Starting phenix.real_space_refine on Sat Mar 16 11:41:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fte_29424/03_2024/8fte_29424.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fte_29424/03_2024/8fte_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fte_29424/03_2024/8fte_29424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fte_29424/03_2024/8fte_29424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fte_29424/03_2024/8fte_29424.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fte_29424/03_2024/8fte_29424.pdb" } 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 Residue "A PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 7.95, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 6.33 Conformation dependent library (CDL) restraints added in 2.9 seconds 3916 Ramachandran restraints generated. 1958 Oldfield, 0 Emsley, 1958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3740 Finding SS restraints... Secondary structure from input PDB file: 66 helices and 22 sheets defined 42.0% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 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: 3.76 Time building geometry restraints manager: 6.75 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: 100.52 - 106.67: 616 106.67 - 112.81: 8493 112.81 - 118.95: 3540 118.95 - 125.10: 7327 125.10 - 131.24: 176 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'V' selection = chain 'W' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.860 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 39.970 Find NCS groups from input model: 0.900 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.370 ------------------------------------------------------------------------------- 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= 0.189 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 *********************** 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 fitting. rotamer outliers: 88 poor density : 423 time to evaluate : 1.577 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: 0.2935 time to fit residues: 188.4133 Evaluate side-chains 254 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 232 time to evaluate : 1.473 ------------------------------------------------------------------------------- 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: 0.0670 chunk 150 optimal weight: 0.8980 chunk 83 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 80 optimal weight: 0.7980 chunk 155 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 chunk 115 optimal weight: 3.9990 chunk 179 optimal weight: 0.5980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 196 HIS B 222 GLN C 156 HIS C 209 ASN C 222 GLN D 156 HIS D 209 ASN D 222 GLN E 156 HIS E 209 ASN E 222 GLN F 156 HIS F 209 ASN F 222 GLN G 156 HIS G 209 ASN G 222 GLN H 209 ASN H 222 GLN I 209 ASN I 222 GLN J 209 ASN J 222 GLN K 209 ASN K 222 GLN L 209 ASN M 209 ASN M 222 GLN N 209 ASN N 222 GLN O 209 ASN 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: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5294 moved from start: 0.4001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14762 Z= 0.203 Angle : 0.640 9.047 20152 Z= 0.296 Chirality : 0.042 0.166 2530 Planarity : 0.005 0.063 2640 Dihedral : 6.390 57.586 2156 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 8.52 % Allowed : 13.70 % Favored : 77.78 % 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: 0.27 (0.21), residues: 1958 helix: 1.97 (0.19), residues: 770 sheet: -1.18 (0.26), residues: 440 loop : -0.79 (0.26), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS A 196 PHE 0.019 0.001 PHE V 126 TYR 0.009 0.001 TYR B 132 ARG 0.014 0.001 ARG N 154 *********************** 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 424 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 289 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 220 LEU cc_start: 0.7006 (mt) cc_final: 0.6736 (mt) REVERT: J 154 ARG cc_start: 0.5523 (mtm-85) cc_final: 0.4913 (mtm-85) REVERT: J 177 THR cc_start: 0.7284 (p) cc_final: 0.6980 (p) REVERT: J 209 ASN cc_start: 0.5080 (OUTLIER) cc_final: 0.4743 (t0) REVERT: K 142 ARG cc_start: 0.8263 (mmp80) cc_final: 0.6890 (ttp80) REVERT: K 159 MET cc_start: 0.6592 (mmt) cc_final: 0.6344 (mmp) REVERT: M 159 MET cc_start: 0.6612 (mmt) cc_final: 0.5881 (mmm) REVERT: N 142 ARG cc_start: 0.7700 (tpp-160) cc_final: 0.7471 (tpp-160) REVERT: N 150 VAL cc_start: 0.5576 (OUTLIER) cc_final: 0.5369 (m) REVERT: N 159 MET cc_start: 0.6731 (mmt) cc_final: 0.5841 (mmm) REVERT: O 142 ARG cc_start: 0.7520 (tpp-160) cc_final: 0.7229 (tpp-160) REVERT: O 159 MET cc_start: 0.6498 (mmt) cc_final: 0.5660 (mmp) REVERT: O 180 LEU cc_start: 0.5166 (tp) cc_final: 0.4873 (mp) REVERT: P 129 GLN cc_start: 0.6356 (tm-30) cc_final: 0.6127 (tm-30) REVERT: P 159 MET cc_start: 0.5651 (mmt) cc_final: 0.5239 (mmm) REVERT: P 180 LEU cc_start: 0.5482 (tp) cc_final: 0.5115 (mp) REVERT: P 184 ARG cc_start: 0.4905 (mmm160) cc_final: 0.4668 (mmm160) REVERT: Q 180 LEU cc_start: 0.5447 (tp) cc_final: 0.4872 (mp) REVERT: R 147 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.7246 (tm) REVERT: V 147 LEU cc_start: 0.7686 (OUTLIER) cc_final: 0.7297 (tm) outliers start: 135 outliers final: 69 residues processed: 374 average time/residue: 0.2752 time to fit residues: 149.4088 Evaluate side-chains 323 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 250 time to evaluate : 1.577 ------------------------------------------------------------------------------- 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 177 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 177 THR 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 175 SER Chi-restraints excluded: chain D residue 177 THR 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 177 THR Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 146 THR Chi-restraints excluded: chain G residue 177 THR 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 177 THR Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain K residue 140 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 L residue 143 THR Chi-restraints excluded: chain L residue 155 VAL 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 197 LEU Chi-restraints excluded: chain N residue 136 