Starting phenix.real_space_refine on Fri Jun 13 00:42:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fte_29424/06_2025/8fte_29424.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fte_29424/06_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_29424/06_2025/8fte_29424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fte_29424/06_2025/8fte_29424.map" model { file = "/net/cci-nas-00/data/ceres_data/8fte_29424/06_2025/8fte_29424.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fte_29424/06_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 9.65, per 1000 atoms: 0.66 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: 3.96 Conformation dependent library (CDL) restraints added in 2.2 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: 1.41 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: 3.89 Time building geometry restraints manager: 4.53 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: 0.16 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: 5.130 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: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 34.820 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.270 ------------------------------------------------------------------------------- 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 : 2.030 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: 0.3360 time to fit residues: 217.0164 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 : 1.575 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.5133 r_free = 0.5133 target = 0.216901 restraints weight = 16060.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.5198 r_free = 0.5198 target = 0.225379 restraints weight = 8566.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.5243 r_free = 0.5243 target = 0.231454 restraints weight = 5338.777| |-----------------------------------------------------------------------------| 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 : 1.804 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: 0.4947 (tt) REVERT: E 180 LEU cc_start: 0.2928 (tp) cc_final: 0.2725 (mp) REVERT: F 220 LEU cc_start: 0.7469 (mt) cc_final: 0.5271 (tt) REVERT: J 142 ARG cc_start: 0.8558 (mmp80) cc_final: 0.8346 (mmp80) REVERT: J 177 THR cc_start: 0.6807 (p) cc_final: 0.6463 (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: 0.6460 (mmt) cc_final: 0.5737 (mmm) REVERT: N 142 ARG cc_start: 0.7804 (tpp-160) cc_final: 0.7496 (tpp-160) REVERT: N 150 VAL cc_start: 0.5154 (OUTLIER) cc_final: 0.4860 (m) REVERT: N 159 MET cc_start: 0.6629 (mmt) cc_final: 0.5849 (mmm) REVERT: O 159 MET cc_start: 0.6193 (mmt) cc_final: 0.5773 (mmm) REVERT: O 180 LEU cc_start: 0.5187 (tp) cc_final: 0.4842 (mp) REVERT: O 181 GLU cc_start: 0.3917 (mt-10) cc_final: 0.3714 (mt-10) REVERT: O 184 ARG cc_start: 0.4156 (mmm160) cc_final: 0.3953 (mmm160) REVERT: P 159 MET cc_start: 0.5439 (mmt) cc_final: 0.5027 (mmm) REVERT: P 180 LEU cc_start: 0.4898 (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: 0.7524 (OUTLIER) cc_final: 0.7178 (tm) outliers start: 107 outliers final: 50 residues processed: 359 average time/residue: 0.3361 time to fit residues: 178.0598 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 : 1.628 ------------------------------------------------------------------------------- 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: 4.9990 chunk 110 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 131 optimal weight: 0.5980 chunk 4 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS D 209 ASN E 209 ASN F 209 ASN G 209 ASN H 156 HIS H 209 ASN I 156 HIS I 209 ASN J 156 HIS J 209 ASN K 125 GLN K 156 HIS K 209 ASN L 156 HIS L 209 ASN M 156 HIS M 209 ASN N 156 HIS N 196 HIS T 196 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5340 r_free = 0.5340 target = 0.243486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.5056 r_free = 0.5056 target = 0.207730 restraints weight = 16549.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.5118 r_free = 0.5118 target = 0.215455 restraints weight = 9144.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5162 r_free = 0.5162 target = 0.221086 restraints weight = 5813.232| |-----------------------------------------------------------------------------| r_work (final): 0.5160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5457 moved from start: 0.5062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14762 Z= 0.154 Angle : 0.689 10.241 20152 Z= 0.324 Chirality : 0.042 0.142 2530 Planarity : 0.005 0.062 2640 Dihedral : 6.083 53.714 2138 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.72 % Favored : 94.23 % Rotamer: Outliers : 7.77 % Allowed : 14.02 % Favored : 78.22 % 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: 0.55 (0.21), residues: 1958 helix: 2.15 (0.19), residues: 748 sheet: -0.57 (0.27), residues: 440 loop : -0.82 (0.26), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS R 196 PHE 0.010 0.001 PHE T 126 TYR 0.014 0.001 TYR A 132 ARG 0.006 0.001 ARG