Starting phenix.real_space_refine on Sun Jun 7 00:00:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ezj_3999/06_2026/6ezj_3999.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ezj_3999/06_2026/6ezj_3999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ezj_3999/06_2026/6ezj_3999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ezj_3999/06_2026/6ezj_3999.map" model { file = "/net/cci-nas-00/data/ceres_data/6ezj_3999/06_2026/6ezj_3999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ezj_3999/06_2026/6ezj_3999.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.050 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: 6 Type Number sf(0) Gaussians Mn 48 7.51 5 P 24 5.49 5 S 48 5.16 5 C 20976 2.51 5 N 6336 2.21 5 O 6168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33600 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "B" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "D" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "E" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "F" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "G" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "H" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "I" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "J" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "K" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "L" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "M" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "N" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "O" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "P" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "Q" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "R" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "S" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "T" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "U" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "V" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "W" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "X" Number of atoms: 1385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1385 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 179} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "U" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "X" Number of atoms: 15 Number of conformers: 1 Conformer: "B" Number of residues, atoms: 3, 15 Unusual residues: {' MN': 2, '5LD': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 8.34, per 1000 atoms: 0.25 Number of scatterers: 33600 At special positions: 0 Unit cell: (125.775, 125.775, 125.775, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Mn 48 24.99 S 48 16.00 P 24 15.00 O 6168 8.00 N 6336 7.00 C 20976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.70 Conformation dependent library (CDL) restraints added in 1.4 seconds 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8064 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 48 sheets defined 35.7% alpha, 23.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 42 through 50 removed outlier: 4.048A pdb=" N ASP A 46 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 55 Processing helix chain 'A' and resid 73 through 91 removed outlier: 3.588A pdb=" N ASP A 78 " --> pdb=" O HIS A 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL A 79 " --> pdb=" O THR A 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 84 " --> pdb=" O ALA A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 155 removed outlier: 3.787A pdb=" N THR A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 184 removed outlier: 3.728A pdb=" N ALA A 180 " --> pdb=" O PHE A 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 removed outlier: 4.048A pdb=" N ASP B 46 " --> pdb=" O ILE B 42 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS B 47 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 55 Processing helix chain 'B' and resid 73 through 91 removed outlier: 3.587A pdb=" N ASP B 78 " --> pdb=" O HIS B 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL B 79 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 84 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 155 removed outlier: 3.787A pdb=" N THR B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 184 removed outlier: 3.729A pdb=" N ALA B 180 " --> pdb=" O PHE B 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 50 removed outlier: 4.047A pdb=" N ASP C 46 " --> pdb=" O ILE C 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS C 47 " --> pdb=" O PRO C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 50 through 55 Processing helix chain 'C' and resid 73 through 91 removed outlier: 3.587A pdb=" N ASP C 78 " --> pdb=" O HIS C 74 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL C 79 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 155 removed outlier: 3.787A pdb=" N THR C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 184 removed outlier: 3.727A pdb=" N ALA C 180 " --> pdb=" O PHE C 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 50 removed outlier: 4.047A pdb=" N ASP D 46 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS D 47 " --> pdb=" O PRO D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 55 Processing helix chain 'D' and resid 73 through 91 removed outlier: 3.587A pdb=" N ASP D 78 " --> pdb=" O HIS D 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL D 79 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 155 removed outlier: 3.786A pdb=" N THR D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 184 removed outlier: 3.728A pdb=" N ALA D 180 " --> pdb=" O PHE D 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 50 removed outlier: 4.048A pdb=" N ASP E 46 " --> pdb=" O ILE E 42 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS E 47 " --> pdb=" O PRO E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 55 Processing helix chain 'E' and resid 73 through 91 removed outlier: 3.587A pdb=" N ASP E 78 " --> pdb=" O HIS E 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL E 79 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY E 84 " --> pdb=" O ALA