LEU Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 150 VAL Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 143 THR Chi-restraints excluded: chain P residue 146 THR Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain R residue 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 197 LEU 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 146 THR 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 99 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 122 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 194 optimal weight: 0.0570 chunk 160 optimal weight: 0.0060 chunk 178 optimal weight: 0.0970 chunk 61 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 overall best weight: 0.3512 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 209 ASN J 209 ASN K 125 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5347 moved from start: 0.4558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 14762 Z= 0.162 Angle : 0.589 11.253 20152 Z= 0.261 Chirality : 0.039 0.163 2530 Planarity : 0.004 0.035 2640 Dihedral : 5.597 57.043 2140 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 6.57 % Allowed : 16.35 % Favored : 77.08 % 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: 0.87 (0.21), residues: 1958 helix: 2.66 (0.19), residues: 748 sheet: -0.63 (0.27), residues: 440 loop : -0.78 (0.26), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS P 196 PHE 0.007 0.001 PHE T 126 TYR 0.010 0.001 TYR S 132 ARG 0.005 0.000 ARG K 184 *********************** 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 371 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 267 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7286 (tm) REVERT: A 209 ASN cc_start: 0.6308 (OUTLIER) cc_final: 0.5849 (t0) REVERT: B 160 PRO cc_start: 0.6534 (Cg_endo) cc_final: 0.6011 (Cg_exo) REVERT: D 209 ASN cc_start: 0.5595 (OUTLIER) cc_final: 0.5209 (t0) REVERT: G 209 ASN cc_start: 0.5356 (OUTLIER) cc_final: 0.4484 (t0) REVERT: H 209 ASN cc_start: 0.5184 (OUTLIER) cc_final: 0.4712 (t0) REVERT: H 220 LEU cc_start: 0.7072 (mt) cc_final: 0.6831 (mt) REVERT: J 154 ARG cc_start: 0.5653 (mtm-85) cc_final: 0.4537 (mtm-85) REVERT: J 159 MET cc_start: 0.6929 (mmm) cc_final: 0.6558 (mmm) REVERT: J 177 THR cc_start: 0.7365 (p) cc_final: 0.6882 (p) REVERT: K 142 ARG cc_start: 0.8248 (mmp80) cc_final: 0.6870 (ttp80) REVERT: K 159 MET cc_start: 0.6819 (mmt) cc_final: 0.6356 (mmm) REVERT: L 159 MET cc_start: 0.6847 (mmm) cc_final: 0.6616 (mmp) REVERT: M 159 MET cc_start: 0.6724 (mmt) cc_final: 0.5726 (mmm) REVERT: N 142 ARG cc_start: 0.7734 (tpp-160) cc_final: 0.7437 (tpp-160) REVERT: N 159 MET cc_start: 0.6907 (mmt) cc_final: 0.5791 (mmp) REVERT: O 142 ARG cc_start: 0.7485 (tpp-160) cc_final: 0.7200 (tpp-160) REVERT: O 159 MET cc_start: 0.6718 (mmt) cc_final: 0.5769 (mmp) REVERT: O 180 LEU cc_start: 0.5132 (tp) cc_final: 0.4815 (mp) REVERT: O 184 ARG cc_start: 0.4033 (mmm160) cc_final: 0.3752 (mmm160) REVERT: P 140 LEU cc_start: 0.5775 (OUTLIER) cc_final: 0.5504 (mm) REVERT: P 142 ARG cc_start: 0.7670 (tpp-160) cc_final: 0.7404 (tpp80) REVERT: P 159 MET cc_start: 0.6025 (mmt) cc_final: 0.5399 (mmm) REVERT: P 180 LEU cc_start: 0.4830 (tp) cc_final: 0.4617 (mp) REVERT: Q 180 LEU cc_start: 0.5438 (tp) cc_final: 0.4897 (mp) REVERT: R 159 MET cc_start: 0.6624 (mmm) cc_final: 0.6364 (mmm) REVERT: S 147 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7362 (tm) REVERT: S 159 MET cc_start: 0.6671 (mmm) cc_final: 0.6219 (mmp) REVERT: T 147 LEU cc_start: 0.7693 (OUTLIER) cc_final: 0.7395 (tm) REVERT: V 147 LEU cc_start: 0.7418 (OUTLIER) cc_final: 0.7113 (tm) REVERT: V 159 MET cc_start: 0.7455 (tpp) cc_final: 0.5283 (mtt) outliers start: 104 outliers final: 63 residues processed: 331 average time/residue: 0.2408 time to fit residues: 117.8620 Evaluate side-chains 305 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 233 time to evaluate : 1.580 ------------------------------------------------------------------------------- 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 177 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 129 GLN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 177 THR 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 D residue 140 LEU Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 177 THR 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 175 SER Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 209 ASN Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 209 ASN Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 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 K residue 202 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 150 VAL Chi-restraints excluded: chain L residue 177 THR Chi-restraints excluded: chain L residue 209 ASN Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 143 THR 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 140 LEU Chi-restraints excluded: chain P residue 146 THR Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 147 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 177 optimal weight: 0.9980 chunk 135 optimal weight: 3.9990 chunk 93 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 85 optimal weight: 0.0070 chunk 120 optimal weight: 0.0010 chunk 180 optimal weight: 2.9990 chunk 191 optimal weight: 0.0020 chunk 94 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.3012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 129 GLN F 209 ASN G 209 ASN I 209 ASN J 222 GLN K 222 GLN N 156 HIS N 209 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5377 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14762 Z= 0.153 Angle : 0.588 12.056 20152 Z= 0.258 Chirality : 0.039 0.221 2530 Planarity : 0.003 0.034 2640 Dihedral : 5.339 58.577 2136 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 6.57 % Allowed : 17.93 % Favored : 75.51 % 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: 1.01 (0.21), residues: 1958 helix: 2.79 (0.19), residues: 748 sheet: -0.30 (0.28), residues: 396 loop : -0.86 (0.26), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 196 PHE 0.004 0.000 PHE T 126 TYR 0.010 0.001 TYR S 132 ARG 0.007 0.000 ARG K 184 *********************** 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 353 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 249 