K 184 Details of bonding type rmsd hydrogen bonds : bond 0.03153 ( 749) hydrogen bonds : angle 4.98733 ( 2247) covalent geometry : bond 0.00343 (14762) covalent geometry : angle 0.68949 (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 375 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 252 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.7854 (OUTLIER) cc_final: 0.7476 (tm) REVERT: A 209 ASN cc_start: 0.6218 (OUTLIER) cc_final: 0.4763 (t0) REVERT: B 160 PRO cc_start: 0.6138 (Cg_endo) cc_final: 0.5516 (Cg_exo) REVERT: C 147 LEU cc_start: 0.7523 (OUTLIER) cc_final: 0.7289 (tt) REVERT: C 209 ASN cc_start: 0.5010 (OUTLIER) cc_final: 0.4525 (t0) REVERT: F 209 ASN cc_start: 0.5592 (OUTLIER) cc_final: 0.4898 (t0) REVERT: G 209 ASN cc_start: 0.6009 (OUTLIER) cc_final: 0.5618 (t0) REVERT: H 209 ASN cc_start: 0.5665 (OUTLIER) cc_final: 0.4949 (t0) REVERT: I 140 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6611 (tt) REVERT: K 142 ARG cc_start: 0.8389 (mmp80) cc_final: 0.6958 (ttp80) REVERT: K 209 ASN cc_start: 0.5290 (OUTLIER) cc_final: 0.4371 (t0) REVERT: K 222 GLN cc_start: 0.8172 (mp10) cc_final: 0.7766 (mp10) REVERT: M 159 MET cc_start: 0.6906 (mmt) cc_final: 0.6016 (mmm) REVERT: N 159 MET cc_start: 0.7088 (mmt) cc_final: 0.5971 (mmp) REVERT: O 159 MET cc_start: 0.6856 (mmt) cc_final: 0.5874 (mmp) REVERT: P 129 GLN cc_start: 0.6423 (tm-30) cc_final: 0.6192 (tm-30) REVERT: P 142 ARG cc_start: 0.7735 (tpp-160) cc_final: 0.7465 (tpp80) REVERT: P 159 MET cc_start: 0.6406 (mmt) cc_final: 0.5695 (mmm) REVERT: Q 147 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7539 (tm) REVERT: Q 180 LEU cc_start: 0.5627 (tp) cc_final: 0.5118 (mp) REVERT: R 159 MET cc_start: 0.7116 (mmm) cc_final: 0.6876 (mmm) REVERT: R 181 GLU cc_start: 0.5357 (tp30) cc_final: 0.4663 (mt-10) REVERT: S 147 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7340 (tm) REVERT: S 154 ARG cc_start: 0.5769 (mpp-170) cc_final: 0.4911 (mpp-170) REVERT: S 159 MET cc_start: 0.7018 (mmm) cc_final: 0.6613 (mmp) REVERT: S 181 GLU cc_start: 0.5260 (tp30) cc_final: 0.4720 (mt-10) REVERT: T 159 MET cc_start: 0.6609 (tpp) cc_final: 0.6266 (mmm) REVERT: V 128 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6377 (tm-30) outliers start: 123 outliers final: 75 residues processed: 343 average time/residue: 0.3001 time to fit residues: 149.7383 Evaluate side-chains 304 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 217 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 147 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 209 ASN Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 140 LEU 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 171 SER 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 155 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 175 SER Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 209 ASN 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 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 143 THR Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain K residue 209 ASN Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain N residue 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 197 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 143 THR Chi-restraints excluded: chain Q 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 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 T residue 220 LEU 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: 0.4980 chunk 188 optimal weight: 0.1980 chunk 193 optimal weight: 2.9990 chunk 2 optimal weight: 0.0870 chunk 182 optimal weight: 0.7980 chunk 92 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 161 optimal weight: 6.9990 chunk 110 optimal weight: 0.0060 chunk 36 optimal weight: 2.9990 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 209 ASN F 209 ASN G 209 ASN H 209 ASN J 125 GLN J 209 ASN K 125 GLN K 209 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5746 r_free = 0.5746 target = 0.312624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5693 r_free = 0.5693 target = 0.302052 restraints weight = 18311.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.5712 r_free = 0.5712 target = 0.304328 restraints weight = 12887.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.5725 r_free = 0.5725 target = 0.305894 restraints weight = 9583.561| |-----------------------------------------------------------------------------| r_work (final): 0.5713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5526 moved from start: 0.5402 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= 0.100 Angle : 0.602 11.849 20152 Z= 0.271 Chirality : 0.041 0.242 2530 Planarity : 0.004 0.030 2640 Dihedral : 5.443 52.522 2134 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.68 % Allowed : 17.68 % Favored : 76.64 % 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: 1.09 (0.21), residues: 1958 helix: 2.47 (0.19), residues: 748 sheet: -0.02 (0.27), residues: 440 loop : -0.56 (0.26), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS R 196 PHE 0.005 0.001 PHE T 126 TYR 0.010 0.001 TYR S 132 ARG 0.005 0.000 ARG N 184 Details of bonding type rmsd hydrogen bonds : bond 0.02532 ( 749) hydrogen bonds : angle 4.48379 ( 2247) covalent geometry : bond 0.00228 (14762) covalent geometry : angle 0.60176 (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 329 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 239 time to evaluate : 1.