E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 155 removed outlier: 3.786A pdb=" N THR E 153 " --> pdb=" O SER E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 184 removed outlier: 3.729A pdb=" N ALA E 180 " --> pdb=" O PHE E 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 50 removed outlier: 4.048A pdb=" N ASP F 46 " --> pdb=" O ILE F 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS F 47 " --> pdb=" O PRO F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 50 through 55 Processing helix chain 'F' and resid 73 through 91 removed outlier: 3.587A pdb=" N ASP F 78 " --> pdb=" O HIS F 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL F 79 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY F 84 " --> pdb=" O ALA F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 155 removed outlier: 3.787A pdb=" N THR F 153 " --> pdb=" O SER F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 184 removed outlier: 3.729A pdb=" N ALA F 180 " --> pdb=" O PHE F 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 50 removed outlier: 4.048A pdb=" N ASP G 46 " --> pdb=" O ILE G 42 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS G 47 " --> pdb=" O PRO G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 50 through 55 Processing helix chain 'G' and resid 73 through 91 removed outlier: 3.587A pdb=" N ASP G 78 " --> pdb=" O HIS G 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL G 79 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY G 84 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 155 removed outlier: 3.788A pdb=" N THR G 153 " --> pdb=" O SER G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 167 through 184 removed outlier: 3.729A pdb=" N ALA G 180 " --> pdb=" O PHE G 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 50 removed outlier: 4.047A pdb=" N ASP H 46 " --> pdb=" O ILE H 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS H 47 " --> pdb=" O PRO H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 55 Processing helix chain 'H' and resid 73 through 91 removed outlier: 3.586A pdb=" N ASP H 78 " --> pdb=" O HIS H 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL H 79 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY H 84 " --> pdb=" O ALA H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 155 removed outlier: 3.788A pdb=" N THR H 153 " --> pdb=" O SER H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 167 through 184 removed outlier: 3.729A pdb=" N ALA H 180 " --> pdb=" O PHE H 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 50 removed outlier: 4.048A pdb=" N ASP I 46 " --> pdb=" O ILE I 42 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS I 47 " --> pdb=" O PRO I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 50 through 55 Processing helix chain 'I' and resid 73 through 91 removed outlier: 3.586A pdb=" N ASP I 78 " --> pdb=" O HIS I 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL I 79 " --> pdb=" O THR I 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY I 84 " --> pdb=" O ALA I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 155 removed outlier: 3.787A pdb=" N THR I 153 " --> pdb=" O SER I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 184 removed outlier: 3.729A pdb=" N ALA I 180 " --> pdb=" O PHE I 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 50 removed outlier: 4.047A pdb=" N ASP J 46 " --> pdb=" O ILE J 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS J 47 " --> pdb=" O PRO J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 50 through 55 Processing helix chain 'J' and resid 73 through 91 removed outlier: 3.587A pdb=" N ASP J 78 " --> pdb=" O HIS J 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL J 79 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY J 84 " --> pdb=" O ALA J 80 " (cutoff:3.500A) Processing helix chain 'J' and resid 142 through 155 removed outlier: 3.787A pdb=" N THR J 153 " --> pdb=" O SER J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 184 removed outlier: 3.728A pdb=" N ALA J 180 " --> pdb=" O PHE J 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 50 removed outlier: 4.047A pdb=" N ASP K 46 " --> pdb=" O ILE K 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS K 47 " --> pdb=" O PRO K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 50 through 55 Processing helix chain 'K' and resid 73 through 91 removed outlier: 3.587A pdb=" N ASP K 78 " --> pdb=" O HIS K 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL K 79 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY K 84 " --> pdb=" O ALA K 80 " (cutoff:3.500A) Processing helix chain 'K' and resid 142 through 155 removed outlier: 3.787A pdb=" N THR K 153 " --> pdb=" O SER K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 184 removed outlier: 3.728A pdb=" N ALA K 180 " --> pdb=" O PHE K 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 50 removed outlier: 4.048A pdb=" N ASP L 46 " --> pdb=" O ILE L 42 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS L 47 " --> pdb=" O PRO L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 50 through 55 Processing helix chain 'L' and resid 73 through 91 removed outlier: 3.588A pdb=" N ASP L 78 " --> pdb=" O HIS L 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL L 79 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY L 84 " --> pdb=" O ALA L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 142 through 155 removed outlier: 3.788A pdb=" N THR L 153 " --> pdb=" O SER L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 184 removed outlier: 3.728A pdb=" N ALA L 180 " --> pdb=" O PHE L 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 50 removed outlier: 4.048A pdb=" N ASP M 46 " --> pdb=" O ILE M 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS M 47 " --> pdb=" O PRO M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 55 Processing helix chain 'M' and resid 73 through 91 removed outlier: 3.587A pdb=" N ASP M 78 " --> pdb=" O HIS M 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL M 79 " --> pdb=" O THR M 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY M 84 " --> pdb=" O