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7349 (tm) REVERT: A 209 ASN cc_start: 0.6270 (OUTLIER) cc_final: 0.4812 (t0) REVERT: B 160 PRO cc_start: 0.6628 (Cg_endo) cc_final: 0.6080 (Cg_exo) REVERT: B 209 ASN cc_start: 0.5823 (OUTLIER) cc_final: 0.5106 (t0) REVERT: D 209 ASN cc_start: 0.5823 (OUTLIER) cc_final: 0.5196 (t0) REVERT: F 209 ASN cc_start: 0.5439 (OUTLIER) cc_final: 0.4998 (t0) REVERT: G 209 ASN cc_start: 0.5434 (OUTLIER) cc_final: 0.4594 (t0) REVERT: H 140 LEU cc_start: 0.6574 (OUTLIER) cc_final: 0.6265 (tt) REVERT: I 209 ASN cc_start: 0.5218 (OUTLIER) cc_final: 0.4346 (t0) REVERT: J 154 ARG cc_start: 0.5836 (mtm-85) cc_final: 0.4862 (mtm-85) REVERT: J 159 MET cc_start: 0.6994 (mmm) cc_final: 0.6752 (mmm) REVERT: J 177 THR cc_start: 0.7575 (p) cc_final: 0.7224 (p) REVERT: K 142 ARG cc_start: 0.8240 (mmp80) cc_final: 0.7017 (ttp80) REVERT: K 222 GLN cc_start: 0.7939 (mp-120) cc_final: 0.7731 (mp10) REVERT: M 159 MET cc_start: 0.6792 (mmt) cc_final: 0.5919 (mmm) REVERT: N 142 ARG cc_start: 0.7667 (tpp-160) cc_final: 0.7372 (tpp-160) REVERT: N 159 MET cc_start: 0.7056 (mmt) cc_final: 0.5922 (mmp) REVERT: O 159 MET cc_start: 0.6801 (mmt) cc_final: 0.5836 (mmp) REVERT: O 180 LEU cc_start: 0.5418 (tp) cc_final: 0.4807 (mp) REVERT: O 184 ARG cc_start: 0.4212 (mmm160) cc_final: 0.3833 (mmm160) REVERT: P 140 LEU cc_start: 0.6226 (OUTLIER) cc_final: 0.5975 (mm) REVERT: P 142 ARG cc_start: 0.7709 (tpp-160) cc_final: 0.7418 (tpp80) REVERT: P 159 MET cc_start: 0.6265 (mmt) cc_final: 0.5635 (mmm) REVERT: P 209 ASN cc_start: 0.6322 (OUTLIER) cc_final: 0.5666 (t0) REVERT: Q 180 LEU cc_start: 0.5572 (tp) cc_final: 0.4985 (mp) REVERT: R 159 MET cc_start: 0.6850 (mmm) cc_final: 0.6551 (mmm) REVERT: S 159 MET cc_start: 0.6703 (mmm) cc_final: 0.6343 (mmp) REVERT: S 194 VAL cc_start: 0.5087 (t) cc_final: 0.4830 (t) REVERT: V 147 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7179 (tm) REVERT: V 159 MET cc_start: 0.7508 (tpp) cc_final: 0.5413 (mtt) outliers start: 104 outliers final: 74 residues processed: 318 average time/residue: 0.2427 time to fit residues: 113.7868 Evaluate side-chains 316 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 231 time to evaluate : 1.578 ------------------------------------------------------------------------------- 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 177 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 209 ASN 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 175 SER Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 209 ASN Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 147 LEU 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 I residue 176 VAL Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 209 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 209 ASN Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain N residue 140 LEU Chi-restraints excluded: chain N residue 146 THR Chi-restraints excluded: chain N residue 209 ASN Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 209 ASN Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 146 THR Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain R residue 146 THR Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 143 THR Chi-restraints excluded: chain S residue 146 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 146 THR Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 197 LEU 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 Chi-restraints excluded: chain W residue 197 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 159 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 2 optimal weight: 0.0030 chunk 142 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 97 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 196 HIS F 209 ASN G 209 ASN H 156 HIS H 209 ASN I 156 HIS I 209 ASN J 209 ASN K 125 GLN N 209 ASN S 209 ASN T 209 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5473 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14762 Z= 0.183 Angle : 0.617 10.902 20152 Z= 0.278 Chirality : 0.040 0.213 2530 Planarity : 0.004 0.036 2640 Dihedral : 5.274 59.973 2132 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 8.08 % Allowed : 17.23 % Favored : 74.68 % 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: 1.15 (0.21), residues: 1958 helix: 2.63 (0.19), residues: 748 sheet: -0.16 (0.28), residues: 440 loop : -0.53 (0.27), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS N 196 PHE 0.005 0.001 PHE K 126 TYR 0.009 0.001 TYR A 132 ARG 0.008 0.000 ARG N 184 *********************** 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 367 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 239 time to evaluate : 1.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ARG cc_start: 0.7412 (mmp80) cc_final: 0.7177 (mmt-90) REVERT: B 209 ASN cc_start: 0.6077 (OUTLIER) cc_final: 0.5428 (t0) REVERT: F 209 ASN cc_start: 0.5966 (OUTLIER) cc_final: 0.4977 (t0) REVERT: G 209 ASN cc_start: 0.5885 (OUTLIER) cc_final: 0.4780 (t0) REVERT: H 140 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6208 (tt) REVERT: H 209 ASN cc_start: 0.5769 (OUTLIER) cc_final: 0.5187 (t0) REVERT: I 140 LEU cc_start: 0.6911 (OUTLIER) cc_final: 0.6583 (tt) REVERT: I 209 ASN cc_start: 0.5656 (OUTLIER) cc_final: 0.4704 (t0) REVERT: J 140 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.6940 (mm) REVERT: J 159 MET cc_start: 0.7076 (mmm) cc_final: 0.6830 (mmm) REVERT: K 142 ARG cc_start: 0.8211 (mmp80) cc_final: 0.6974 (ttp80) REVERT: K 159 MET cc_start: 0.7116 (mmt) cc_final: 0.5918 (mmp) REVERT: K 222 GLN cc_start: 0.8162 (mp-120) cc_final: 0.7875 (mp10) REVERT: M 159 MET cc_start: 0.7015 (mmt) cc_final: 0.6081 (mmm) REVERT: N 142 ARG cc_start: 0.7800 (tpp-160) cc_final: 0.7537 (tpp-160) REVERT: N 159 MET cc_start: 0.7180 (mmt) cc_final: 0.6301 (mmm) REVERT: N 181 GLU cc_start: 0.3828 (mt-10) cc_final: 0.3594 (mt-10) REVERT: N 209 ASN cc_start: 0.5901 (OUTLIER) cc_final: 0.5583 (t0) REVERT: O 159 MET cc_start: 0.6983 (mmt) cc_final: 0.6266 (mmm) REVERT: O 180 LEU cc_start: 0.5575 (tp) cc_final: 0.4883 (mp) REVERT: O 184 ARG cc_start: 0.4105 (mmm160) cc_final: 0.3713 (mmm160) REVERT: P 129 GLN cc_start: 0.6626 (tm-30) cc_final: 0.6396 (tm-30) REVERT: P 140 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.6109 (mm) REVERT: P 142 ARG cc_start: 0.7702 (tpp-160) cc_final: 0.7397 (tpp80) REVERT: P 159 MET cc_start: 0.6897 (mmt) cc_final: 0.6025 (mmm) REVERT: P 209 ASN cc_start: 0.6511 (OUTLIER) cc_final: 0.5853 (t0) REVERT: R 159 MET cc_start: 0.7245 (mmm) cc_final: 0.6977 (mmm) REVERT: S 159 MET cc_start: 0.6983 (mmm) cc_final: 0.6673 (mmp) REVERT: V 147 LEU cc_start: 0.7433 (OUTLIER) cc_final: 0.7187 (tm) REVERT: W 209 ASN cc_start: 0.6302 (OUTLIER) cc_final: 0.5378 (m-40) outliers start: 128 outliers final: 86 residues processed: 323 average time/residue: 0.2326 time to fit residues: 112.5471 Evaluate side-chains 320 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 221 time to evaluate : 1.490 ------------------------------------------------------------------------------- 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 177 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain C residue 146 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 177 THR 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 175 SER Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 209 ASN Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 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 178 VAL Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 209 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 155 VAL Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 197 LEU Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 209 ASN Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 143 THR 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 209 ASN 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 140 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 143 THR Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 125 GLN Chi-restraints excluded: chain S residue 143 THR Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain 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 146 THR Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 197 LEU Chi-restraints excluded: chain W residue 209 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 64 optimal weight: 0.7980 chunk 172 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 112 optimal weight: 2.9990 chunk 47 optimal weight: 0.0770 chunk 191 optimal weight: 0.5980 chunk 159 optimal weight: 0.9990 chunk 88 optimal weight: 0.0270 chunk 15 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 ASN F 209 ASN G 209 ASN H 209 ASN I 209 ASN N 209 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5484 moved from start: 0.5855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14762 Z= 0.156 Angle : 0.606 11.721 20152 Z= 0.266 Chirality : 0.040 0.207 2530 Planarity : 0.003 0.026 2640 Dihedral : 5.201 59.900 2132 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 7.45 % Allowed : 18.50 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.13 (0.21), residues: 1958 helix: 2.68 (0.19), residues: 748 sheet: 0.04 (0.29), residues: 396 loop : -0.75 (0.26), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS N 196 PHE 0.003 0.000 PHE K 126 TYR 0.008 0.001 TYR T 132 ARG 0.007 0.000 ARG N 184 *********************** 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 350 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 232 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 147 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7413 (tm) REVERT: A 209 ASN cc_start: 0.6215 (OUTLIER) cc_final: 0.4744 (t0) REVERT: D 159 MET cc_start: 0.7504 (tpp) cc_final: 0.6815 (mmm) REVERT: F 209 ASN cc_start: 0.5480 (OUTLIER) cc_final: 0.4415 (t0) REVERT: G 209 ASN cc_start: 0.6012 (OUTLIER) cc_final: 0.5181 (t0) REVERT: H 140 LEU cc_start: 0.6577 (OUTLIER) cc_final: 0.6284 (tt) REVERT: H 159 MET cc_start: 0.6383 (mmm) cc_final: 0.5857 (mmm) REVERT: H 209 ASN cc_start: 0.5784 (OUTLIER) cc_final: 0.5072 (t0) REVERT: I 140 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6586 (tt) REVERT: I 209 ASN cc_start: 0.4736 (OUTLIER) cc_final: 0.3745 (t0) REVERT: J 140 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6951 (mm) REVERT: J 154 ARG cc_start: 0.6116 (mtm-85) cc_final: 0.5198 (mtm-85) REVERT: J 159 MET cc_start: 0.6989 (mmm) cc_final: 0.6725 (mmm) REVERT: K 142 ARG cc_start: 0.8195 (mmp80) cc_final: 0.6954 (ttp80) REVERT: K 159 MET cc_start: 0.7156 (mmt) cc_final: 0.6130 (mmp) REVERT: K 222 GLN cc_start: 0.8058 (mp-120) cc_final: 0.7822 (mp10) REVERT: L 180 LEU cc_start: 0.4797 (tt) cc_final: 0.4463 (mt) REVERT: M 159 MET cc_start: 0.7063 (mmt) cc_final: 0.6122 (mmm) REVERT: N 159 MET cc_start: 0.7232 (mmt) cc_final: 0.6341 (mmm) REVERT: O 159 MET cc_start: 0.7042 (mmt) cc_final: 0.6315 (mmm) REVERT: O 180 LEU cc_start: 0.5573 (tp) cc_final: 0.4875 (mp) REVERT: O 184 ARG cc_start: 0.4181 (mmm160) cc_final: 0.3862 (mmm160) REVERT: O 209 ASN cc_start: 0.6034 (OUTLIER) cc_final: 0.5451 (m-40) REVERT: P 129 GLN cc_start: 0.6629 (tm-30) cc_final: 0.6426 (tm-30) REVERT: P 140 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.6133 (mm) REVERT: P 159 MET cc_start: 0.6957 (mmt) cc_final: 0.6062 (mmm) REVERT: P 209 ASN cc_start: 0.6527 (OUTLIER) cc_final: 0.5920 (t0) REVERT: Q 181 GLU cc_start: 0.3661 (tp30) cc_final: 0.3452 (pt0) REVERT: R 159 MET cc_start: 0.7279 (mmm) cc_final: 0.6980 (mmm) REVERT: S 159 MET cc_start: 0.7041 (mmm) cc_final: 0.6759 (mmp) REVERT: W 209 ASN cc_start: 0.6259 (OUTLIER) cc_final: 0.5318 (t0) outliers start: 118 outliers final: 85 residues processed: 315 average time/residue: 0.2318 time to fit residues: 110.2701 Evaluate side-chains 317 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 219 time to evaluate : 1.462 ------------------------------------------------------------------------------- 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 177 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 209 ASN 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 F residue 142 ARG Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain G residue 147 LEU 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 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 I residue 209 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 197 LEU Chi-restraints excluded: chain J residue 202 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 146 THR 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 