Starting phenix.real_space_refine on Fri May 16 13:43:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fte_29424/05_2025/8fte_29424.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fte_29424/05_2025/8fte_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8fte_29424/05_2025/8fte_29424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fte_29424/05_2025/8fte_29424.map" model { file = "/net/cci-nas-00/data/ceres_data/8fte_29424/05_2025/8fte_29424.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fte_29424/05_2025/8fte_29424.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 1} 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: {'GLN:plan1': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 8.82, per 1000 atoms: 0.61 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: 3.22 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.42 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: 3.74 Time building geometry restraints manager: 3.81 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'T' selection = chain 'W' selection = chain 'V' } 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: 5.090 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 31.680 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.680 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 HIS 0.002 0.001 HIS C 196 PHE 0.001 0.001 PHE K 126 TYR 0.004 0.001 TYR C 132 ARG 0.001 0.000 ARG H 184 Details of bonding type rmsd hydrogen bonds : bond 0.17722 ( 749) hydrogen bonds : angle 7.28947 ( 2247) covalent geometry : bond 0.00279 (14762) covalent geometry : angle 0.62702 (20152) *********************** 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 : 1.691 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: 0.7176 (m) REVERT: D 160 PRO cc_start: 0.5619 (Cg_exo) cc_final: 0.5317 (Cg_endo) REVERT: F 220 LEU cc_start: 0.7565 (mt) cc_final: 0.5267 (tt) REVERT: I 220 LEU cc_start: 0.6616 (mt) cc_final: 0.6401 (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: 0.5476 (mmm) REVERT: N 159 MET cc_start: 0.6330 (mmt) cc_final: 0.5560 (mmm) REVERT: O 159 MET cc_start: 0.5642 (mmt) cc_final: 0.5000 (mmp) REVERT: P 159 MET cc_start: 0.4903 (mmt) cc_final: 0.4684 (mmm) REVERT: Q 147 LEU cc_start: 0.6749 (OUTLIER) cc_final: 0.6379 (tm) REVERT: T 129 GLN cc_start: 0.5664 (mm-40) cc_final: 0.4997 (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: 0.2930 time to fit residues: 188.9233 Evaluate side-chains 254 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 232 time to evaluate : 1.644 ------------------------------------------------------------------------------- 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 167 optimal weight: 1.9990 chunk 150 optimal weight: 0.6980 chunk 83 optimal weight: 0.3980 chunk 51 optimal weight: 2.9990 chunk 101 optimal weight: 0.0470 chunk 80 optimal weight: 0.0020 chunk 155 optimal weight: 3.9990 chunk 60 optimal weight: 0.6980 chunk 94 optimal weight: 0.0040 chunk 115 optimal weight: 2.9990 chunk 179 optimal weight: 0.0370 overall best weight: 0.0976 ------------------------------------------------------------------------------- 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 156 HIS W 222 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5405 r_free = 0.5405 target = 0.253053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.5133 r_free = 0.5133 target = 0.216889 restraints weight = 16060.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5198 r_free = 0.5198 target = 0.225387 restraints weight = 8570.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5243 r_free = 0.5243 target = 0.231456 restraints weight = 5336.478| |-----------------------------------------------------------------------------| r_work (final): 0.5266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5080 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14762 Z= 0.115 Angle : 0.617 10.113 20152 Z= 0.282 Chirality : 0.041 0.134 2530 Planarity : 0.005 0.047 2640 Dihedral : 6.129 56.781 2156 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 6.76 % Allowed : 13.26 % Favored : 79.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.21), residues: 1958 helix: 2.40 (0.19), residues: 770 sheet: -0.21 (0.28), residues: 440 loop : -0.66 (0.25), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS T 156 PHE 0.019 0.001 PHE V 126 TYR 0.005 0.001 TYR B 132 ARG 0.015 0.001 ARG N 154 Details of bonding type rmsd hydrogen bonds : bond 0.02768 ( 749) hydrogen bonds : angle 5.16595 ( 2247) covalent geometry : bond 0.00248 (14762) covalent geometry : angle 0.61650 (20152) *********************** 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 397 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 290 time to evaluate : 1.727 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: C 212 LEU cc_start: 0.5302 (OUTLIER) cc_final: 0.5026 (tp) REVERT: C 220 LEU cc_start: 0.7220 (mt) cc_final: 0.5455 (tt) REVERT: D 220 LEU cc_start: 0.7175 (mt) cc_final: 0.4946 (tt) REVERT: E 180 LEU cc_start: 0.2929 (tp) cc_final: 0.2725 (mp) REVERT: F 220 LEU cc_start: 0.7470 (mt) cc_final: 0.5271 (tt) REVERT: J 142 ARG cc_start: 0.8557 (mmp80) cc_final: 0.8346 (mmp80) REVERT: J 177 THR cc_start: 0.6806 (p) cc_final: 0.6462 (p) REVERT: K 142 ARG cc_start: 0.8328 (mmp80) cc_final: 0.6933 (ttp80) REVERT: K 159 MET cc_start: 0.6433 (mmt) cc_final: 0.5591 (mmp) REVERT: M 159 MET cc_start: 0.6459 (mmt) cc_final: 0.5736 (mmm) REVERT: N 142 ARG cc_start: 0.7804 (tpp-160) cc_final: 0.7497 (tpp-160) REVERT: N 150 VAL cc_start: 0.5155 (OUTLIER) cc_final: 0.4860 (m) REVERT: N 159 MET cc_start: 0.6628 (mmt) cc_final: 0.5848 (mmm) REVERT: O 159 MET cc_start: 0.6193 (mmt) cc_final: 0.5773 (mmm) REVERT: O 180 LEU cc_start: 0.5186 (tp) cc_final: 0.4840 (mp) REVERT: O 181 GLU cc_start: 