618 (t0) REVERT: E 142 ARG cc_start: 0.8309 (mmp80) cc_final: 0.8056 (mmp80) REVERT: E 159 MET cc_start: 0.7777 (mmm) cc_final: 0.7427 (mmm) REVERT: F 191 ILE cc_start: 0.4791 (OUTLIER) cc_final: 0.4353 (mt) REVERT: G 142 ARG cc_start: 0.8510 (mmp80) cc_final: 0.8208 (mmp80) REVERT: H 140 LEU cc_start: 0.6021 (OUTLIER) cc_final: 0.5776 (tt) REVERT: I 140 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6312 (tt) REVERT: K 140 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7076 (mm) REVERT: K 159 MET cc_start: 0.7110 (mmt) cc_final: 0.6229 (mmp) REVERT: M 131 ASN cc_start: 0.6832 (t0) cc_final: 0.6626 (m-40) REVERT: M 159 MET cc_start: 0.7119 (mmt) cc_final: 0.6277 (mmm) REVERT: N 159 MET cc_start: 0.7568 (mmt) cc_final: 0.6684 (mmm) REVERT: O 159 MET cc_start: 0.7205 (mmt) cc_final: 0.6232 (mmp) REVERT: P 159 MET cc_start: 0.7312 (mmt) cc_final: 0.6477 (mmm) REVERT: P 209 ASN cc_start: 0.6245 (OUTLIER) cc_final: 0.5234 (t0) REVERT: Q 159 MET cc_start: 0.6513 (mmp) cc_final: 0.5886 (mmm) REVERT: R 159 MET cc_start: 0.6420 (mmm) cc_final: 0.6092 (mmm) REVERT: R 209 ASN cc_start: 0.6128 (OUTLIER) cc_final: 0.5460 (m-40) REVERT: W 159 MET cc_start: 0.7505 (tpp) cc_final: 0.7063 (mmm) REVERT: W 209 ASN cc_start: 0.6035 (OUTLIER) cc_final: 0.5531 (t0) outliers start: 104 outliers final: 84 residues processed: 300 average time/residue: 0.1061 time to fit residues: 48.2952 Evaluate side-chains 312 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 220 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain K residue 126 PHE Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 209 ASN Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain R residue 144 ILE Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 209 ASN Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 125 GLN Chi-restraints excluded: chain S residue 143 THR Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain T residue 220 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 197 LEU Chi-restraints excluded: chain V residue 209 ASN Chi-restraints excluded: chain W residue 136 LEU Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 176 VAL Chi-restraints excluded: chain W residue 197 LEU Chi-restraints excluded: chain W residue 209 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 107 optimal weight: 0.9990 chunk 180 optimal weight: 0.0270 chunk 93 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 0.0370 chunk 34 optimal weight: 0.8980 chunk 124 optimal weight: 0.4980 chunk 63 optimal weight: 0.1980 chunk 82 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 209 ASN J 222 GLN P 209 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5720 r_free = 0.5720 target = 0.308588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.5669 r_free = 0.5669 target = 0.298018 restraints weight = 18306.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.5685 r_free = 0.5685 target = 0.300220 restraints weight = 12934.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5697 r_free = 0.5697 target = 0.301771 restraints weight = 9603.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.5711 r_free = 0.5711 target = 0.303003 restraints weight = 7398.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.5721 r_free = 0.5721 target = 0.303826 restraints weight = 5833.261| |-----------------------------------------------------------------------------| r_work (final): 0.5701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5684 moved from start: 0.7166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14762 Z= 0.099 Angle : 0.654 12.076 20152 Z= 0.281 Chirality : 0.041 0.239 2530 Planarity : 0.004 0.031 2640 Dihedral : 4.554 59.646 2120 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 6.25 % Allowed : 19.70 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.59 (0.22), residues: 1958 helix: 2.55 (0.19), residues: 748 sheet: 1.07 (0.29), residues: 440 loop : -0.47 (0.27), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 184 TYR 0.008 0.001 TYR T 132 PHE 0.003 0.000 PHE T 126 HIS 0.003 0.001 HIS P 196 Details of bonding type rmsd covalent geometry : bond 0.00223 (14762) covalent geometry : angle 0.65439 (20152) hydrogen bonds : bond 