ALA M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 155 removed outlier: 3.787A pdb=" N THR M 153 " --> pdb=" O SER M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 167 through 184 removed outlier: 3.729A pdb=" N ALA M 180 " --> pdb=" O PHE M 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 50 removed outlier: 4.047A pdb=" N ASP N 46 " --> pdb=" O ILE N 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS N 47 " --> pdb=" O PRO N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 55 Processing helix chain 'N' and resid 73 through 91 removed outlier: 3.588A pdb=" N ASP N 78 " --> pdb=" O HIS N 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL N 79 " --> pdb=" O THR N 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY N 84 " --> pdb=" O ALA N 80 " (cutoff:3.500A) Processing helix chain 'N' and resid 142 through 155 removed outlier: 3.787A pdb=" N THR N 153 " --> pdb=" O SER N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 184 removed outlier: 3.729A pdb=" N ALA N 180 " --> pdb=" O PHE N 176 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 50 removed outlier: 4.048A pdb=" N ASP O 46 " --> pdb=" O ILE O 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS O 47 " --> pdb=" O PRO O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 55 Processing helix chain 'O' and resid 73 through 91 removed outlier: 3.588A pdb=" N ASP O 78 " --> pdb=" O HIS O 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL O 79 " --> pdb=" O THR O 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY O 84 " --> pdb=" O ALA O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 155 removed outlier: 3.787A pdb=" N THR O 153 " --> pdb=" O SER O 149 " (cutoff:3.500A) Processing helix chain 'O' and resid 167 through 184 removed outlier: 3.728A pdb=" N ALA O 180 " --> pdb=" O PHE O 176 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 50 removed outlier: 4.048A pdb=" N ASP P 46 " --> pdb=" O ILE P 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS P 47 " --> pdb=" O PRO P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 50 through 55 Processing helix chain 'P' and resid 73 through 91 removed outlier: 3.587A pdb=" N ASP P 78 " --> pdb=" O HIS P 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL P 79 " --> pdb=" O THR P 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY P 84 " --> pdb=" O ALA P 80 " (cutoff:3.500A) Processing helix chain 'P' and resid 142 through 155 removed outlier: 3.787A pdb=" N THR P 153 " --> pdb=" O SER P 149 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 184 removed outlier: 3.728A pdb=" N ALA P 180 " --> pdb=" O PHE P 176 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 50 removed outlier: 4.047A pdb=" N ASP Q 46 " --> pdb=" O ILE Q 42 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS Q 47 " --> pdb=" O PRO Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 55 Processing helix chain 'Q' and resid 73 through 91 removed outlier: 3.587A pdb=" N ASP Q 78 " --> pdb=" O HIS Q 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL Q 79 " --> pdb=" O THR Q 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY Q 84 " --> pdb=" O ALA Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 142 through 155 removed outlier: 3.787A pdb=" N THR Q 153 " --> pdb=" O SER Q 149 " (cutoff:3.500A) Processing helix chain 'Q' and resid 167 through 184 removed outlier: 3.728A pdb=" N ALA Q 180 " --> pdb=" O PHE Q 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 50 removed outlier: 4.048A pdb=" N ASP R 46 " --> pdb=" O ILE R 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS R 47 " --> pdb=" O PRO R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 55 Processing helix chain 'R' and resid 73 through 91 removed outlier: 3.587A pdb=" N ASP R 78 " --> pdb=" O HIS R 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL R 79 " --> pdb=" O THR R 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY R 84 " --> pdb=" O ALA R 80 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 155 removed outlier: 3.787A pdb=" N THR R 153 " --> pdb=" O SER R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 184 removed outlier: 3.729A pdb=" N ALA R 180 " --> pdb=" O PHE R 176 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 50 removed outlier: 4.047A pdb=" N ASP S 46 " --> pdb=" O ILE S 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS S 47 " --> pdb=" O PRO S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 50 through 55 Processing helix chain 'S' and resid 73 through 91 removed outlier: 3.588A pdb=" N ASP S 78 " --> pdb=" O HIS S 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL S 79 " --> pdb=" O THR S 75 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY S 84 " --> pdb=" O ALA S 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 142 through 155 removed outlier: 3.787A pdb=" N THR S 153 " --> pdb=" O SER S 149 " (cutoff:3.500A) Processing helix chain 'S' and resid 167 through 184 removed outlier: 3.729A pdb=" N ALA S 180 " --> pdb=" O PHE S 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 50 removed outlier: 4.047A pdb=" N ASP T 46 " --> pdb=" O ILE T 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS T 47 " --> pdb=" O PRO T 43 " (cutoff:3.500A) Processing helix chain 'T' and resid 50 through 55 Processing helix chain 'T' and resid 73 through 91 removed outlier: 3.587A pdb=" N ASP T 78 " --> pdb=" O HIS T 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL T 79 " --> pdb=" O THR T 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY T 84 " --> pdb=" O ALA T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 142 through 155 removed outlier: 3.787A pdb=" N THR T 153 " --> pdb=" O SER T 149 " (cutoff:3.500A) Processing helix chain 'T' and resid 167 through 184 removed outlier: 3.729A pdb=" N ALA T 180 " --> pdb=" O PHE T 176 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 50 removed outlier: 4.047A pdb=" N ASP U 46 " --> pdb=" O ILE U 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS U 47 " --> pdb=" O PRO U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 50 through 55 Processing helix