0.3916 (mt-10) cc_final: 0.3714 (mt-10) REVERT: O 184 ARG cc_start: 0.4154 (mmm160) cc_final: 0.3951 (mmm160) REVERT: P 159 MET cc_start: 0.5438 (mmt) cc_final: 0.5027 (mmm) REVERT: P 180 LEU cc_start: 0.4899 (tp) cc_final: 0.4587 (mp) REVERT: R 147 LEU cc_start: 0.7144 (OUTLIER) cc_final: 0.6868 (tm) REVERT: V 147 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7177 (tm) outliers start: 107 outliers final: 50 residues processed: 359 average time/residue: 0.2903 time to fit residues: 150.6833 Evaluate side-chains 294 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 240 time to evaluate : 1.593 ------------------------------------------------------------------------------- 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 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 C residue 212 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 136 LEU Chi-restraints excluded: chain P residue 146 THR Chi-restraints excluded: chain P 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 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 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 181 optimal weight: 0.4980 chunk 73 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 146 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 0.0370 chunk 110 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 131 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 0.6060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS G 209 ASN H 156 HIS H 209 ASN I 156 HIS J 156 HIS J 209 ASN K 125 GLN K 209 ASN L 156 HIS L 209 ASN M 156 HIS M 209 ASN N 156 HIS N 196 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5353 r_free = 0.5353 target = 0.246763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.5072 r_free = 0.5072 target = 0.210717 restraints weight = 16517.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5136 r_free = 0.5136 target = 0.218701 restraints weight = 9130.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5180 r_free = 0.5180 target = 0.224485 restraints weight = 5802.287| |-----------------------------------------------------------------------------| r_work (final): 0.5184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5382 moved from start: 0.4690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14762 Z= 0.137 Angle : 0.643 10.789 20152 Z= 0.298 Chirality : 0.041 0.148 2530 Planarity : 0.004 0.039 2640 Dihedral : 5.776 53.007 2138 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 6.69 % Allowed : 14.58 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.21), residues: 1958 helix: 2.40 (0.19), residues: 748 sheet: -0.33 (0.27), residues: 440 loop : -0.67 (0.26), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS A 196 PHE 0.010 0.001 PHE T 126 TYR 0.011 0.001 TYR B 132 ARG 0.007 0.001 ARG L 184 Details of bonding type rmsd hydrogen bonds : bond 0.02827 ( 749) hydrogen bonds : angle 4.79009 ( 2247) covalent geometry : bond 0.00306 (14762) covalent geometry : angle 0.64297 (20152) *********************** 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 366 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 260 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7527 (tpp-160) cc_final: 0.7277 (mmp80) REVERT: A 147 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7408 (tm) REVERT: B 160 PRO cc_start: 0.6055 (Cg_endo) cc_final: 0.5409 (Cg_exo) REVERT: C 147 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7238 (tt) REVERT: C 209 ASN cc_start: 0.5097 (OUTLIER) cc_final: 0.4580 (t0) REVERT: E 209 ASN cc_start: 0.5549 (OUTLIER) cc_final: 0.5142 (t0) REVERT: F 209 ASN cc_start: 0.5525 (m-40) cc_final: 0.4963 (t0) REVERT: H 220 LEU cc_start: 0.7109 (mt) cc_final: 0.6789 (mt) REVERT: J 142 ARG cc_start: 0.8623 (mmp80) cc_final: 0.8357 (mmp80) REVERT: J 209 ASN cc_start: 0.5370 (OUTLIER) cc_final: 0.5093 (t0) REVERT: K 142 ARG cc_start: 0.8361 (mmp80) cc_final: 0.6937 (ttp80) REVERT: K 209 ASN cc_start: 0.5126 (OUTLIER) cc_final: 0.4617 (t0) REVERT: K 222 GLN cc_start: 0.8086 (mp10) cc_final: 0.7731 (mp10) REVERT: M 159 MET cc_start: 0.6851 (mmt) cc_final: 0.5950 (mmm) REVERT: N 159 MET cc_start: 0.6965 (mmt) cc_final: 0.5814 (mmp) REVERT: O 159 MET cc_start: 0.6731 (mmt) cc_final: 0.5729 (mmp) REVERT: O 180 LEU cc_start: 0.5555 (tp) cc_final: 0.4969 (mp) REVERT: O 184 ARG cc_start: 0.4181 (mmm160) cc_final: 0.3906 (mmm160) REVERT: P 129 GLN cc_start: 0.6400 (tm-30) cc_final: 0.6143 (tm-30) REVERT: P 142 ARG cc_start: 0.7687 (tpp-160) cc_final: 0.7366 (tpp80) REVERT: P 159 MET cc_start: 0.6166 (mmt) cc_final: 0.5449 (mmm) REVERT: Q 180 LEU cc_start: 0.5705 (tp) cc_final: 0.5123 (mp) REVERT: R 181 GLU cc_start: 0.5214 (tp30) cc_final: 0.4623 (mt-10) REVERT: S 147 LEU cc_start: 0.7531 (OUTLIER) cc_final: 0.7303 (tm) REVERT: S 154 ARG cc_start: 0.5717 (mpp-170) cc_final: 0.4940 (mpp-170) REVERT: S 159 MET cc_start: 0.6773 (mmm) cc_final: 0.6344 (mmp) REVERT: S 181 GLU cc_start: 0.5291 (tp30) cc_final: 0.4705 (mt-10) REVERT: T 147 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7287 (tm) REVERT: T 159 MET cc_start: 0.6394 (tpp) cc_final: 0.6056 (mmm) REVERT: V 128 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6350 (tm-30) REVERT: V 147 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7156 (tm) REVERT: V 159 MET cc_start: 0.7493 (tpp) cc_final: 0.5345 (mtt) outliers start: 106 outliers final: 59 residues processed: 330 average time/residue: 0.2499 time to fit residues: 120.0952 Evaluate side-chains 297 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 228 time to evaluate : 1.502 ------------------------------------------------------------------------------- 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 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 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 