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6736 (tm) REVERT: B 160 PRO cc_start: 0.7707 (Cg_endo) cc_final: 0.7058 (Cg_exo) REVERT: B 209 ASN cc_start: 0.5958 (OUTLIER) cc_final: 0.5245 (t0) REVERT: C 147 LEU cc_start: 0.6560 (OUTLIER) cc_final: 0.6226 (tt) REVERT: F 220 LEU cc_start: 0.6322 (mt) cc_final: 0.5752 (mt) REVERT: H 140 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6947 (tt) REVERT: I 209 ASN cc_start: 0.6186 (OUTLIER) cc_final: 0.5808 (t0) REVERT: J 140 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7612 (mm) REVERT: J 154 ARG cc_start: 0.5814 (mtm-85) cc_final: 0.5355 (mtm-85) REVERT: K 142 ARG cc_start: 0.6489 (mmp80) cc_final: 0.6056 (ttp80) REVERT: K 159 MET cc_start: 0.6022 (mmt) cc_final: 0.5203 (mmp) REVERT: M 159 MET cc_start: 0.6087 (mmt) cc_final: 0.5254 (mmm) REVERT: N 159 MET cc_start: 0.5862 (mmt) cc_final: 0.4917 (mmp) REVERT: O 159 MET cc_start: 0.6424 (mmt) cc_final: 0.5369 (mmp) REVERT: P 159 MET cc_start: 0.5821 (mmt) cc_final: 0.5231 (mmm) REVERT: Q 180 LEU cc_start: 0.6696 (tp) cc_final: 0.6067 (mp) REVERT: S 132 TYR cc_start: 0.4174 (t80) cc_final: 0.3966 (t80) REVERT: S 147 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.7006 (tm) REVERT: S 159 MET cc_start: 0.6307 (mmm) cc_final: 0.6074 (mmp) REVERT: S 194 VAL cc_start: 0.6292 (t) cc_final: 0.5993 (t) REVERT: T 159 MET cc_start: 0.6512 (tpp) cc_final: 0.6109 (mmm) REVERT: V 147 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6860 (tm) outliers start: 90 outliers final: 62 residues processed: 297 average time/residue: 0.2347 time to fit residues: 104.8780 Evaluate side-chains 291 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 221 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain C residue 147 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 197 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 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 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 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 I residue 209 ASN 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 147 LEU Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain L residue 140 LEU 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 144 ILE Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 180 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 125 GLN 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 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=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: 0.8980 chunk 194 optimal weight: 0.6980 chunk 165 optimal weight: 5.9990 chunk 80 optimal weight: 0.0980 chunk 187 optimal weight: 0.6980 chunk 171 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 59 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 209 ASN D 209 ASN O 209 ASN P 209 ASN S 209 ASN T 196 HIS T 209 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5716 r_free = 0.5716 target = 0.307264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.5657 r_free = 0.5657 target = 0.295879 restraints weight = 18488.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.5677 r_free = 0.5677 target = 0.298188 restraints weight = 13263.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.5692 r_free = 0.5692 target = 0.299837 restraints weight = 10003.496| |-----------------------------------------------------------------------------| r_work (final): 0.5681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5691 moved from start: 0.6212 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= 0.121 Angle : 0.644 11.360 20152 Z= 0.292 Chirality : 0.042 0.231 2530 Planarity : 0.004 0.032 2640 Dihedral : 5.520 55.355 2132 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 7.32 % Allowed : 16.86 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.07 (0.21), residues: 1958 helix: 2.37 (0.19), residues: 748 sheet: 0.24 (0.28), residues: 440 loop : -0.67 (0.26), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS R 196 PHE 0.006 0.001 PHE Q 126 TYR 0.009 0.001 TYR B 132 ARG 0.007 0.000 ARG N 184 Details of bonding type rmsd hydrogen bonds : bond 0.02582 ( 749) hydrogen bonds : angle 4.47524 ( 2247) covalent geometry : bond 0.00275 (14762) covalent geometry : angle 0.64423 (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 353 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 237 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASN cc_start: 0.6564 (OUTLIER) cc_final: 0.5565 (t0) REVERT: B 209 ASN cc_start: 0.6106 (OUTLIER) cc_final: 0.5759 (t0) REVERT: C 209 ASN cc_start: 0.6543 (OUTLIER) cc_final: 0.6271 (t0) REVERT: D 159 MET cc_start: 0.7035 (tpp) cc_final: 0.6617 (mmm) REVERT: E 209 ASN cc_start: 0.6273 (OUTLIER) cc_final: 0.5528 (t0) REVERT: F 209 ASN cc_start: 0.6286 (OUTLIER) cc_final: 0.5562 (t0) REVERT: G 209 ASN cc_start: 0.6484 (OUTLIER) cc_final: 0.5694 (t0) REVERT: H 140 LEU cc_start: 0.7365 (OUTLIER) cc_final: 0.7036 (tt) REVERT: H 209 ASN cc_start: 0.5622 (OUTLIER) cc_final: 0.5278 (t0) REVERT: I 140 LEU cc_start: 0.7358 (OUTLIER) cc_final: 0.7113 (tt) REVERT: J 209 ASN cc_start: 0.5160 (OUTLIER) cc_final: 0.4727 (t0) REVERT: J 222 GLN cc_start: 0.7171 (mp10) cc_final: 0.6889 (mp10) REVERT: K 142 ARG cc_start: 0.6359 (mmp80) cc_final: 0.6018 (ttp80) REVERT: K 159 MET cc_start: 0.6204 (mmt) cc_final: 0.5464 (mmp) REVERT: K 209 ASN cc_start: 0.5414 (OUTLIER) cc_final: 0.4911 (t0) REVERT: N 159 MET cc_start: 0.6306 (mmt) cc_final: 0.5587 (mmm) REVERT: O 159 MET cc_start: 0.6643 (mmt) cc_final: 0.5925 (mmm) REVERT: P 159 MET cc_start: 0.6110 (mmt) cc_final: 0.5444 (mmm) REVERT: P 209 ASN cc_start: 0.6647 (OUTLIER) cc_final: 0.6346 (t0) REVERT: Q 129 GLN cc_start: 0.6707 (tp-100) cc_final: 0.6335 (mm110) REVERT: R 159 MET cc_start: 0.6480 (mmm) cc_final: 0.6014 (mmm) REVERT: R 209 ASN cc_start: 0.6280 (OUTLIER) cc_final: 0.5720 (m-40) REVERT: S 132 TYR cc_start: 0.4360 (t80) cc_final: 0.4095 (t80) REVERT: T 159 MET cc_start: 0.7192 (tpp) cc_final: 0.4850 (mtt) outliers start: 116 outliers final: 76 residues processed: 321 average time/residue: 0.2695 time to fit residues: 133.7872 Evaluate side-chains 310 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 221 time to evaluate : 2.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 197 LEU 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 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 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 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 F residue 209 ASN Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 209 ASN Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 209 ASN Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 209 ASN Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain 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 209 ASN Chi-restraints excluded: chain Q residue 140 LEU 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 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 W residue 147 LEU Chi-restraints excluded: chain W residue 197 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 108 optimal weight: 0.9980 chunk 66 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 134 optimal weight: 0.0070 chunk 149 optimal weight: 0.7980 chunk 184 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 80 optimal weight: 0.0980 chunk 92 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- 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 = 0.309617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5672 r_free = 0.5672 target = 0.297759 restraints weight = 18341.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.5691 r_free = 0.5691 target = 0.300293 restraints weight = 12852.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.5705 r_free = 0.5705 target = 0.302073 restraints weight = 9452.162| |-----------------------------------------------------------------------------| r_work (final): 0.5693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5669 moved from start: 0.6446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14762 Z= 0.102 Angle : 0.616 12.036 20152 Z= 0.272 Chirality : 0.040 0.191 2530 Planarity : 0.004 0.024 2640 Dihedral : 5.360 56.390 2132 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 6.38 % Allowed : 18.37 % Favored : 75.25 % 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: 1.39 (0.22), residues: 1958 helix: 2.51 (0.19), residues: 748 sheet: 0.63 (0.29), residues: 440 loop : -0.49 (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 K 126 TYR 0.007 0.001 TYR B 132 ARG 0.007 0.000 ARG N 184 Details of bonding type rmsd hydrogen bonds : bond 0.02459 ( 749) hydrogen bonds : angle 4.30062 ( 2247) covalent geometry : bond 0.00234 (14762) covalent geometry : angle 0.61612 (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 337 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 236 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6752 (tm) REVERT: D 147 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6154 (tt) REVERT: D 159 MET cc_start: 0.7342 (tpp) cc_final: 0.6883 (mmm) REVERT: F 159 MET cc_start: 0.7492 (mmm) cc_final: 0.7292 (mmm) REVERT: H 140 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.6995 (tt) REVERT: K 159 MET cc_start: 0.6220 (mmt) cc_final: 0.5496 (mmp) REVERT: L 222 GLN cc_start: 0.7364 (mp-120) cc_final: 0.7127 (mp10) REVERT: N 159 MET cc_start: 0.6289 (mmt) cc_final: 0.5604 (mmm) REVERT: O 159 MET cc_start: 0.6631 (mmt) cc_final: 0.5933 (mmm) REVERT: P 159 MET cc_start: 0.6071 (mmt) cc_final: 0.5478 (mmm) REVERT: R 159 MET cc_start: 