chain 'U' and resid 73 through 91 removed outlier: 3.587A pdb=" N ASP U 78 " --> pdb=" O HIS U 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL U 79 " --> pdb=" O THR U 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY U 84 " --> pdb=" O ALA U 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 142 through 155 removed outlier: 3.786A pdb=" N THR U 153 " --> pdb=" O SER U 149 " (cutoff:3.500A) Processing helix chain 'U' and resid 167 through 184 removed outlier: 3.729A pdb=" N ALA U 180 " --> pdb=" O PHE U 176 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 50 removed outlier: 4.047A pdb=" N ASP V 46 " --> pdb=" O ILE V 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS V 47 " --> pdb=" O PRO V 43 " (cutoff:3.500A) Processing helix chain 'V' and resid 50 through 55 Processing helix chain 'V' and resid 73 through 91 removed outlier: 3.587A pdb=" N ASP V 78 " --> pdb=" O HIS V 74 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL V 79 " --> pdb=" O THR V 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY V 84 " --> pdb=" O ALA V 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 142 through 155 removed outlier: 3.787A pdb=" N THR V 153 " --> pdb=" O SER V 149 " (cutoff:3.500A) Processing helix chain 'V' and resid 167 through 184 removed outlier: 3.729A pdb=" N ALA V 180 " --> pdb=" O PHE V 176 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 50 removed outlier: 4.048A pdb=" N ASP W 46 " --> pdb=" O ILE W 42 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS W 47 " --> pdb=" O PRO W 43 " (cutoff:3.500A) Processing helix chain 'W' and resid 50 through 55 Processing helix chain 'W' and resid 73 through 91 removed outlier: 3.587A pdb=" N ASP W 78 " --> pdb=" O HIS W 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL W 79 " --> pdb=" O THR W 75 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY W 84 " --> pdb=" O ALA W 80 " (cutoff:3.500A) Processing helix chain 'W' and resid 142 through 155 removed outlier: 3.787A pdb=" N THR W 153 " --> pdb=" O SER W 149 " (cutoff:3.500A) Processing helix chain 'W' and resid 167 through 184 removed outlier: 3.728A pdb=" N ALA W 180 " --> pdb=" O PHE W 176 " (cutoff:3.500A) Processing helix chain 'X' and resid 42 through 50 removed outlier: 4.047A pdb=" N ASP X 46 " --> pdb=" O ILE X 42 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N HIS X 47 " --> pdb=" O PRO X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 50 through 55 Processing helix chain 'X' and resid 73 through 91 removed outlier: 3.587A pdb=" N ASP X 78 " --> pdb=" O HIS X 74 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL X 79 " --> pdb=" O THR X 75 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY X 84 " --> pdb=" O ALA X 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 142 through 155 removed outlier: 3.787A pdb=" N THR X 153 " --> pdb=" O SER X 149 " (cutoff:3.500A) Processing helix chain 'X' and resid 167 through 184 removed outlier: 3.729A pdb=" N ALA X 180 " --> pdb=" O PHE X 176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP A 37 " --> pdb=" O VAL A 60 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL A 62 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 64 " --> pdb=" O SER A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE A 112 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU A 111 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 12 through 18 removed outlier: 3.716A pdb=" N ASP B 37 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 62 " --> pdb=" O ASP B 37 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA B 64 " --> pdb=" O SER B 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 106 removed outlier: 3.831A pdb=" N ILE B 112 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU B 111 " --> pdb=" O LEU B 163 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP C 37 " --> pdb=" O VAL C 60 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL C 62 " --> pdb=" O ASP C 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA C 64 " --> pdb=" O SER C 39 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE C 112 " --> pdb=" O ALA C 105 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU C 111 " --> pdb=" O LEU C 163 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP D 37 " --> pdb=" O VAL D 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL D 62 " --> pdb=" O ASP D 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA D 64 " --> pdb=" O SER D 39 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE D 112 " --> pdb=" O ALA D 105 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU D 111 " --> pdb=" O LEU D 163 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP E 37 " --> pdb=" O VAL E 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL E 62 " --> pdb=" O ASP E 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA E 64 " --> pdb=" O SER E 39 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 101 through 106 removed outlier: 3.831A pdb=" N ILE E 112 " --> pdb=" O ALA E 105 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU E 111 " --> pdb=" O LEU E 163 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP F 37 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL F 62 " --> pdb=" O ASP F 37 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA F 64 " --> pdb=" O SER F 39 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 101 through 106 removed outlier: 3.831A pdb=" N ILE F 112 " --> pdb=" O ALA F 105 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU F 111 " --> pdb=" O LEU F 163 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP G 37 " --> pdb=" O VAL G 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL G 62 " --> pdb=" O ASP G 37 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA G 64 " --> pdb=" O SER G 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 101 through 106 removed outlier: 3.831A pdb=" N ILE G 112 " --> pdb=" O ALA G 105 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU G 111 " --> pdb=" O LEU G 163 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP H 37 " --> pdb=" O VAL H 