C residue 209 ASN Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 213 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 209 ASN 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 G 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 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 197 LEU 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 209 ASN Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 197 LEU 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 M residue 140 LEU Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain Q residue 143 THR 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 155 VAL Chi-restraints excluded: chain V residue 128 GLU Chi-restraints excluded: chain V residue 147 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 177 THR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 187 optimal weight: 0.5980 chunk 188 optimal weight: 0.9990 chunk 193 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 182 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 0.2980 chunk 161 optimal weight: 0.9980 chunk 110 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN E 209 ASN F 209 ASN I 209 ASN J 125 GLN J 209 ASN K 209 ASN N 209 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5714 r_free = 0.5714 target = 0.307391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.5657 r_free = 0.5657 target = 0.296188 restraints weight = 18268.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5666 r_free = 0.5666 target = 0.298019 restraints weight = 13210.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.5691 r_free = 0.5691 target = 0.299974 restraints weight = 10178.629| |-----------------------------------------------------------------------------| r_work (final): 0.5679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5639 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14762 Z= 0.145 Angle : 0.639 10.697 20152 Z= 0.296 Chirality : 0.042 0.231 2530 Planarity : 0.004 0.048 2640 Dihedral : 5.656 52.222 2134 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 7.26 % Allowed : 15.72 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.21), residues: 1958 helix: 2.27 (0.19), residues: 748 sheet: -0.19 (0.27), residues: 440 loop : -0.72 (0.26), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS P 196 PHE 0.011 0.001 PHE K 126 TYR 0.011 0.001 TYR B 132 ARG 0.008 0.001 ARG R 184 Details of bonding type rmsd hydrogen bonds : bond 0.02760 ( 749) hydrogen bonds : angle 4.64665 ( 2247) covalent geometry : bond 0.00322 (14762) covalent geometry : angle 0.63917 (20152) *********************** 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 356 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 241 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.7441 (OUTLIER) cc_final: 0.7003 (tm) REVERT: A 209 ASN cc_start: 0.6586 (OUTLIER) cc_final: 0.5488 (t0) REVERT: B 209 ASN cc_start: 0.6036 (OUTLIER) cc_final: 0.5529 (t0) REVERT: C 147 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6423 (tt) REVERT: C 209 ASN cc_start: 0.6137 (OUTLIER) cc_final: 0.5932 (t0) REVERT: C 212 LEU cc_start: 0.4660 (OUTLIER) cc_final: 0.4233 (tp) REVERT: E 131 ASN cc_start: 0.6573 (m-40) cc_final: 0.6359 (m-40) REVERT: F 209 ASN cc_start: 0.6117 (OUTLIER) cc_final: 0.5778 (t0) REVERT: H 140 LEU cc_start: 0.7209 (OUTLIER) cc_final: 0.6846 (tt) REVERT: H 209 ASN cc_start: 0.5801 (OUTLIER) cc_final: 0.5562 (t0) REVERT: I 140 LEU cc_start: 0.7375 (OUTLIER) cc_final: 0.7081 (tt) REVERT: J 154 ARG cc_start: 0.6360 (mtm-85) cc_final: 0.5788 (mtm-85) REVERT: K 142 ARG cc_start: 0.6600 (mmp80) cc_final: 0.6146 (ttp80) REVERT: L 209 ASN cc_start: 0.4875 (OUTLIER) cc_final: 0.4673 (t0) REVERT: N 159 MET cc_start: 0.6029 (mmt) cc_final: 0.5351 (mmm) REVERT: O 144 ILE cc_start: 0.6193 (OUTLIER) cc_final: 0.4927 (mt) REVERT: O 159 MET cc_start: 0.6472 (mmt) cc_final: 0.5852 (mmp) REVERT: P 159 MET cc_start: 0.5954 (mmt) cc_final: 0.5298 (mmm) REVERT: Q 180 LEU cc_start: 0.6372 (tp) cc_final: 0.5882 (mp) REVERT: R 159 MET cc_start: 0.7005 (mmm) cc_final: 0.6494 (mmm) REVERT: S 132 TYR cc_start: 0.4426 (t80) cc_final: 0.4196 (t80) REVERT: S 159 MET cc_start: 0.6565 (mmm) cc_final: 0.6337 (mmp) REVERT: T 159 MET cc_start: 0.6834 (tpp) cc_final: 0.6362 (mmm) REVERT: V 147 LEU cc_start: 0.7140 (OUTLIER) cc_final: 0.6800 (tm) outliers start: 115 outliers final: 78 residues processed: 323 average time/residue: 0.2311 time to fit residues: 111.4078 Evaluate side-chains 310 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 219 time to evaluate : 1.556 ------------------------------------------------------------------------------- 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 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 B residue 209 ASN 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 C residue 209 ASN Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 202 VAL Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 213 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 202 VAL 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 147 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 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 176 VAL Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 143 THR 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 209 ASN 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 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 144 ILE 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 P residue 147 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 180 LEU Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 147 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 143 THR 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 158 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 chunk 194 optimal weight: 0.0060 chunk 165 optimal weight: 0.9980 chunk 80 optimal weight: 0.9980 chunk 187 optimal weight: 0.0020 chunk 171 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 157 optimal weight: 0.6980 chunk 59 optimal weight: 0.9990 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 125 GLN J 222 GLN K 125 GLN O 209 ASN S 209 ASN T 209 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5726 r_free = 0.5726 target = 0.309388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.5671 r_free = 0.5671 target = 0.298347 restraints weight = 18414.