0.7271 (mmm) cc_final: 0.7001 (mmm) REVERT: S 132 TYR cc_start: 0.4420 (t80) cc_final: 0.4154 (t80) REVERT: S 159 MET cc_start: 0.6687 (mmp) cc_final: 0.6136 (mmm) REVERT: T 159 MET cc_start: 0.7204 (tpp) cc_final: 0.6888 (mmm) REVERT: V 147 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6905 (tm) REVERT: W 159 MET cc_start: 0.6886 (tpp) cc_final: 0.6387 (mmm) outliers start: 101 outliers final: 82 residues processed: 300 average time/residue: 0.2301 time to fit residues: 105.6465 Evaluate side-chains 311 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 225 time to evaluate : 1.611 ------------------------------------------------------------------------------- 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 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 197 LEU 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 175 SER Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 213 VAL 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 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 K residue 125 GLN Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 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 L residue 177 THR Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 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 O residue 197 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 209 ASN Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain 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 125 GLN 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 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 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: 7.9990 chunk 68 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 111 optimal weight: 0.0870 chunk 27 optimal weight: 0.7980 chunk 110 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 51 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 125 GLN J 222 GLN K 125 GLN K 222 GLN P 209 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5326 r_free = 0.5326 target = 0.242295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5029 r_free = 0.5029 target = 0.204741 restraints weight = 16508.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5095 r_free = 0.5095 target = 0.212756 restraints weight = 8835.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5140 r_free = 0.5140 target = 0.218670 restraints weight = 5550.665| |-----------------------------------------------------------------------------| r_work (final): 0.5135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5480 moved from start: 0.6803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14762 Z= 0.114 Angle : 0.628 11.722 20152 Z= 0.280 Chirality : 0.041 0.217 2530 Planarity : 0.004 0.026 2640 Dihedral : 5.259 57.768 2130 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 7.01 % Allowed : 18.18 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.42 (0.22), residues: 1958 helix: 2.48 (0.19), residues: 748 sheet: 0.82 (0.29), residues: 440 loop : -0.54 (0.27), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS R 196 PHE 0.009 0.001 PHE K 126 TYR 0.010 0.001 TYR V 132 ARG 0.008 0.000 ARG N 184 Details of bonding type rmsd hydrogen bonds : bond 0.02509 ( 749) hydrogen bonds : angle 4.25513 ( 2247) covalent geometry : bond 0.00261 (14762) covalent geometry : angle 0.62785 (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 342 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 231 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.6892 (mmm) cc_final: 0.6682 (mmm) REVERT: B 209 ASN cc_start: 0.5788 (OUTLIER) cc_final: 0.5238 (t0) REVERT: C 140 LEU cc_start: 0.6598 (OUTLIER) cc_final: 0.6285 (mp) REVERT: E 159 MET cc_start: 0.7886 (mmm) cc_final: 0.7605 (mmm) REVERT: E 209 ASN cc_start: 0.5675 (OUTLIER) cc_final: 0.4784 (t0) REVERT: G 213 VAL cc_start: 0.6159 (p) cc_final: 0.5948 (t) REVERT: H 140 LEU cc_start: 0.6101 (OUTLIER) cc_final: 0.5876 (tt) REVERT: J 209 ASN cc_start: 0.5164 (OUTLIER) cc_final: 0.4488 (t0) REVERT: K 126 PHE cc_start: 0.4568 (t80) cc_final: 0.4301 (t80) REVERT: K 140 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7256 (mm) REVERT: K 159 MET cc_start: 0.7219 (mmt) cc_final: 0.6188 (mmp) REVERT: N 159 MET cc_start: 0.7560 (mmt) cc_final: 0.6646 (mmm) REVERT: O 159 MET cc_start: 0.7287 (mmt) cc_final: 0.6604 (mmm) REVERT: P 159 MET cc_start: 0.7340 (mmt) cc_final: 0.6494 (mmm) REVERT: Q 129 GLN cc_start: 0.6405 (tp-100) cc_final: 0.5487 (mm110) REVERT: R 159 MET cc_start: 0.7664 (mmm) cc_final: 0.7132 (mmm) REVERT: S 159 MET cc_start: 0.6449 (mmp) cc_final: 0.6079 (mmm) REVERT: V 142 ARG cc_start: 0.7925 (tpp-160) cc_final: 0.7707 (mmp80) REVERT: W 159 MET cc_start: 0.7535 (tpp) cc_final: 0.7035 (mmm) outliers start: 111 outliers final: 82 residues processed: 305 average time/residue: 0.2219 time to fit residues: 102.8422 Evaluate side-chains 304 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 216 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 221 