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL H 62 " --> pdb=" O ASP H 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA H 64 " --> pdb=" O SER H 39 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE H 112 " --> pdb=" O ALA H 105 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU H 111 " --> pdb=" O LEU H 163 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP I 37 " --> pdb=" O VAL I 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL I 62 " --> pdb=" O ASP I 37 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA I 64 " --> pdb=" O SER I 39 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 101 through 106 removed outlier: 3.829A pdb=" N ILE I 112 " --> pdb=" O ALA I 105 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU I 111 " --> pdb=" O LEU I 163 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP J 37 " --> pdb=" O VAL J 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL J 62 " --> pdb=" O ASP J 37 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA J 64 " --> pdb=" O SER J 39 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE J 112 " --> pdb=" O ALA J 105 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU J 111 " --> pdb=" O LEU J 163 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP K 37 " --> pdb=" O VAL K 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL K 62 " --> pdb=" O ASP K 37 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA K 64 " --> pdb=" O SER K 39 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE K 112 " --> pdb=" O ALA K 105 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU K 111 " --> pdb=" O LEU K 163 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 12 through 18 removed outlier: 3.716A pdb=" N ASP L 37 " --> pdb=" O VAL L 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL L 62 " --> pdb=" O ASP L 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA L 64 " --> pdb=" O SER L 39 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE L 112 " --> pdb=" O ALA L 105 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU L 111 " --> pdb=" O LEU L 163 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP M 37 " --> pdb=" O VAL M 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL M 62 " --> pdb=" O ASP M 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA M 64 " --> pdb=" O SER M 39 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE M 112 " --> pdb=" O ALA M 105 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU M 111 " --> pdb=" O LEU M 163 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 12 through 18 removed outlier: 3.716A pdb=" N ASP N 37 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL N 62 " --> pdb=" O ASP N 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA N 64 " --> pdb=" O SER N 39 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 101 through 106 removed outlier: 3.829A pdb=" N ILE N 112 " --> pdb=" O ALA N 105 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU N 111 " --> pdb=" O LEU N 163 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP O 37 " --> pdb=" O VAL O 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL O 62 " --> pdb=" O ASP O 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA O 64 " --> pdb=" O SER O 39 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE O 112 " --> pdb=" O ALA O 105 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU O 111 " --> pdb=" O LEU O 163 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 12 through 18 removed outlier: 3.716A pdb=" N ASP P 37 " --> pdb=" O VAL P 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL P 62 " --> pdb=" O ASP P 37 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA P 64 " --> pdb=" O SER P 39 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 101 through 106 removed outlier: 3.831A pdb=" N ILE P 112 " --> pdb=" O ALA P 105 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU P 111 " --> pdb=" O LEU P 163 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 12 through 18 removed outlier: 3.716A pdb=" N ASP Q 37 " --> pdb=" O VAL Q 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL Q 62 " --> pdb=" O ASP Q 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA Q 64 " --> pdb=" O SER Q 39 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE Q 112 " --> pdb=" O ALA Q 105 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU Q 111 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 12 through 18 removed outlier: 3.716A pdb=" N ASP R 37 " --> pdb=" O VAL R 60 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL R 62 " --> pdb=" O ASP R 37 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA R 64 " --> pdb=" O SER R 39 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE R 112 " --> pdb=" O ALA R 105 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU R 111 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'S' and resid 12 through 18 removed outlier: 3.716A pdb=" N ASP S 37 " --> pdb=" O VAL S 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL S 62 " --> pdb=" O ASP S 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA S 64 " --> pdb=" O SER S 39 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 101 through 106 removed outlier: 3.831A pdb=" N ILE S 112 " --> pdb=" O ALA S 105 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU S 111 " --> pdb=" O LEU S 163 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 12 through 18 removed outlier: 3.716A pdb=" N ASP T 37 " --> pdb=" O VAL T 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL T 62 " --> pdb=" O ASP T 37 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA T 64 " --> pdb=" O SER T 39 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 101 through 106 removed outlier: 3.831A pdb=" N ILE T 112 " --> pdb=" O ALA T 105 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU T 111 " --> pdb=" O LEU T 163 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'U' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP U 37 " --> pdb=" O VAL U 60 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL U 62 " --> pdb=" O ASP U 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA U 64 " --> pdb=" O SER U 39 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'U' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE U 112 " --> pdb=" O ALA U 105 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU U 111 " --> pdb=" O LEU U 163 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 12 through 18 removed outlier: 3.716A pdb=" N ASP V 37 " --> pdb=" O VAL V 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL V 62 " --> pdb=" O ASP V 37 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA V 64 " --> pdb=" O SER V 39 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'V' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE V 112 " --> pdb=" O ALA V 105 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU V 111 " --> pdb=" O LEU V 163 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'W' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP W 37 " --> pdb=" O VAL W 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL W 62 " --> pdb=" O ASP W 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA W 64 " --> pdb=" O SER W 39 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'W' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE W 112 " --> pdb=" O ALA W 105 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU W 111 " --> pdb=" O LEU W 163 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 12 through 18 removed outlier: 3.715A pdb=" N ASP X 37 " --> pdb=" O VAL X 60 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL X 62 " --> pdb=" O ASP X 37 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA X 64 " --> pdb=" O SER X 39 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'X' and resid 101 through 106 removed outlier: 3.830A pdb=" N ILE X 112 " --> pdb=" O ALA X 105 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU X 111 " --> pdb=" O LEU X 163 " (cutoff:3.500A) 1608 hydrogen bonds defined for protein. 4680 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: 6.41 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11541 1.34 - 1.46: 6395 1.46 - 1.58: 16144 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 34200 Sorted by residual: bond pdb=" N1 5LD U 303 " pdb=" N2 5LD U 303 " ideal model delta sigma weight residual 1.334 1.391 -0.057 2.00e-02 2.50e+03 8.01e+00 bond pdb=" N1 5LD N 303 " pdb=" N2 5LD N 303 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.00e-02 2.50e+03 7.90e+00 bond pdb=" N1 5LD V 303 " pdb=" N2 5LD V 303 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.00e-02 2.50e+03 7.90e+00 bond pdb=" N1 5LD Q 303 " pdb=" N2 5LD Q 303 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.00e-02 2.50e+03 7.79e+00 bond pdb=" N1 5LD X 303 " pdb=" N2 5LD X 303 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.00e-02 2.50e+03 7.78e+00 ... (remaining 34195 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 42330 1.75 - 3.50: 3270 3.50 - 5.25: 540 5.25 - 7.00: 180 7.00 - 8.75: 120 Bond angle restraints: 46440 Sorted by residual: angle pdb=" C ASP V 108 " pdb=" N GLU V 109 " pdb=" CA GLU V 109 " ideal model delta sigma weight residual 121.54 130.29 -8.75 1.91e+00 2.74e-01 2.10e+01 angle pdb=" C ASP R 108 " pdb=" N GLU R 109 " pdb=" CA GLU R 109 " ideal model delta sigma weight residual 121.54 130.28 -8.74 1.91e+00 2.74e-01 2.10e+01 angle pdb=" C ASP U 108 " pdb=" N GLU U 109 " pdb=" CA GLU U 109 " ideal model delta sigma weight residual 121.54 130.28 -8.74 1.91e+00 2.74e-01 2.09e+01 angle pdb=" C ASP Q 108 " pdb=" N GLU Q 109 " pdb=" CA GLU Q 109 " ideal model delta sigma weight residual 121.54 130.27 -8.73 1.91e+00 2.74e-01 2.09e+01 angle pdb=" C ASP B 108 " pdb=" N GLU B 109 " pdb=" CA GLU B 109 " ideal model delta sigma weight residual 121.54 130.26 -8.72 1.91e+00 2.74e-01 2.09e+01 ... (remaining 46435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.23: 18596 15.23 - 30.45: 1036 30.45 - 45.68: 264 45.68 - 60.91: 72 60.91 - 76.13: 24 Dihedral angle restraints: 19992 sinusoidal: 7440 harmonic: 12552 Sorted by residual: dihedral pdb=" CA PRO K 106 " pdb=" C PRO K 106 " pdb=" N LEU K 107 " pdb=" CA LEU K 107 " ideal model delta harmonic sigma weight residual 180.00 150.72 29.28 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA PRO G 106 " pdb=" C PRO G 106 " pdb=" N LEU G 107 " pdb=" CA LEU G 107 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA PRO E 106 " pdb=" C PRO E 106 " pdb=" N LEU E 107 " pdb=" CA LEU E 107 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 19989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3644 0.047 - 0.094: 1264 0.094 - 0.142: 354 0.142 - 0.189: 138 0.189 - 0.236: 24 Chirality restraints: 5424 Sorted by residual: chirality pdb=" C7 5LD L 303 " pdb=" C6 5LD L 303 " pdb=" C8 5LD L 303 " pdb=" O13 5LD L 303 " both_signs ideal model delta sigma weight residual False 2.41 2.64 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C7 5LD M 402 " pdb=" C6 5LD M 402 " pdb=" C8 5LD M 402 " pdb=" O13 5LD M 402 " both_signs ideal model delta sigma weight residual False 2.41 2.64 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C7 5LD O 402 " pdb=" C6 5LD O 402 " pdb=" C8 5LD O 402 " pdb=" O13 5LD O 402 " both_signs ideal model delta sigma weight residual False 2.41 2.64 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 5421 not shown) Planarity restraints: 6024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP N 108 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C ASP N 108 " -0.048 2.00e-02 2.50e+03 pdb=" O ASP N 108 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU N 109 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP Q 108 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.74e+00 pdb=" C ASP Q 108 " -0.048 2.00e-02 2.50e+03 pdb=" O ASP Q 108 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU Q 109 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 108 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.73e+00 pdb=" C ASP I 108 " 0.048 2.00e-02 2.50e+03 pdb=" O ASP I 108 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU I 109 " -0.016 2.00e-02 2.50e+03 ... (remaining 6021 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 