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.5689 r_free = 0.5689 target = 0.300558 restraints weight = 13109.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.5702 r_free = 0.5702 target = 0.302168 restraints weight = 9917.377| |-----------------------------------------------------------------------------| r_work (final): 0.5692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5639 moved from start: 0.5986 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= 0.108 Angle : 0.619 11.688 20152 Z= 0.277 Chirality : 0.041 0.246 2530 Planarity : 0.004 0.060 2640 Dihedral : 5.378 53.432 2132 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 6.76 % Allowed : 17.36 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.21), residues: 1958 helix: 2.45 (0.19), residues: 748 sheet: 0.23 (0.28), residues: 440 loop : -0.55 (0.27), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS R 196 PHE 0.003 0.001 PHE T 126 TYR 0.009 0.001 TYR B 132 ARG 0.017 0.000 ARG O 184 Details of bonding type rmsd hydrogen bonds : bond 0.02557 ( 749) hydrogen bonds : angle 4.42341 ( 2247) covalent geometry : bond 0.00249 (14762) covalent geometry : angle 0.61936 (20152) *********************** 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 346 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 239 time to evaluate : 2.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.6982 (tm) REVERT: A 209 ASN cc_start: 0.6541 (OUTLIER) cc_final: 0.5528 (t0) REVERT: C 147 LEU cc_start: 0.6724 (OUTLIER) cc_final: 0.6441 (tt) REVERT: D 159 MET cc_start: 0.7338 (tpp) cc_final: 0.6479 (mmm) REVERT: D 209 ASN cc_start: 0.5864 (OUTLIER) cc_final: 0.5169 (t0) REVERT: E 131 ASN cc_start: 0.6553 (m-40) cc_final: 0.6326 (m-40) REVERT: F 209 ASN cc_start: 0.6520 (OUTLIER) cc_final: 0.5802 (t0) REVERT: H 140 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.7005 (tt) REVERT: I 140 LEU cc_start: 0.7319 (OUTLIER) cc_final: 0.7008 (tt) REVERT: K 142 ARG cc_start: 0.6444 (mmp80) cc_final: 0.6036 (ttp80) REVERT: K 159 MET cc_start: 0.6094 (mmt) cc_final: 0.5251 (mmp) REVERT: N 159 MET cc_start: 0.6103 (mmt) cc_final: 0.5421 (mmm) REVERT: O 136 LEU cc_start: 0.7783 (OUTLIER) cc_final: 0.7507 (tp) REVERT: O 159 MET cc_start: 0.6510 (mmt) cc_final: 0.5434 (mmp) REVERT: P 159 MET cc_start: 0.5983 (mmt) cc_final: 0.5399 (mmm) REVERT: P 209 ASN cc_start: 0.6559 (OUTLIER) cc_final: 0.6304 (t0) REVERT: R 159 MET cc_start: 0.7245 (mmm) cc_final: 0.6901 (mmm) REVERT: S 132 TYR cc_start: 0.4330 (t80) cc_final: 0.4074 (t80) REVERT: T 159 MET cc_start: 0.7079 (tpp) cc_final: 0.6736 (mmm) REVERT: V 147 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6858 (tm) REVERT: W 209 ASN cc_start: 0.6195 (OUTLIER) cc_final: 0.5695 (t0) outliers start: 107 outliers final: 71 residues processed: 313 average time/residue: 0.2262 time to fit residues: 108.8791 Evaluate side-chains 308 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 226 time to evaluate : 1.607 ------------------------------------------------------------------------------- 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 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 C residue 147 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 213 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 202 VAL 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 147 LEU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 197 LEU 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 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 143 THR 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 176 VAL Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 176 VAL 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 143 THR Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain O residue 136 LEU 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 155 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 P residue 209 ASN Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain R residue 147 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 143 THR 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 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 209 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 108 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 141 optimal weight: 0.6980 chunk 134 optimal weight: 0.7980 chunk 149 optimal weight: 2.9990 chunk 184 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 80 optimal weight: 0.0070 chunk 92 optimal weight: 0.9980 chunk 44 optimal weight: 0.0470 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 125 GLN L 222 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5728 r_free = 0.5728 target = 0.309518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.5672 r_free = 0.5672 target = 0.298639 restraints weight = 18544.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.5692 r_free = 0.5692 target = 0.300942 restraints weight = 13171.