THR Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain C residue 140 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 D residue 140 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 197 LEU 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 175 SER Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 191 ILE 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 176 VAL Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 144 ILE Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 144 ILE Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 221 THR 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 125 GLN Chi-restraints excluded: chain S residue 143 THR Chi-restraints excluded: chain S residue 144 ILE Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain T residue 220 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 197 LEU Chi-restraints excluded: chain V residue 209 ASN Chi-restraints excluded: chain W residue 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: 0.9980 chunk 170 optimal weight: 2.9990 chunk 2 optimal weight: 0.0770 chunk 157 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 42 optimal weight: 0.0070 chunk 171 optimal weight: 0.2980 chunk 147 optimal weight: 1.9990 chunk 61 optimal weight: 0.0970 chunk 14 optimal weight: 0.9990 chunk 152 optimal weight: 0.0020 overall best weight: 0.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5760 r_free = 0.5760 target = 0.314666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.5709 r_free = 0.5709 target = 0.303636 restraints weight = 18170.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.5726 r_free = 0.5726 target = 0.306177 restraints weight = 12405.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.5744 r_free = 0.5744 target = 0.307997 restraints weight = 8938.721| |-----------------------------------------------------------------------------| r_work (final): 0.5729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5607 moved from start: 0.6926 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= 0.093 Angle : 0.641 12.305 20152 Z= 0.274 Chirality : 0.040 0.211 2530 Planarity : 0.003 0.026 2640 Dihedral : 4.620 59.918 2124 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 5.37 % Allowed : 20.20 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.97 (0.22), residues: 1958 helix: 2.51 (0.19), residues: 770 sheet: 1.30 (0.29), residues: 440 loop : 0.07 (0.29), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS H 196 PHE 0.003 0.000 PHE T 126 TYR 0.006 0.000 TYR V 132 ARG 0.007 0.000 ARG N 184 Details of bonding type rmsd hydrogen bonds : bond 0.02368 ( 749) hydrogen bonds : angle 3.96751 ( 2247) covalent geometry : bond 0.00214 (14762) covalent geometry : angle 0.64104 (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 323 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 238 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 142 ARG cc_start: 0.7043 (mmp80) cc_final: 0.6723 (mmp80) REVERT: E 159 MET cc_start: 0.7193 (mmm) cc_final: 0.6877 (mmm) REVERT: F 209 ASN cc_start: 0.5827 (m110) cc_final: 0.5576 (t0) REVERT: K 140 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7520 (mm) REVERT: K 159 MET cc_start: 0.5972 (mmt) cc_final: 0.5465 (mmp) REVERT: L 140 LEU cc_start: 0.8095 (OUTLIER) cc_final: 0.7757 (mm) REVERT: M 159 MET cc_start: 0.6538 (mmm) cc_final: 0.5587 (mmm) REVERT: M 180 LEU cc_start: 0.4772 (OUTLIER) cc_final: 0.4541 (mp) REVERT: N 159 MET cc_start: 0.6293 (mmt) cc_final: 0.5650 (mmm) REVERT: O 159 MET cc_start: 0.6642 (mmt) cc_final: 0.5556 (mmp) REVERT: P 159 MET cc_start: 0.6193 (mmt) cc_final: 0.5555 (mmm) REVERT: R 159 MET cc_start: 0.7246 (mmm) cc_final: 0.6867 (mmm) REVERT: W 159 MET cc_start: 0.6945 (tpp) cc_final: 0.6575 (mmm) outliers start: 85 outliers final: 62 residues processed: 295 average time/residue: 0.2344 time to fit residues: 104.1541 Evaluate side-chains 291 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 226 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 197 LEU 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 197 LEU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 191 ILE Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL 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 J residue 202 VAL Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 210 VAL Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 155 VAL 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 125 GLN Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 220 LEU Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 155 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 61 optimal weight: 0.9990 chunk 97 optimal weight: 0.1980 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 0.3980 chunk 179 optimal weight: 1.9990 chunk 25 optimal weight: 0.0020 chunk 189 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 16 optimal weight: 0.0470 chunk 178 optimal weight: 0.8980 chunk 38 optimal weight: 0.0050 overall best weight: 0.