0.02440 ( 749) hydrogen bonds : angle 4.21013 ( 2247) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 233 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 147 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6401 (tt) REVERT: E 159 MET cc_start: 0.7343 (mmm) cc_final: 0.6921 (mmm) REVERT: F 191 ILE cc_start: 0.5026 (OUTLIER) cc_final: 0.4549 (mt) REVERT: G 142 ARG cc_start: 0.6916 (mmp80) cc_final: 0.6385 (ttp-170) REVERT: H 140 LEU cc_start: 0.6790 (OUTLIER) cc_final: 0.6496 (tt) REVERT: H 191 ILE cc_start: 0.5680 (OUTLIER) cc_final: 0.4990 (mt) REVERT: I 140 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6949 (tt) REVERT: K 140 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7861 (mm) REVERT: K 159 MET cc_start: 0.5984 (mmt) cc_final: 0.5560 (mmp) REVERT: L 140 LEU cc_start: 0.8157 (OUTLIER) cc_final: 0.7820 (mm) REVERT: M 131 ASN cc_start: 0.5835 (t0) cc_final: 0.5542 (m-40) REVERT: M 159 MET cc_start: 0.6390 (mmt) cc_final: 0.5618 (mmm) REVERT: N 159 MET cc_start: 0.6387 (mmt) cc_final: 0.5754 (mmm) REVERT: O 159 MET cc_start: 0.6617 (mmt) cc_final: 0.5554 (mmp) REVERT: P 159 MET cc_start: 0.6255 (mmt) cc_final: 0.5632 (mmm) REVERT: P 209 ASN cc_start: 0.6097 (OUTLIER) cc_final: 0.5481 (t0) REVERT: R 159 MET cc_start: 0.6320 (mmm) cc_final: 0.6044 (mmm) REVERT: R 209 ASN cc_start: 0.6442 (OUTLIER) cc_final: 0.5870 (m-40) REVERT: W 159 MET cc_start: 0.7190 (tpp) cc_final: 0.6769 (mmm) outliers start: 99 outliers final: 75 residues processed: 303 average time/residue: 0.1080 time to fit residues: 49.4492 Evaluate side-chains 307 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 223 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 209 ASN Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 191 ILE Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 209 ASN Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 209 ASN Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 125 GLN Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 209 ASN Chi-restraints excluded: chain W residue 136 LEU Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 197 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 37 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 7 optimal weight: 0.4980 chunk 84 optimal weight: 0.0000 chunk 46 optimal weight: 0.6980 chunk 195 optimal weight: 1.9990 chunk 66 optimal weight: 0.0670 chunk 61 optimal weight: 0.0060 chunk 56 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 185 optimal weight: 0.5980 overall best weight: 0.2338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5708 r_free = 0.5708 target = 0.307450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5651 r_free = 0.5651 target = 0.294681 restraints weight = 18309.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.5670 r_free = 0.5670 target = 0.297581 restraints weight = 12309.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5684 r_free = 0.5684 target = 0.299617 restraints weight = 8777.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.5699 r_free = 0.5699 target = 0.301115 restraints weight = 6547.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5705 r_free = 0.5705 target = 0.302065 restraints weight = 5031.488| |-----------------------------------------------------------------------------| r_work (final): 0.5684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5688 moved from start: 0.7291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 14762 Z= 0.097 Angle : 0.670 12.605 20152 Z= 0.286 Chirality : 0.041 0.214 2530 Planarity : 0.004 0.035 2640 Dihedral : 4.455 59.281 2120 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 5.74 % Allowed : 20.45 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.75 (0.22), residues: 1958 helix: 2.61 (0.19), residues: 748 sheet: 1.25 (0.30), residues: 440 loop : -0.37 (0.27), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 184 TYR 0.015 0.001 TYR S 132 PHE 0.003 0.000 PHE T 126 HIS 0.003 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00225 (14762) covalent geometry : angle 0.67026 (20152) hydrogen bonds : bond 0.02412 ( 749) hydrogen bonds : angle 4.12982 ( 2247) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 233 