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.5707 r_free = 0.5707 target = 0.302559 restraints weight = 9843.249| |-----------------------------------------------------------------------------| r_work (final): 0.5695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5667 moved from start: 0.6494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 14762 Z= 0.103 Angle : 0.614 11.358 20152 Z= 0.274 Chirality : 0.041 0.224 2530 Planarity : 0.004 0.024 2640 Dihedral : 5.068 51.241 2128 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 7.26 % Allowed : 17.68 % Favored : 75.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.22), residues: 1958 helix: 2.27 (0.19), residues: 770 sheet: 0.68 (0.29), residues: 440 loop : -0.22 (0.27), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS R 196 PHE 0.004 0.001 PHE Q 126 TYR 0.007 0.001 TYR B 132 ARG 0.006 0.000 ARG N 184 Details of bonding type rmsd hydrogen bonds : bond 0.02489 ( 749) hydrogen bonds : angle 4.27039 ( 2247) covalent geometry : bond 0.00237 (14762) covalent geometry : angle 0.61411 (20152) *********************** 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 354 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 239 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.7497 (OUTLIER) cc_final: 0.7206 (tm) REVERT: A 209 ASN cc_start: 0.6540 (OUTLIER) cc_final: 0.5562 (t0) REVERT: D 159 MET cc_start: 0.7310 (tpp) cc_final: 0.6805 (mmm) REVERT: D 209 ASN cc_start: 0.5903 (OUTLIER) cc_final: 0.5442 (t0) REVERT: E 191 ILE cc_start: 0.4438 (OUTLIER) cc_final: 0.4163 (tt) REVERT: F 209 ASN cc_start: 0.6589 (m-40) cc_final: 0.5870 (t0) REVERT: G 176 VAL cc_start: 0.7597 (OUTLIER) cc_final: 0.7385 (p) REVERT: H 140 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7000 (tt) REVERT: I 140 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.7030 (tt) REVERT: K 140 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7684 (mm) REVERT: K 159 MET cc_start: 0.6165 (mmt) cc_final: 0.5442 (mmp) REVERT: M 159 MET cc_start: 0.6628 (OUTLIER) cc_final: 0.5554 (mmm) REVERT: N 159 MET cc_start: 0.6360 (mmt) cc_final: 0.5645 (mmm) REVERT: O 159 MET cc_start: 0.6650 (mmt) cc_final: 0.5963 (mmm) REVERT: P 159 MET cc_start: 0.6132 (mmt) cc_final: 0.5471 (mmm) REVERT: Q 129 GLN cc_start: 0.6602 (tp-100) cc_final: 0.6370 (mm110) REVERT: R 159 MET cc_start: 0.7269 (mmm) cc_final: 0.6949 (mmm) REVERT: R 209 ASN cc_start: 0.6164 (OUTLIER) cc_final: 0.5578 (m-40) REVERT: S 132 TYR cc_start: 0.4431 (t80) cc_final: 0.4179 (t80) REVERT: T 159 MET cc_start: 0.7239 (tpp) cc_final: 0.6922 (mmm) REVERT: V 147 LEU cc_start: 0.7071 (OUTLIER) cc_final: 0.6813 (tm) REVERT: W 159 MET cc_start: 0.6828 (tpp) cc_final: 0.6383 (mmm) outliers start: 115 outliers final: 80 residues processed: 319 average time/residue: 0.2461 time to fit residues: 119.6441 Evaluate side-chains 310 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 219 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 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 C residue 212 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 202 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 G residue 140 LEU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain H residue 140 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 140 LEU Chi-restraints excluded: chain I residue 143 THR 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 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 143 THR Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 159 MET Chi-restraints excluded: chain M residue 176 VAL 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 144 ILE 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 Q residue 140 LEU Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q residue 155 VAL 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 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 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 155 VAL 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 209 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 27 optimal weight: 0.7980 chunk 110 optimal weight: 0.5980 chunk 64 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 65 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 125 GLN F 209 ASN K 222 GLN L 222 GLN Q 209 ASN R 209 ASN T 196 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5707 r_free = 0.5707 target = 0.305394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.5655 r_free = 0.5655 target = 0.294905 restraints weight = 18392.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.5670 r_free = 0.5670 target = 0.296918 restraints weight = 13245.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5687 r_free = 0.5687 target = 0.298473 restraints weight = 10034.562| |-----------------------------------------------------------------------------| r_work (final): 0.5328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5740 moved from start: 0.7065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14762 Z= 0.117 Angle : 0.652 11.889 20152 Z= 0.289 Chirality : 0.041 0.247 2530 Planarity : 0.004 0.039 2640 Dihedral : 5.288 54.804 2128 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 6.88 % Allowed : 18.56 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.22), residues: 1958 helix: 2.34 (0.19), residues: 748 sheet: 0.82 (0.29), residues: 440 loop : -0.53 (0.27), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS P 196 PHE 0.010 0.001 PHE D 126 TYR 0.012 0.001 TYR V 132 ARG 0.010 0.000 ARG M 184 Details of bonding type rmsd hydrogen bonds : bond 0.02665 ( 749) hydrogen bonds : angle 4.39458 ( 2247) covalent geometry : bond 0.00270 (14762) covalent geometry : angle 0.65172 (20152) *********************** 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 344 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 235 time to evaluate : 1.