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: W 156 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5765 r_free = 0.5765 target = 0.313622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.5727 r_free = 0.5727 target = 0.304126 restraints weight = 18606.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.5745 r_free = 0.5745 target = 0.306397 restraints weight = 12696.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.5754 r_free = 0.5754 target = 0.307813 restraints weight = 9081.805| |-----------------------------------------------------------------------------| r_work (final): 0.5741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5596 moved from start: 0.7041 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= 0.095 Angle : 0.663 13.065 20152 Z= 0.283 Chirality : 0.041 0.232 2530 Planarity : 0.004 0.035 2640 Dihedral : 4.542 59.703 2124 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 4.36 % Allowed : 20.71 % Favored : 74.94 % 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: 2.02 (0.22), residues: 1958 helix: 2.75 (0.19), residues: 748 sheet: 1.40 (0.30), residues: 440 loop : -0.13 (0.28), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.000 HIS W 156 PHE 0.002 0.000 PHE S 126 TYR 0.017 0.001 TYR S 132 ARG 0.010 0.000 ARG W 154 Details of bonding type rmsd hydrogen bonds : bond 0.02319 ( 749) hydrogen bonds : angle 3.95015 ( 2247) covalent geometry : bond 0.00219 (14762) covalent geometry : angle 0.66256 (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 300 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 231 time to evaluate : 1.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 159 MET cc_start: 0.7278 (mmm) cc_final: 0.7027 (mmm) REVERT: I 142 ARG cc_start: 0.6481 (mmp80) cc_final: 0.6169 (ttp-170) REVERT: I 146 THR cc_start: 0.5439 (t) cc_final: 0.5168 (t) REVERT: J 222 GLN cc_start: 0.6448 (mp10) cc_final: 0.6244 (mp10) REVERT: K 140 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7562 (mm) REVERT: K 159 MET cc_start: 0.6025 (mmt) cc_final: 0.5497 (mmp) REVERT: L 140 LEU cc_start: 0.8114 (OUTLIER) cc_final: 0.7726 (mm) REVERT: M 159 MET cc_start: 0.6601 (mmm) cc_final: 0.5608 (mmm) REVERT: M 180 LEU cc_start: 0.4704 (OUTLIER) cc_final: 0.4464 (mp) REVERT: N 159 MET cc_start: 0.6333 (mmt) cc_final: 0.5669 (mmm) REVERT: O 159 MET cc_start: 0.6694 (mmt) cc_final: 0.6012 (mmm) REVERT: P 159 MET cc_start: 0.6158 (mmt) cc_final: 0.5523 (mmm) REVERT: R 159 MET cc_start: 0.7228 (mmm) cc_final: 0.6897 (mmm) REVERT: R 209 ASN cc_start: 0.6496 (OUTLIER) cc_final: 0.5785 (m-40) REVERT: S 159 MET cc_start: 0.5599 (mmm) cc_final: 0.4737 (mmt) REVERT: S 194 VAL cc_start: 0.5336 (t) cc_final: 0.4990 (t) REVERT: V 209 ASN cc_start: 0.6691 (OUTLIER) cc_final: 0.5929 (t0) REVERT: W 159 MET cc_start: 0.7058 (tpp) cc_final: 0.6856 (mmm) outliers start: 69 outliers final: 58 residues processed: 279 average time/residue: 0.2313 time to fit residues: 98.2714 Evaluate side-chains 282 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 219 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 197 LEU 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 213 VAL 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 191 ILE Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 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 L residue 177 THR Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain N residue 140 LEU 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 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 209 ASN Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain V residue 155 VAL 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 155 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 14 optimal weight: 0.9980 chunk 7 optimal weight: 0.0270 chunk 123 optimal weight: 0.6980 chunk 173 optimal weight: 0.5980 chunk 46 optimal weight: 0.1980 chunk 158 optimal weight: 0.5980 chunk 192 optimal weight: 0.8980 chunk 197 optimal weight: 1.9990 chunk 8 optimal weight: 0.0270 chunk 163 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.2896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5752 r_free = 0.5752 target = 0.311759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5712 r_free = 0.5712 target = 0.302273 restraints weight = 18722.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.5729 r_free = 0.5729 target = 0.304453 restraints weight = 12896.