time to evaluate : 0.623 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 147 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6445 (tt) REVERT: E 159 MET cc_start: 0.7579 (mmm) cc_final: 0.7300 (mmm) REVERT: F 191 ILE cc_start: 0.4913 (OUTLIER) cc_final: 0.4414 (mt) REVERT: H 140 LEU cc_start: 0.6754 (OUTLIER) cc_final: 0.6438 (tt) REVERT: H 191 ILE cc_start: 0.5690 (OUTLIER) cc_final: 0.5013 (mt) REVERT: I 140 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6992 (tt) REVERT: K 140 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7864 (mm) REVERT: K 159 MET cc_start: 0.6060 (mmt) cc_final: 0.5641 (mmp) REVERT: L 140 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7788 (mm) REVERT: M 131 ASN cc_start: 0.5962 (t0) cc_final: 0.5692 (m-40) REVERT: M 159 MET cc_start: 0.6477 (mmt) cc_final: 0.5714 (mmm) REVERT: M 180 LEU cc_start: 0.4905 (OUTLIER) cc_final: 0.4546 (mp) REVERT: N 159 MET cc_start: 0.6491 (mmt) cc_final: 0.5864 (mmm) REVERT: O 159 MET cc_start: 0.6656 (mmt) cc_final: 0.5613 (mmp) REVERT: P 159 MET cc_start: 0.6331 (mmt) cc_final: 0.5742 (mmm) REVERT: R 159 MET cc_start: 0.6475 (mmm) cc_final: 0.6215 (mmm) REVERT: R 209 ASN cc_start: 0.6481 (OUTLIER) cc_final: 0.5869 (m-40) REVERT: W 159 MET cc_start: 0.7205 (tpp) cc_final: 0.6937 (mmm) outliers start: 91 outliers final: 72 residues processed: 299 average time/residue: 0.1125 time to fit residues: 50.8514 Evaluate side-chains 303 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 222 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 191 ILE Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 191 ILE Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 209 ASN Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 125 GLN Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 209 ASN Chi-restraints excluded: chain W residue 136 LEU Chi-restraints excluded: chain W residue 147 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 138 optimal weight: 0.0670 chunk 188 optimal weight: 0.0670 chunk 94 optimal weight: 0.9980 chunk 146 optimal weight: 0.0270 chunk 16 optimal weight: 0.0170 chunk 144 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 59 optimal weight: 0.4980 chunk 124 optimal weight: 0.9980 overall best weight: 0.1352 ------------------------------------------------------------------------------- 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 = 0.5730 r_free = 0.5730 target = 0.310710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.5685 r_free = 0.5685 target = 0.300742 restraints weight = 18253.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.5695 r_free = 0.5695 target = 0.302851 restraints weight = 12778.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.5717 r_free = 0.5717 target = 0.304617 restraints weight = 9349.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.5724 r_free = 0.5724 target = 0.305662 restraints weight = 7089.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.5732 r_free = 0.5732 target = 0.306527 restraints weight = 5559.776| |-----------------------------------------------------------------------------| r_work (final): 0.5737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5617 moved from start: 0.7400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 14762 Z= 0.095 Angle : 0.674 12.435 20152 Z= 0.285 Chirality : 0.041 0.211 2530 Planarity : 0.004 0.048 2640 Dihedral : 4.292 57.271 2120 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 5.18 % Allowed : 20.64 % Favored : 74.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.22), residues: 1958 helix: 2.77 (0.19), residues: 748 sheet: 1.44 (0.30), residues: 440 loop : -0.15 (0.28), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 184 TYR 0.015 0.001 TYR S 132 PHE 0.003 0.000 PHE T 126 HIS 0.002 0.000 HIS W 156 Details of bonding type rmsd covalent geometry : bond 0.00217 (14762) covalent geometry : angle 0.67377 (20152) hydrogen bonds : bond 0.02357 ( 749) hydrogen bonds : angle 3.95764 ( 2247) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 235 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 147 LEU cc_start: 0.6858 (OUTLIER) cc_final: 0.6547 (tt) REVERT: E 159 MET cc_start: 0.7521 (mmm) cc_final: 0.7259 (mmm) REVERT: F 191 ILE cc_start: 0.4816 (OUTLIER) cc_final: 0.4355 (mt) REVERT: H 140 LEU cc_start: 0.6627 (OUTLIER) cc_final: 0.6354 (tt) REVERT: H 159 MET cc_start: 0.6736 (mmm) cc_final: 0.5530 (mmm) REVERT: H 191 ILE cc_start: 0.5594 (OUTLIER) cc_final: 0.4921 (mt) REVERT: K 140 LEU cc_start: 0.7836 (OUTLIER) cc_final: 0.7574 (mm) REVERT: K 159 MET cc_start: 0.6101 (mmt) cc_final: 0.5752 (mmp) REVERT: L 140 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7728 (mm) REVERT: L 142 ARG cc_start: 0.6637 (mmp80) cc_final: 0.6309 (mmp80) REVERT: M 131 ASN cc_start: 0.5838 (t0) cc_final: 0.5540 (m-40) REVERT: M 159 MET cc_start: 0.6356 (mmt) cc_final: 0.5634 (mmm) REVERT: M 180 LEU cc_start: 0.4839 (OUTLIER) cc_final: 0.4522 (mp) REVERT: N 159 MET cc_start: 0.6343 (mmt) cc_final: 0.5462 (mmp) REVERT: O 159 MET cc_start: 0.6558 (mmt) cc_final: 0.5544 (mmp) REVERT: P 159 MET cc_start: 0.6204 (mmt) cc_final: 0.5640 (mmm) REVERT: R 159 MET cc_start: 0.7038 (mmm) cc_final: 0.6653 (mmm) REVERT: R 209 ASN cc_start: 0.6536 (OUTLIER) cc_final: 0.5877 (m-40) REVERT: V 209 ASN cc_start: 0.6360 (OUTLIER) cc_final: 0.5752 (t0) outliers start: 82 outliers final: 67 residues processed: 293 average time/residue: 0.0946 time to fit residues: 43.7827 Evaluate side-chains 297 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 221 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain E residue 220 LEU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 191 ILE Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 191 ILE Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 191 ILE Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 220 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain L residue 126 PHE Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 202 VAL Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 147 LEU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 176 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 209 ASN Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 125 GLN Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 209 ASN Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 155 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 37 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 190 optimal weight: 1.9990 chunk 79 optimal weight: 0.0170 chunk 131 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 chunk 197 optimal weight: 0.0980 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5736 r_free = 0.5736 target = 0.311316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5687 r_free = 0.5687 target = 0.300291 restraints weight = 18097.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5706 r_free = 0.5706 target = 0.302791 restraints weight = 12480.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.5721 r_free = 0.5721 target = 0.304544 restraints weight = 9063.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.5727 r_free = 0.5727 target = 0.305664 restraints weight = 6851.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.5738 r_free = 0.5738 target = 0.306672 restraints weight = 5360.733| |-----------------------------------------------------------------------------| r_work (final): 0.5717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5655 moved from start: 0.7528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14762 Z= 0.099 Angle : 0.676 12.194 20152 Z= 0.286 Chirality : 0.041 0.230 2530 Planarity : 0.004 0.037 2640 Dihedral : 4.299 56.245 2120 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 5.05 % Allowed : 21.09 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.22), residues: 1958 helix: 2.70 (0.19), residues: 748 sheet: 1.45 (0.30), residues: 440 loop : -0.20 (0.28), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG N 184 TYR 0.015 0.001 TYR S 132 PHE 0.003 0.000 PHE F 126 HIS 0.004 0.001 HIS C 196 Details of bonding type rmsd covalent geometry : bond 0.00232 (14762) covalent geometry : angle 0.67562 (20152) hydrogen bonds : bond 0.02277 ( 749) hydrogen bonds : angle 4.01381 ( 2247) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2365.31 seconds wall clock time: 41 minutes 47.56 seconds (2507.56 seconds total)