209 ASN 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 O residue 209 ASN Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 146 THR Chi-restraints excluded: chain P residue 150 VAL 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 143 THR Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 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 155 VAL Chi-restraints excluded: chain T residue 197 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 Chi-restraints excluded: chain W residue 197 LEU Chi-restraints excluded: chain W residue 209 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 184 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 139 optimal weight: 0.4980 chunk 108 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 106 optimal weight: 0.0980 chunk 190 optimal weight: 1.9990 chunk 119 optimal weight: 2.9990 chunk 116 optimal weight: 0.0030 chunk 88 optimal weight: 0.6980 overall best weight: 0.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 209 ASN F 209 ASN G 209 ASN H 209 ASN I 209 ASN ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 209 ASN N 209 ASN T 209 ASN V 209 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5501 moved from start: 0.6083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14762 Z= 0.157 Angle : 0.610 11.961 20152 Z= 0.265 Chirality : 0.040 0.230 2530 Planarity : 0.003 0.030 2640 Dihedral : 5.071 59.762 2130 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 7.58 % Allowed : 18.50 % Favored : 73.93 % 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: 1.23 (0.21), residues: 1958 helix: 2.70 (0.19), residues: 748 sheet: 0.28 (0.29), residues: 396 loop : -0.72 (0.26), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 196 PHE 0.003 0.001 PHE K 126 TYR 0.007 0.001 TYR T 132 ARG 0.008 0.000 ARG N 184 *********************** 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 350 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 230 time to evaluate : 1.613 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASN cc_start: 0.6223 (OUTLIER) cc_final: 0.4777 (t0) REVERT: D 159 MET cc_start: 0.7638 (tpp) cc_final: 0.7021 (mmm) REVERT: F 209 ASN cc_start: 0.5807 (OUTLIER) cc_final: 0.4862 (t0) REVERT: G 209 ASN cc_start: 0.5668 (OUTLIER) cc_final: 0.5379 (t0) REVERT: H 140 LEU cc_start: 0.6570 (OUTLIER) cc_final: 0.6282 (tt) REVERT: H 159 MET cc_start: 0.6723 (mmm) cc_final: 0.6259 (mmm) REVERT: H 209 ASN cc_start: 0.5744 (OUTLIER) cc_final: 0.5049 (t0) REVERT: I 140 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6582 (tt) REVERT: I 209 ASN cc_start: 0.5059 (OUTLIER) cc_final: 0.4289 (t0) REVERT: J 140 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6960 (mm) REVERT: J 154 ARG cc_start: 0.6120 (mtm-85) cc_final: 0.5174 (mtm-85) REVERT: J 159 MET cc_start: 0.7015 (mmm) cc_final: 0.6769 (mmm) REVERT: J 209 ASN cc_start: 0.5067 (OUTLIER) cc_final: 0.4284 (t0) REVERT: K 142 ARG cc_start: 0.8195 (mmp80) cc_final: 0.6977 (ttp80) REVERT: K 159 MET cc_start: 0.7076 (mmt) cc_final: 0.6120 (mmp) REVERT: L 180 LEU cc_start: 0.4755 (tt) cc_final: 0.4435 (mt) REVERT: L 209 ASN cc_start: 0.5922 (OUTLIER) cc_final: 0.5659 (t0) REVERT: M 159 MET cc_start: 0.7101 (mmt) cc_final: 0.6168 (mmm) REVERT: N 159 MET cc_start: 0.7277 (mmt) cc_final: 0.6374 (mmm) REVERT: O 159 MET cc_start: 0.7084 (mmt) cc_final: 0.6342 (mmm) REVERT: O 180 LEU cc_start: 0.5499 (tp) cc_final: 0.4832 (mp) REVERT: O 184 ARG cc_start: 0.4129 (mmm160) cc_final: 0.3821 (mmm160) REVERT: O 209 ASN cc_start: 0.6097 (OUTLIER) cc_final: 0.5472 (m-40) REVERT: P 140 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6164 (mm) REVERT: P 159 MET cc_start: 0.7013 (mmt) cc_final: 0.6251 (mmm) REVERT: P 209 ASN cc_start: 0.6560 (OUTLIER) cc_final: 0.5981 (t0) REVERT: Q 129 GLN cc_start: 0.6712 (tp-100) cc_final: 0.5483 (mm-40) REVERT: Q 180 LEU cc_start: 0.5100 (tp) cc_final: 0.4664 (mp) REVERT: R 159 MET cc_start: 0.7388 (mmm) cc_final: 0.7146 (mmm) REVERT: R 209 ASN cc_start: 0.6283 (OUTLIER) cc_final: 0.5687 (m-40) REVERT: S 159 MET cc_start: 0.7107 (mmm) cc_final: 0.6834 (mmp) REVERT: W 209 ASN cc_start: 0.6302 (OUTLIER) cc_final: 0.5896 (t0) outliers start: 120 outliers final: 90 residues processed: 316 average time/residue: 0.2253 time to fit residues: 109.2655 Evaluate side-chains 324 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 219 time to evaluate : 1.836 ------------------------------------------------------------------------------- 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 177 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 209 ASN 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 F residue 142 ARG Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 147 LEU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 209 ASN Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 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 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 J residue 202 VAL Chi-restraints excluded: chain J residue 209 ASN Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 209 ASN Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 146 THR 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 209 ASN Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 209 ASN Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 146 THR Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 150 VAL 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 143 THR Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 209 ASN Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 143 THR Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain T residue 209 ASN 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 Chi-restraints excluded: chain W residue 197 LEU Chi-restraints excluded: chain W residue 209 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 118 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 113 optimal weight: 0.3980 chunk 57 optimal weight: 0.4980 chunk 37 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 121 optimal weight: 0.6980 chunk 130 optimal weight: 0.0970 chunk 94 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 150 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 209 ASN G 209 ASN H 209 ASN I 209 ASN N 209 ASN Q 209 ASN T 209 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5523 moved from start: 0.6297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 14762 Z= 0.167 Angle : 0.629 11.977 20152 Z= 0.274 Chirality : 0.040 0.233 2530 Planarity : 0.003 0.034 2640 Dihedral : 5.103 59.608 2130 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 7.45 % Allowed : 18.94 % Favored : 73.61 % 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: 1.23 (0.22), residues: 1958 helix: 2.67 (0.19), residues: 748 sheet: 0.36 (0.29), residues: 396 loop : -0.74 (0.26), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS N 196 PHE 0.003 0.001 PHE J 126 TYR 0.010 0.001 TYR T 132 ARG 0.008 0.000 ARG M 184 *********************** 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 348 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 230 time to evaluate : 1.