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.5740 r_free = 0.5740 target = 0.305962 restraints weight = 9291.179| |-----------------------------------------------------------------------------| r_work (final): 0.5728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5636 moved from start: 0.7209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 14762 Z= 0.096 Angle : 0.660 12.538 20152 Z= 0.282 Chirality : 0.040 0.200 2530 Planarity : 0.004 0.039 2640 Dihedral : 4.543 59.455 2124 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 4.42 % Allowed : 21.02 % 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: 2.00 (0.22), residues: 1958 helix: 2.68 (0.19), residues: 748 sheet: 1.47 (0.30), residues: 440 loop : -0.13 (0.28), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 196 PHE 0.002 0.000 PHE M 126 TYR 0.015 0.001 TYR S 132 ARG 0.009 0.000 ARG M 184 Details of bonding type rmsd hydrogen bonds : bond 0.02261 ( 749) hydrogen bonds : angle 3.98120 ( 2247) covalent geometry : bond 0.00227 (14762) covalent geometry : angle 0.65965 (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 302 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 232 time to evaluate : 2.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 220 LEU cc_start: 0.6307 (mp) cc_final: 0.5990 (mp) REVERT: E 142 ARG cc_start: 0.6794 (mmp80) cc_final: 0.6449 (mmp80) REVERT: E 209 ASN cc_start: 0.5858 (OUTLIER) cc_final: 0.5545 (t0) REVERT: F 209 ASN cc_start: 0.5181 (t0) cc_final: 0.4934 (t0) REVERT: I 142 ARG cc_start: 0.6523 (mmp80) cc_final: 0.6211 (ttp-170) REVERT: I 146 THR cc_start: 0.5509 (t) cc_final: 0.5243 (t) REVERT: K 140 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7794 (mm) REVERT: K 159 MET cc_start: 0.6072 (mmt) cc_final: 0.5514 (mmp) REVERT: L 140 LEU cc_start: 0.8132 (OUTLIER) cc_final: 0.7771 (mm) REVERT: M 159 MET cc_start: 0.6665 (mmm) cc_final: 0.5541 (mmm) REVERT: M 180 LEU cc_start: 0.4718 (OUTLIER) cc_final: 0.4481 (mp) REVERT: N 159 MET cc_start: 0.6401 (mmt) cc_final: 0.5753 (mmm) REVERT: O 159 MET cc_start: 0.6713 (mmt) cc_final: 0.6037 (mmm) REVERT: P 159 MET cc_start: 0.6203 (mmt) cc_final: 0.5577 (mmm) REVERT: R 159 MET cc_start: 0.7289 (mmm) cc_final: 0.6913 (mmm) REVERT: R 209 ASN cc_start: 0.6603 (OUTLIER) cc_final: 0.6020 (m-40) REVERT: S 159 MET cc_start: 0.5929 (mmm) cc_final: 0.5381 (mmm) REVERT: S 194 VAL cc_start: 0.5591 (t) cc_final: 0.5256 (t) outliers start: 70 outliers final: 58 residues processed: 280 average time/residue: 0.3361 time to fit residues: 148.1281 Evaluate side-chains 287 residues out of total 1672 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 224 time to evaluate : 2.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 LEU 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 D residue 140 LEU Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 197 LEU 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 197 LEU Chi-restraints excluded: chain E residue 209 ASN Chi-restraints excluded: chain E residue 213 VAL Chi-restraints excluded: chain F residue 176 VAL Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 191 ILE Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain J residue 220 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 176 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain N residue 140 LEU 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 155 VAL Chi-restraints excluded: chain Q residue 221 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 209 ASN Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 125 GLN Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain 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 15 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 52 optimal weight: 0.9990 chunk 171 optimal weight: 0.1980 chunk 63 optimal weight: 0.4980 chunk 111 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 chunk 72 optimal weight: 0.0170 chunk 20 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN K 125 GLN R 209 ASN T 196 HIS V 209 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5723 r_free = 0.5723 target = 0.307406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5679 r_free = 0.5679 target = 0.297369 restraints weight = 18687.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.5696 r_free = 0.5696 target = 0.299599 restraints weight = 13209.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5704 r_free = 0.5704 target = 0.300951 restraints weight = 9654.225| |-----------------------------------------------------------------------------| r_work (final): 0.5693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5721 moved from start: 0.7497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14762 Z= 0.108 Angle : 0.674 12.537 20152 Z= 0.291 Chirality : 0.041 0.234 2530 Planarity : 0.004 0.078 2640 Dihedral : 4.714 57.290 2124 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 4.80 % Allowed : 20.58 % Favored : 74.62 % 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: 1.83 (0.22), residues: 1958 helix: 2.51 (0.19), residues: 748 sheet: 1.42 (0.29), residues: 440 loop : -0.22 (0.28), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 196 PHE 0.004 0.001 PHE M 126 TYR 0.016 0.001 TYR S 132 ARG 0.009 0.000 ARG M 184 Details of bonding type rmsd hydrogen bonds : bond 0.02392 ( 749) hydrogen bonds : angle 4.11418 ( 2247) covalent geometry : bond 0.00252 (14762) covalent geometry : angle 0.67354 (20152) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5444.41 seconds wall clock time: 99 minutes 43.32 seconds (5983.32 seconds total)