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASN cc_start: 0.6728 (OUTLIER) cc_final: 0.5277 (t0) REVERT: B 159 MET cc_start: 0.6663 (mmm) cc_final: 0.6421 (mmm) REVERT: B 209 ASN cc_start: 0.6019 (OUTLIER) cc_final: 0.5498 (t0) REVERT: E 159 MET cc_start: 0.7904 (mmm) cc_final: 0.7346 (mmm) REVERT: F 159 MET cc_start: 0.8011 (mmm) cc_final: 0.7780 (mmm) REVERT: F 209 ASN cc_start: 0.6414 (m110) cc_final: 0.5656 (t0) REVERT: H 140 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.6365 (tt) REVERT: I 140 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.7031 (tt) REVERT: K 140 LEU cc_start: 0.8234 (OUTLIER) cc_final: 0.7751 (mm) REVERT: K 159 MET cc_start: 0.6591 (mmt) cc_final: 0.5815 (mmp) REVERT: L 209 ASN cc_start: 0.6132 (OUTLIER) cc_final: 0.5765 (t0) REVERT: M 131 ASN cc_start: 0.6648 (t0) cc_final: 0.6334 (m-40) REVERT: N 159 MET cc_start: 0.7125 (mmt) cc_final: 0.6269 (mmm) REVERT: O 159 MET cc_start: 0.7043 (mmt) cc_final: 0.6362 (mmm) REVERT: P 159 MET cc_start: 0.6927 (mmt) cc_final: 0.6158 (mmm) REVERT: R 159 MET cc_start: 0.7586 (mmm) cc_final: 0.7181 (mmm) REVERT: S 132 TYR cc_start: 0.4943 (t80) cc_final: 0.4719 (t80) REVERT: S 159 MET cc_start: 0.6010 (mmm) cc_final: 0.5625 (mmm) REVERT: W 159 MET cc_start: 0.7535 (tpp) cc_final: 0.7289 (mmm) outliers start: 109 outliers final: 81 residues processed: 317 average time/residue: 0.2284 time to fit residues: 108.9839 Evaluate side-chains 307 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 220 time to evaluate : 1.485 ------------------------------------------------------------------------------- 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 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 209 ASN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 213 VAL 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 F residue 142 ARG Chi-restraints excluded: chain F residue 175 SER 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 176 VAL Chi-restraints excluded: chain G residue 213 VAL 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 197 LEU 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 209 ASN 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 159 MET 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 144 ILE 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 Q residue 140 LEU Chi-restraints excluded: chain Q residue 144 ILE Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain R residue 143 THR 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 197 LEU Chi-restraints excluded: chain R residue 220 LEU 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 W residue 155 VAL Chi-restraints excluded: chain W residue 197 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 56 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 2 optimal weight: 0.0010 chunk 157 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 171 optimal weight: 0.5980 chunk 147 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 152 optimal weight: 0.0030 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 196 HIS V 209 ASN W 156 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5710 r_free = 0.5710 target = 0.306819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.5656 r_free = 0.5656 target = 0.295988 restraints weight = 18324.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.5675 r_free = 0.5675 target = 0.298239 restraints weight = 13112.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.5690 r_free = 0.5690 target = 0.299829 restraints weight = 9843.632| |-----------------------------------------------------------------------------| r_work (final): 0.5337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5734 moved from start: 0.7313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14762 Z= 0.107 Angle : 0.670 12.489 20152 Z= 0.291 Chirality : 0.042 0.246 2530 Planarity : 0.004 0.057 2640 Dihedral : 4.885 50.622 2124 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 6.31 % Allowed : 19.38 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.22), residues: 1958 helix: 2.41 (0.19), residues: 748 sheet: 1.08 (0.29), residues: 440 loop : -0.38 (0.27), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS W 156 PHE 0.004 0.001 PHE Q 126 TYR 0.007 0.001 TYR V 132 ARG 0.007 0.000 ARG M 184 Details of bonding type rmsd hydrogen bonds : bond 0.02535 ( 749) hydrogen bonds : angle 4.26880 ( 2247) covalent geometry : bond 0.00246 (14762) covalent geometry : angle 0.67006 (20152) *********************** 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 331 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 231 time to evaluate : 1.519 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASN cc_start: 0.6705 (OUTLIER) cc_final: 0.5392 (t0) REVERT: B 159 MET cc_start: 0.6841 (mmm) cc_final: 0.6640 (mmm) REVERT: B 209 ASN cc_start: 0.6004 (OUTLIER) cc_final: 0.5585 (t0) REVERT: E 159 MET cc_start: 0.8065 (mmm) cc_final: 0.7612 (mmm) REVERT: F 191 ILE cc_start: 0.5813 (OUTLIER) cc_final: 0.5360 (mt) REVERT: F 209 ASN cc_start: 0.5936 (m110) cc_final: 0.5278 (t0) REVERT: H 140 LEU cc_start: 0.6703 (OUTLIER) cc_final: 0.6423 (tt) REVERT: I 140 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7196 (tt) REVERT: K 140 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7779 (mm) REVERT: K 159 MET cc_start: 0.6576 (mmt) cc_final: 0.5873 (mmp) REVERT: L 209 ASN cc_start: 0.6231 (OUTLIER) cc_final: 0.5949 (t0) REVERT: M 131 ASN cc_start: 0.6666 (t0) cc_final: 0.6344 (m-40) REVERT: M 159 MET cc_start: 0.7108 (OUTLIER) cc_final: 0.5878 (mmm) REVERT: N 159 MET cc_start: 0.7123 (mmt) cc_final: 0.6309 (mmm) REVERT: O 159 MET cc_start: 0.7048 (mmt) cc_final: 0.5958 (mmp) REVERT: P 159 MET cc_start: 0.6930 (mmt) cc_final: 0.6176 (mmm) REVERT: Q 129 GLN cc_start: 0.6818 (tp-100) cc_final: 0.6204 (tm-30) REVERT: R 159 MET cc_start: 0.7586 (mmm) cc_final: 0.7193 (mmm) REVERT: W 159 MET cc_start: 0.7417 (tpp) cc_final: 0.7183 (mmm) outliers start: 100 outliers final: 77 residues processed: 307 average time/residue: 0.2269 time to fit residues: 105.5153 Evaluate side-chains 304 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 219 time to evaluate : 1.