846 2.67 - 3.23: 28021 3.23 - 3.78: 51546 3.78 - 4.34: 70994 4.34 - 4.90: 118819 Nonbonded interactions: 270226 Sorted by model distance: nonbonded pdb=" NE2 HIS C 73 " pdb="MN MN C 403 " model vdw 2.111 2.400 nonbonded pdb=" NE2 HIS R 73 " pdb="MN MN R 301 " model vdw 2.114 2.400 nonbonded pdb=" NE2 HIS B 73 " pdb="MN MN B 403 " model vdw 2.118 2.400 nonbonded pdb=" NE2 HIS Q 73 " pdb="MN MN Q 301 " model vdw 2.119 2.400 nonbonded pdb=" NE2 HIS L 73 " pdb="MN MN L 301 " model vdw 2.120 2.400 ... (remaining 270221 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and resid 11 through 401) selection = (chain 'B' and resid 11 through 401) selection = (chain 'C' and resid 11 through 401) selection = (chain 'D' and resid 11 through 401) selection = (chain 'E' and resid 11 through 401) selection = (chain 'F' and resid 11 through 401) selection = (chain 'G' and resid 11 through 401) selection = (chain 'H' and resid 11 through 301) selection = (chain 'I' and resid 11 through 401) selection = (chain 'J' and resid 11 through 401) selection = (chain 'K' and resid 11 through 401) selection = (chain 'L' and resid 11 through 301) selection = (chain 'M' and resid 11 through 401) selection = (chain 'N' and resid 11 through 301) selection = (chain 'O' and resid 11 through 401) selection = (chain 'P' and resid 11 through 301) selection = (chain 'Q' and resid 11 through 301) selection = (chain 'R' and resid 11 through 301) selection = (chain 'S' and resid 11 through 301) selection = (chain 'T' and resid 11 through 301) selection = (chain 'U' and resid 11 through 301) selection = (chain 'V' and resid 11 through 301) selection = (chain 'W' and resid 11 through 301) selection = (chain 'X' and resid 11 through 301) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 30.590 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 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 : 0.007 0.057 34200 Z= 0.308 Angle : 1.124 8.754 46440 Z= 0.605 Chirality : 0.057 0.236 5424 Planarity : 0.007 0.051 6024 Dihedral : 11.613 76.133 11928 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.02 (0.09), residues: 4392 helix: -4.65 (0.04), residues: 1536 sheet: -0.55 (0.13), residues: 1248 loop : -4.12 (0.10), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 17 TYR 0.021 0.004 TYR E 138 PHE 0.008 0.002 PHE B 176 HIS 0.010 0.003 HIS J 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00655 / 0.31 (34200) covalent geometry : angle 1.12403 / 0.60 (46440) hydrogen bonds : bond 0.28574 / 19.56 ( 1608) hydrogen bonds : angle 9.21131 / 6.47 ( 4680) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 882 time to evaluate : 1.403 Fit side-chains REVERT: G 166 LYS cc_start: 0.7714 (ptpt) cc_final: 0.7448 (pttp) REVERT: M 166 LYS cc_start: 0.7805 (ptpt) cc_final: 0.7590 (pttp) REVERT: R 30 LEU cc_start: 0.8462 (tt) cc_final: 0.8259 (tp) REVERT: U 166 LYS cc_start: 0.7664 (ptpt) cc_final: 0.7362 (pttp) REVERT: X 166 LYS cc_start: 0.7792 (ptpt) cc_final: 0.7573 (pttp) outliers start: 0 outliers final: 0 residues processed: 882 average time/residue: 0.2731 time to fit residues: 355.3514 Evaluate side-chains 625 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 625 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 9.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 30.0000 chunk 424 optimal weight: 3.9990 chunk 155 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN B 133 GLN B 185 GLN C 185 GLN D 133 GLN D 185 GLN E 185 GLN F 133 GLN F 185 GLN G 185 GLN H 133 GLN H 185 GLN I 185 GLN J 133 GLN J 185 GLN K 185 GLN L 133 GLN L 185 GLN M 133 GLN N 133 GLN N 185 GLN O 133 GLN O 185 GLN P 133 GLN P 185 GLN Q 133 GLN Q 185 GLN R 185 GLN S 185 GLN T 133 GLN T 185 GLN U 185 GLN V 185 GLN W 185 GLN X 133 GLN X 185 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.203668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.182937 restraints weight = 32749.862| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 1.27 r_work: 0.3893 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3767 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3767 r_free = 0.3767 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 34200 Z= 0.245 Angle : 0.857 7.584 46440 Z= 0.449 Chirality : 0.050 0.134 5424 Planarity : 0.008 0.051 6024 Dihedral : 9.515 59.965 4920 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 3.24 % Allowed : 7.52 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.44 (0.11), residues: 4392 helix: -2.68 (0.09), residues: 1608 sheet: 0.02 (0.15), residues: 1200 loop : -3.62 (0.12), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 134 TYR 0.018 0.003 TYR E 138 PHE 0.008 0.002 PHE N 100 HIS 0.007 0.002 HIS S 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00567 / 0.24 (34200) covalent geometry : angle 0.85666 / 0.45 (46440) hydrogen bonds : bond 0.05578 / 3.79 ( 1608) hydrogen bonds : angle 5.13394 / 3.60 ( 4680) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 718 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 610 time to evaluate : 1.092 Fit side-chains REVERT: A 133 GLN cc_start: 0.8393 (mt0) cc_final: 0.8123 (mt0) REVERT: C 133 GLN cc_start: 0.8447 (mt0) cc_final: 0.8177 (mt0) REVERT: R 133 GLN cc_start: 0.8393 (mt0) cc_final: 0.8065 (mt0) REVERT: S 26 VAL cc_start: 0.8033 (p) cc_final: 0.7775 (p) REVERT: S 133 GLN cc_start: 0.8433 (mt0) cc_final: 0.8197 (mt0) REVERT: U 166 LYS cc_start: 0.8246 (ptpt) cc_final: 0.8044 (ptmt) REVERT: W 133 GLN cc_start: 0.8470 (mt0) cc_final: 0.8164 (mt0) outliers start: 108 outliers final: 60 residues processed: 672 average time/residue: 0.2760 time to fit residues: 274.5556 Evaluate side-chains 554 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 494 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain U residue 26 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 104 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 420 optimal weight: 9.9990 chunk 375 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 368 optimal weight: 1.9990 chunk 423 optimal weight: 10.0000 chunk 141 optimal weight: 6.9990 chunk 112 optimal weight: 10.0000 chunk 173 optimal weight: 7.9990 chunk 108 optimal weight: 40.0000 chunk 89 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.199973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.178640 restraints weight = 35620.173| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 1.35 r_work: 0.3903 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3788 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3792 r_free = 0.3792 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3791 r_free = 0.3791 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3791 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 34200 Z= 0.176 Angle : 0.744 7.036 46440 Z= 0.395 Chirality : 0.047 0.129 5424 Planarity : 0.006 0.039 6024 Dihedral : 8.898 59.687 4920 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % Rotamer: Outliers : 4.56 % Allowed : 11.42 % Favored : 84.