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASN cc_start: 0.6253 (OUTLIER) cc_final: 0.4812 (t0) REVERT: D 159 MET cc_start: 0.7659 (tpp) cc_final: 0.7088 (mmm) REVERT: E 159 MET cc_start: 0.7561 (mmm) cc_final: 0.7106 (mmm) REVERT: F 209 ASN cc_start: 0.5467 (OUTLIER) cc_final: 0.4523 (t0) REVERT: G 209 ASN cc_start: 0.5575 (OUTLIER) cc_final: 0.5153 (t0) REVERT: H 140 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6284 (tt) REVERT: H 209 ASN cc_start: 0.5595 (OUTLIER) cc_final: 0.4919 (t0) REVERT: I 140 LEU cc_start: 0.6901 (OUTLIER) cc_final: 0.6592 (tt) REVERT: I 209 ASN cc_start: 0.5431 (OUTLIER) cc_final: 0.4623 (t0) REVERT: J 140 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.7039 (mm) REVERT: J 154 ARG cc_start: 0.6119 (mtm-85) cc_final: 0.5255 (mtm-85) REVERT: J 159 MET cc_start: 0.7142 (mmm) cc_final: 0.6937 (mmm) REVERT: K 142 ARG cc_start: 0.8087 (mmp80) cc_final: 0.6926 (ttp80) REVERT: K 159 MET cc_start: 0.7092 (mmt) cc_final: 0.6150 (mmp) REVERT: K 222 GLN cc_start: 0.7913 (mp-120) cc_final: 0.7684 (mp10) REVERT: L 180 LEU cc_start: 0.4727 (tt) cc_final: 0.4418 (mt) REVERT: L 209 ASN cc_start: 0.5902 (OUTLIER) cc_final: 0.5587 (t0) REVERT: L 222 GLN cc_start: 0.8056 (mp-120) cc_final: 0.7586 (mp10) REVERT: M 159 MET cc_start: 0.7145 (mmt) cc_final: 0.6204 (mmm) REVERT: N 159 MET cc_start: 0.7405 (mmt) cc_final: 0.6528 (mmm) REVERT: O 159 MET cc_start: 0.7118 (mmt) cc_final: 0.6405 (mmm) REVERT: O 180 LEU cc_start: 0.5518 (tp) cc_final: 0.4902 (mp) REVERT: O 184 ARG cc_start: 0.4092 (mmm160) cc_final: 0.3789 (mmm160) REVERT: O 209 ASN cc_start: 0.6050 (OUTLIER) cc_final: 0.5398 (m-40) REVERT: P 140 LEU cc_start: 0.6542 (OUTLIER) cc_final: 0.6224 (mm) REVERT: P 159 MET cc_start: 0.7068 (mmt) cc_final: 0.6301 (mmm) REVERT: P 209 ASN cc_start: 0.6514 (OUTLIER) cc_final: 0.5957 (t0) REVERT: R 159 MET cc_start: 0.7447 (mmm) cc_final: 0.7204 (mmm) REVERT: R 209 ASN cc_start: 0.6318 (OUTLIER) cc_final: 0.5728 (m-40) REVERT: W 159 MET cc_start: 0.7429 (tpp) cc_final: 0.6786 (mmm) REVERT: W 209 ASN cc_start: 0.6301 (OUTLIER) cc_final: 0.5929 (t0) outliers start: 118 outliers final: 88 residues processed: 316 average time/residue: 0.2163 time to fit residues: 104.5746 Evaluate side-chains 324 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 222 time to evaluate : 1.647 ------------------------------------------------------------------------------- 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 177 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain F residue 213 VAL Chi-restraints excluded: chain G residue 140 LEU 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 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 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 J residue 202 VAL Chi-restraints excluded: chain K residue 140 LEU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 146 THR Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 209 ASN Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 155 VAL Chi-restraints excluded: chain M residue 177 THR Chi-restraints excluded: chain M residue 180 LEU Chi-restraints excluded: chain M residue 197 LEU Chi-restraints excluded: chain M residue 202 VAL Chi-restraints excluded: chain N residue 143 THR Chi-restraints excluded: chain N residue 209 ASN Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 209 ASN Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 146 THR Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 150 VAL 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 143 THR Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 197 LEU Chi-restraints excluded: chain R residue 209 ASN Chi-restraints excluded: chain R residue 220 LEU Chi-restraints excluded: chain S residue 125 GLN Chi-restraints excluded: chain S residue 143 THR Chi-restraints excluded: chain S residue 147 LEU Chi-restraints excluded: chain S residue 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain T residue 209 ASN 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 Chi-restraints excluded: chain W residue 197 LEU Chi-restraints excluded: chain W residue 209 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 173 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 166 optimal weight: 0.1980 chunk 177 optimal weight: 0.9990 chunk 107 optimal weight: 0.9990 chunk 77 optimal weight: 0.1980 chunk 139 optimal weight: 0.3980 chunk 54 optimal weight: 0.9980 chunk 160 optimal weight: 0.9980 chunk 168 optimal weight: 0.7980 chunk 116 optimal weight: 0.0470 overall best weight: 0.3278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 ASN ** D 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 ASN G 209 ASN H 209 ASN I 209 ASN J 209 ASN M 156 HIS N 209 ASN T 209 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5520 moved from start: 0.6451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 14762 Z= 0.153 Angle : 0.630 12.055 20152 Z= 0.271 Chirality : 0.040 0.244 2530 Planarity : 0.003 0.036 2640 Dihedral : 4.900 55.429 2128 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 6.88 % Allowed : 19.89 % Favored : 73.23 % 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: 1.38 (0.22), residues: 1958 helix: 2.74 (0.19), residues: 748 sheet: 0.57 (0.30), residues: 396 loop : -0.68 (0.26), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 196 PHE 0.003 0.001 PHE D 126 TYR 0.008 0.001 TYR T 132 ARG 0.008 0.000 ARG N 184 *********************** 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 341 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 232 time to evaluate : 1.