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 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 B residue 209 ASN Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 213 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 E residue 202 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 191 ILE 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 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 J residue 197 LEU Chi-restraints excluded: chain J residue 220 LEU 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 126 PHE 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 209 ASN 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 159 MET 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 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 Q residue 140 LEU Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain R residue 143 THR 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 197 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 143 THR 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 209 ASN Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 155 VAL 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 61 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 25 optimal weight: 0.0870 chunk 189 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 16 optimal weight: 0.0670 chunk 178 optimal weight: 0.0770 chunk 38 optimal weight: 2.9990 overall best weight: 0.3654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 125 GLN V 209 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5720 r_free = 0.5720 target = 0.308061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5670 r_free = 0.5670 target = 0.297577 restraints weight = 18205.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5684 r_free = 0.5684 target = 0.299646 restraints weight = 12882.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.5702 r_free = 0.5702 target = 0.301275 restraints weight = 9655.456| |-----------------------------------------------------------------------------| r_work (final): 0.5689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5734 moved from start: 0.7485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14762 Z= 0.102 Angle : 0.675 12.490 20152 Z= 0.292 Chirality : 0.041 0.281 2530 Planarity : 0.004 0.036 2640 Dihedral : 4.526 51.395 2120 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.62 % Allowed : 20.90 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.22), residues: 1958 helix: 2.44 (0.19), residues: 748 sheet: 1.19 (0.29), residues: 440 loop : -0.34 (0.27), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 196 PHE 0.007 0.001 PHE D 126 TYR 0.007 0.001 TYR V 132 ARG 0.008 0.000 ARG N 184 Details of bonding type rmsd hydrogen bonds : bond 0.02485 ( 749) hydrogen bonds : angle 4.21943 ( 2247) covalent geometry : bond 0.00236 (14762) covalent geometry : angle 0.67503 (20152) *********************** 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 317 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 228 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASN cc_start: 0.6623 (OUTLIER) cc_final: 0.5559 (t0) REVERT: C 191 ILE cc_start: 0.5605 (OUTLIER) cc_final: 0.4832 (mt) REVERT: D 209 ASN cc_start: 0.6158 (OUTLIER) cc_final: 0.5553 (t0) REVERT: E 159 MET cc_start: 0.7592 (mmm) cc_final: 0.7138 (mmm) REVERT: F 209 ASN cc_start: 0.5784 (m110) cc_final: 0.5547 (t0) REVERT: H 140 LEU cc_start: 0.6828 (OUTLIER) cc_final: 0.6553 (tt) REVERT: K 140 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7906 (mm) REVERT: K 159 MET cc_start: 0.6062 (mmt) cc_final: 0.5650 (mmp) REVERT: L 209 ASN cc_start: 0.6012 (OUTLIER) cc_final: 0.5787 (t0) REVERT: M 131 ASN cc_start: 0.5807 (t0) cc_final: 0.5550 (m-40) REVERT: M 159 MET cc_start: 0.6897 (OUTLIER) cc_final: 0.5655 (mmm) REVERT: N 159 MET cc_start: 0.6446 (mmt) cc_final: 0.5798 (mmm) REVERT: O 159 MET cc_start: 0.6694 (mmt) cc_final: 0.5584 (mmp) REVERT: P 159 MET cc_start: 0.6295 (mmt) cc_final: 0.5697 (mmm) REVERT: R 159 MET cc_start: 0.7100 (mmm) cc_final: 0.6886 (mmm) outliers start: 89 outliers final: 75 residues processed: 296 average time/residue: 0.2152 time to fit residues: 97.1612 Evaluate side-chains 302 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 220 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 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 C residue 176 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 176 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 175 SER Chi-restraints excluded: chain F residue 176 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 197 LEU Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 220 LEU 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 126 PHE Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 209 ASN 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 159 MET 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 143 THR 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 143 THR 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 197 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 143 THR 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 209 ASN Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 197 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 0.1980 chunk 123 optimal weight: 1.9990 chunk 173 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 192 optimal weight: 0.0970 chunk 197 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 43 optimal weight: 0.0470 overall best weight: 0.3476 ------------------------------------------------------------------------------- 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 = 0.5729 r_free = 0.5729 target = 0.308329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.5681 r_free = 0.5681 target = 0.298321 restraints weight = 18219.