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASN cc_start: 0.6227 (OUTLIER) cc_final: 0.4790 (t0) REVERT: B 209 ASN cc_start: 0.5656 (OUTLIER) cc_final: 0.4592 (t0) REVERT: D 159 MET cc_start: 0.7598 (tpp) cc_final: 0.7122 (mmm) REVERT: E 159 MET cc_start: 0.7697 (mmm) cc_final: 0.7230 (mmm) REVERT: F 209 ASN cc_start: 0.5461 (OUTLIER) cc_final: 0.4663 (t0) REVERT: G 209 ASN cc_start: 0.5972 (OUTLIER) cc_final: 0.5294 (t0) REVERT: H 140 LEU cc_start: 0.6550 (OUTLIER) cc_final: 0.6257 (tt) REVERT: H 159 MET cc_start: 0.7635 (mmm) cc_final: 0.6597 (mmm) REVERT: H 209 ASN cc_start: 0.5686 (OUTLIER) cc_final: 0.5338 (t0) REVERT: I 140 LEU cc_start: 0.6881 (OUTLIER) cc_final: 0.6585 (tt) REVERT: I 209 ASN cc_start: 0.5266 (OUTLIER) cc_final: 0.4496 (t0) REVERT: J 140 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.7045 (mm) REVERT: J 159 MET cc_start: 0.7926 (mmm) cc_final: 0.7551 (mmm) REVERT: J 209 ASN cc_start: 0.5332 (OUTLIER) cc_final: 0.4598 (t0) REVERT: K 142 ARG cc_start: 0.8066 (mmp80) cc_final: 0.6921 (ttp80) REVERT: K 159 MET cc_start: 0.7077 (mmt) cc_final: 0.6162 (mmp) REVERT: K 180 LEU cc_start: 0.4962 (tp) cc_final: 0.4726 (mp) REVERT: K 222 GLN cc_start: 0.7855 (mp-120) cc_final: 0.7652 (mp10) REVERT: L 180 LEU cc_start: 0.4695 (tt) cc_final: 0.4403 (mt) REVERT: L 209 ASN cc_start: 0.5854 (OUTLIER) cc_final: 0.5563 (t0) REVERT: L 222 GLN cc_start: 0.8042 (mp-120) cc_final: 0.7550 (mp10) REVERT: M 159 MET cc_start: 0.7154 (mmt) cc_final: 0.6219 (mmm) REVERT: N 159 MET cc_start: 0.7415 (mmt) cc_final: 0.6539 (mmm) REVERT: O 159 MET cc_start: 0.7125 (mmt) cc_final: 0.6417 (mmm) REVERT: O 180 LEU cc_start: 0.5503 (tp) cc_final: 0.4906 (mp) REVERT: O 184 ARG cc_start: 0.4016 (mmm160) cc_final: 0.3724 (mmm160) REVERT: O 209 ASN cc_start: 0.6308 (OUTLIER) cc_final: 0.5619 (m-40) REVERT: P 140 LEU cc_start: 0.6553 (OUTLIER) cc_final: 0.6238 (mm) REVERT: P 159 MET cc_start: 0.7080 (mmt) cc_final: 0.6311 (mmm) REVERT: P 209 ASN cc_start: 0.6510 (OUTLIER) cc_final: 0.5978 (t0) REVERT: Q 129 GLN cc_start: 0.6713 (tp-100) cc_final: 0.5653 (mm110) REVERT: R 209 ASN cc_start: 0.6258 (OUTLIER) cc_final: 0.5666 (m-40) REVERT: S 159 MET cc_start: 0.7281 (mmm) cc_final: 0.6725 (mmp) REVERT: W 159 MET cc_start: 0.7393 (tpp) cc_final: 0.6870 (mmm) REVERT: W 209 ASN cc_start: 0.6214 (OUTLIER) cc_final: 0.5949 (t0) outliers start: 109 outliers final: 86 residues processed: 318 average time/residue: 0.2220 time to fit residues: 107.4943 Evaluate side-chains 328 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 226 time to evaluate : 1.557 ------------------------------------------------------------------------------- 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 177 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain B residue 209 ASN Chi-restraints excluded: chain B residue 221 THR 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 175 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 175 SER Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain F residue 142 ARG Chi-restraints excluded: chain F residue 146 THR Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 209 ASN Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 197 LEU Chi-restraints excluded: chain G residue 209 ASN Chi-restraints excluded: chain H residue 140 LEU Chi-restraints excluded: chain H residue 175 SER Chi-restraints excluded: chain H residue 176 VAL Chi-restraints excluded: chain H residue 209 ASN Chi-restraints excluded: chain I residue 140 LEU Chi-restraints excluded: chain I residue 143 THR Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 209 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 176 VAL 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 146 THR Chi-restraints excluded: chain K residue 147 LEU Chi-restraints excluded: chain K residue 176 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain L residue 143 THR Chi-restraints excluded: chain L residue 176 VAL Chi-restraints excluded: chain L residue 209 ASN Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 143 THR Chi-restraints excluded: chain M residue 146 THR Chi-restraints excluded: chain M residue 155 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 209 ASN Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain O residue 209 ASN Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 146 THR Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain P residue 155 VAL Chi-restraints excluded: chain P residue 209 ASN Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 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 155 VAL Chi-restraints excluded: chain S residue 197 LEU Chi-restraints excluded: chain S residue 220 LEU Chi-restraints excluded: chain T residue 155 VAL Chi-restraints excluded: chain T residue 197 LEU Chi-restraints excluded: chain V residue 155 VAL Chi-restraints excluded: chain V residue 177 THR Chi-restraints excluded: chain V residue 197 LEU Chi-restraints excluded: chain V residue 209 ASN Chi-restraints excluded: chain V residue 220 LEU Chi-restraints excluded: chain W residue 147 LEU Chi-restraints excluded: chain W residue 197 LEU Chi-restraints excluded: chain W residue 209 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 188 optimal weight: 0.0070 chunk 114 optimal weight: 0.9990 chunk 89 optimal weight: 3.9990 chunk 130 optimal weight: 0.0370 chunk 197 optimal weight: 0.8980 chunk 181 optimal weight: 1.9990 chunk 157 optimal weight: 0.9980 chunk 16 optimal weight: 0.0040 chunk 121 optimal weight: 0.0870 chunk 96 optimal weight: 0.0070 chunk 124 optimal weight: 0.5980 overall best weight: 0.0284 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 209 ASN D 125 GLN F 209 ASN H 209 ASN I 209 ASN N 196 HIS N 209 ASN T 129 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5481 moved from start: 0.6510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14762 Z= 0.144 Angle : 0.640 12.667 20152 Z= 0.273 Chirality : 0.040 0.253 2530 Planarity : 0.003 0.039 2640 Dihedral : 4.782 56.252 2128 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 5.56 % Allowed : 21.15 % Favored : 73.30 % 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: 1.68 (0.22), residues: 1958 helix: 2.90 (0.19), residues: 748 sheet: 0.92 (0.30), residues: 396 loop : -0.52 (0.27), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 196 PHE 0.003 0.000 PHE S 126 TYR 0.007 0.000 TYR T 132 ARG 0.009 0.000 ARG N 184 ********************** 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 321 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 233 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 ASN cc_start: 0.6136 (OUTLIER) cc_final: 0.4737 (t0) REVERT: D 159 MET cc_start: 0.7434 (tpp) cc_final: 0.7105 (mmm) REVERT: E 159 MET cc_start: 0.7587 (mmm) cc_final: 0.7076 (mmm) REVERT: F 209 ASN cc_start: 0.5709 (OUTLIER) cc_final: 0.5172 (t0) REVERT: H 140 LEU cc_start: 0.6446 (OUTLIER) cc_final: 0.6227 (tt) REVERT: H 154 ARG cc_start: 0.6257 (mtm-85) cc_final: 0.5718 (mtm-85) REVERT: H 159 MET cc_start: 0.7731 (mmm) cc_final: 0.6760 (mmm) REVERT: I 209 ASN cc_start: 0.4877 (OUTLIER) cc_final: 0.4389 (t0) REVERT: J 140 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.7126 (mm) REVERT: J 154 ARG cc_start: 0.6175 (mtm-85) cc_final: 0.4880 (mtm-85) REVERT: J 159 MET cc_start: 0.7893 (mmm) cc_final: 0.7522 (mmm) REVERT: K 142 ARG cc_start: 0.8041 (mmp80) cc_final: 0.6928 (ttp80) REVERT: K 159 MET cc_start: 0.7151 (mmt) cc_final: 0.6231 (mmp) REVERT: K 180 LEU cc_start: 0.4943 (tp) cc_final: 0.4713 (mp) REVERT: L 140 LEU cc_start: 0.7241 (OUTLIER) cc_final: 0.6791 (mm) REVERT: L 180 LEU cc_start: 0.4636 (tt) cc_final: 0.4385 (mt) REVERT: M 159 MET cc_start: 0.7125 (mmt) cc_final: 0.6319 (mmm) REVERT: N 159 MET cc_start: 0.7375 (mmt) cc_final: 0.6511 (mmm) REVERT: N 209 ASN cc_start: 0.5310 (OUTLIER) cc_final: 0.4146 (t0) REVERT: O 159 MET cc_start: 0.7093 (mmt) cc_final: 0.6361 (mmm) REVERT: O 180 LEU cc_start: 0.5585 (tp) cc_final: 0.4950 (mp) REVERT: O 184 ARG cc_start: 0.3998 (mmm160) cc_final: 0.3797 (mmm160) REVERT: P 140 LEU cc_start: 0.6696 (OUTLIER) cc_final: 0.6336 (mm) REVERT: P 159 MET cc_start: 0.7042 (mmt) cc_final: 0.6294 (mmm) REVERT: Q 129 GLN cc_start: 0.6720 (tp-100) cc_final: 0.5625 (mm110) REVERT: S 159 MET cc_start: 0.7328 (mmm) cc_final: 0.6801 (mmp) REVERT: W 159 MET cc_start: 0.7370 (tpp) cc_final: 0.6856 (mmm) REVERT: W 209 ASN cc_start: 0.6262 (OUTLIER) cc_final: 0.5910 (t0) outliers start: 88 outliers final: 67 residues processed: 295 average time/residue: 0.2255 time to fit residues: 100.6909 Evaluate side-chains 301 residues out of total 1672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 225 time to evaluate : 1.507 ------------------------------------------------------------------------------- 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 177 THR Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 175 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 140 LEU Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain F residue 146 THR 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 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 176 VAL Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 176 VAL Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 209 ASN Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain J residue 176 VAL Chi-restraints excluded: chain J residue 197 LEU 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 176 VAL Chi-restraints excluded: chain K residue 202 VAL Chi-restraints excluded: chain L residue 140 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 155 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 209 ASN Chi-restraints excluded: chain O residue 140 LEU Chi-restraints excluded: chain O residue 155 VAL Chi-restraints excluded: chain O residue 197 LEU Chi-restraints excluded: chain P residue 140 LEU Chi-restraints excluded: chain P residue 147 LEU Chi-restraints excluded: chain Q residue 140 LEU Chi-restraints excluded: chain Q residue 155 VAL Chi-restraints excluded: chain Q residue 197 LEU Chi-restraints excluded: chain R residue 147 LEU Chi-restraints excluded: chain R residue 155 VAL Chi-restraints excluded: chain R residue 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 T residue 197 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 209 ASN Chi-restraints excluded: chain V residue 220 LEU Chi-restraints excluded: chain W residue 197 LEU Chi-restraints excluded: chain W residue 209 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 198 random chunks: chunk 167 optimal weight: 0.0000 chunk 48 optimal weight: 0.8980 chunk 144 optimal weight: 0.9980 chunk 23 optimal weight: 0.2980 chunk 43 optimal weight: 0.0770 chunk 157 optimal weight: 0.9990 chunk 65 optimal weight: 0.0000 chunk 161 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 overall best weight: 0.2546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 125 GLN ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 209 ASN W 156 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5751 r_free = 0.5751 target = 0.313116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.5698 r_free = 0.5698 target = 0.301933 restraints weight = 18237.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.5717 r_free = 0.5717 target = 0.304451 restraints weight = 12617.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.5733 r_free = 0.5733 target = 0.306256 restraints weight = 9197.001| |-----------------------------------------------------------------------------| r_work (final): 0.5720 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5601 moved from start: 0.6627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 14762 Z= 0.156 Angle : 0.645 12.812 20152 Z= 0.275 Chirality : 0.040 0.252 2530 Planarity : 0.003 0.038 2640 Dihedral : 4.641 56.570 2126 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 5.11 % Allowed : 21.72 % Favored : 73.17 % 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: 1.70 (0.22), residues: 1958 helix: 2.91 (0.19), residues: 748 sheet: 0.93 (0.30), residues: 396 loop : -0.50 (0.27), residues: 814 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS W 156 PHE 0.009 0.001 PHE D 126 TYR 0.010 0.001 TYR V 132 ARG 0.009 0.000 ARG N 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3226.30 seconds wall clock time: 58 minutes 46.11 seconds (3526.11 seconds total)