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.5699 r_free = 0.5699 target = 0.300408 restraints weight = 12964.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.5712 r_free = 0.5712 target = 0.301860 restraints weight = 9727.025| |-----------------------------------------------------------------------------| r_work (final): 0.5696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5729 moved from start: 0.7592 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= 0.102 Angle : 0.679 12.830 20152 Z= 0.292 Chirality : 0.041 0.254 2530 Planarity : 0.004 0.042 2640 Dihedral : 4.481 51.642 2120 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.86 % Allowed : 21.59 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.22), residues: 1958 helix: 2.47 (0.19), residues: 748 sheet: 1.33 (0.29), residues: 440 loop : -0.26 (0.28), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 196 PHE 0.003 0.001 PHE Q 126 TYR 0.006 0.001 TYR V 132 ARG 0.010 0.000 ARG R 184 Details of bonding type rmsd hydrogen bonds : bond 0.02453 ( 749) hydrogen bonds : angle 4.16232 ( 2247) covalent geometry : bond 0.00237 (14762) covalent geometry : angle 0.67906 (20152) ********************** 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 301 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 224 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASN cc_start: 0.6651 (OUTLIER) cc_final: 0.5608 (t0) REVERT: C 191 ILE cc_start: 0.5466 (OUTLIER) cc_final: 0.5186 (mt) REVERT: C 212 LEU cc_start: 0.4306 (OUTLIER) cc_final: 0.4050 (tp) REVERT: D 209 ASN cc_start: 0.6080 (OUTLIER) cc_final: 0.5536 (t0) REVERT: E 159 MET cc_start: 0.7586 (mmm) cc_final: 0.7166 (mmm) REVERT: F 147 LEU cc_start: 0.6593 (tt) cc_final: 0.6321 (tt) REVERT: H 140 LEU cc_start: 0.6799 (OUTLIER) cc_final: 0.6548 (tt) REVERT: K 140 LEU cc_start: 0.8145 (OUTLIER) cc_final: 0.7847 (mm) REVERT: K 159 MET cc_start: 0.6225 (mmt) cc_final: 0.5734 (mmp) REVERT: L 140 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8048 (mm) REVERT: M 131 ASN cc_start: 0.5710 (t0) cc_final: 0.5438 (m-40) REVERT: M 159 MET cc_start: 0.6901 (OUTLIER) cc_final: 0.5682 (mmm) REVERT: N 159 MET cc_start: 0.6427 (mmt) cc_final: 0.5792 (mmm) REVERT: O 159 MET cc_start: 0.6676 (mmt) cc_final: 0.6031 (mmm) REVERT: P 159 MET cc_start: 0.6322 (mmt) cc_final: 0.5739 (mmm) REVERT: R 159 MET cc_start: 0.7092 (mmm) cc_final: 0.6870 (mmm) outliers start: 77 outliers final: 67 residues processed: 282 average time/residue: 0.2194 time to fit residues: 95.1506 Evaluate side-chains 296 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 221 time to evaluate : 1.482 ------------------------------------------------------------------------------- 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 209 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 220 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain D residue 213 VAL Chi-restraints excluded: chain D residue 220 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 176 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 175 SER Chi-restraints excluded: chain F residue 176 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 197 LEU Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 220 LEU 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 202 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 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 159 MET 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 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 197 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 143 THR 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 W residue 147 LEU Chi-restraints excluded: chain W residue 197 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 15 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 chunk 171 optimal weight: 0.4980 chunk 63 optimal weight: 0.0170 chunk 111 optimal weight: 0.9980 chunk 174 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN L 209 ASN V 209 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5703 r_free = 0.5703 target = 0.304537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.5654 r_free = 0.5654 target = 0.294094 restraints weight = 18230.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.5664 r_free = 0.5664 target = 0.296028 restraints weight = 13332.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.5683 r_free = 0.5683 target = 0.297551 restraints weight = 10063.807| |-----------------------------------------------------------------------------| r_work (final): 0.5666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5803 moved from start: 0.7910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14762 Z= 0.115 Angle : 0.689 12.233 20152 Z= 0.300 Chirality : 0.041 0.204 2530 Planarity : 0.004 0.038 2640 Dihedral : 4.655 51.123 2120 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 5.62 % Allowed : 20.83 % Favored : 73.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.22), residues: 1958 helix: 2.30 (0.19), residues: 748 sheet: 1.27 (0.29), residues: 440 loop : -0.44 (0.27), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS O 196 PHE 0.004 0.001 PHE M 126 TYR 0.007 0.001 TYR B 132 ARG 0.009 0.001 ARG N 184 Details of bonding type rmsd hydrogen bonds : bond 0.02565 ( 749) hydrogen bonds : angle 4.33874 ( 2247) covalent geometry : bond 0.00270 (14762) covalent geometry : angle 0.68942 (20152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4550.59 seconds wall clock time: 80 minutes 45.46 seconds (4845.46 seconds total)