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.12), residues: 4392 helix: -1.33 (0.11), residues: 1608 sheet: -0.22 (0.15), residues: 1248 loop : -3.54 (0.13), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG Q 63 TYR 0.012 0.002 TYR A 138 PHE 0.006 0.001 PHE U 176 HIS 0.005 0.001 HIS V 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (34200) covalent geometry : angle 0.74383 / 0.39 (46440) hydrogen bonds : bond 0.04511 / 3.06 ( 1608) hydrogen bonds : angle 4.70789 / 3.30 ( 4680) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 552 time to evaluate : 1.189 Fit side-chains REVERT: A 133 GLN cc_start: 0.8437 (mt0) cc_final: 0.8202 (mt0) REVERT: C 133 GLN cc_start: 0.8421 (mt0) cc_final: 0.8202 (mt0) REVERT: F 173 GLU cc_start: 0.8562 (tt0) cc_final: 0.8336 (tt0) REVERT: G 166 LYS cc_start: 0.8591 (ptmt) cc_final: 0.8367 (pttp) REVERT: O 26 VAL cc_start: 0.8036 (p) cc_final: 0.7829 (p) REVERT: S 26 VAL cc_start: 0.8070 (p) cc_final: 0.7862 (p) REVERT: V 133 GLN cc_start: 0.8455 (mt0) cc_final: 0.8223 (mt0) REVERT: W 133 GLN cc_start: 0.8454 (mt0) cc_final: 0.8189 (mt0) outliers start: 152 outliers final: 83 residues processed: 631 average time/residue: 0.2410 time to fit residues: 235.4979 Evaluate side-chains 562 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 479 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain U residue 26 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 151 VAL Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 104 THR Chi-restraints excluded: chain X residue 151 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 166 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 225 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 407 optimal weight: 0.0170 chunk 48 optimal weight: 7.9990 chunk 239 optimal weight: 30.0000 chunk 18 optimal weight: 40.0000 chunk 291 optimal weight: 4.9990 overall best weight: 2.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 76 ASN D 76 ASN F 76 ASN J 76 ASN K 76 ASN L 76 ASN M 76 ASN N 76 ASN O 76 ASN P 76 ASN Q 76 ASN R 76 ASN S 76 ASN U 76 ASN V 76 ASN X 76 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.209556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.190828 restraints weight = 34974.644| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 1.20 r_work: 0.3957 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3848 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3838 r_free = 0.3838 target_work(ls_wunit_k1) = 0.164 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34200 Z= 0.142 Angle : 0.670 7.032 46440 Z= 0.359 Chirality : 0.045 0.136 5424 Planarity : 0.005 0.043 6024 Dihedral : 8.240 57.612 4920 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 4.47 % Allowed : 13.58 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.19 (0.12), residues: 4392 helix: -0.52 (0.12), residues: 1584 sheet: -0.37 (0.15), residues: 1272 loop : -3.39 (0.12), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 63 TYR 0.010 0.002 TYR E 138 PHE 0.006 0.001 PHE W 146 HIS 0.004 0.001 HIS T 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (34200) covalent geometry : angle 0.67021 / 0.36 (46440) hydrogen bonds : bond 0.03857 / 2.62 ( 1608) hydrogen bonds : angle 4.48480 / 3.14 ( 4680) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 541 time to evaluate : 1.191 Fit side-chains REVERT: A 109 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.5875 (pm20) REVERT: B 109 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.5863 (pm20) REVERT: C 30 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8454 (mp) REVERT: C 109 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.5787 (pm20) REVERT: C 166 LYS cc_start: 0.8502 (pttt) cc_final: 0.8224 (pttt) REVERT: D 109 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.5814 (pm20) REVERT: D 166 LYS cc_start: 0.8405 (pttt) cc_final: 0.8170 (pttp) REVERT: E 109 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.5846 (pm20) REVERT: F 109 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.5831 (pm20) REVERT: G 109 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.5839 (pm20) REVERT: H 72 ASP cc_start: 0.7828 (m-30) cc_final: 0.7311 (t0) REVERT: H 109 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.5781 (pm20) REVERT: I 109 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.5766 (pm20) REVERT: J 109 GLU cc_start: 0.6828 (OUTLIER) cc_final: 0.5874 (pm20) REVERT: J 166 LYS cc_start: 0.8501 (pttt) cc_final: 0.8205 (pttp) REVERT: K 109 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.5848 (pm20) REVERT: L 109 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.5878 (pm20) REVERT: M 109 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.5896 (pm20) REVERT: N 109 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.5827 (pm20) REVERT: O 109 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.5800 (pm20) REVERT: O 166 LYS cc_start: 0.8501 (pttt) cc_final: 0.8261 (pttp) REVERT: P 109 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.5909 (pm20) REVERT: Q 109 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.5917 (pm20) REVERT: R 109 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.5925 (pm20) REVERT: R 166 LYS cc_start: 0.8476 (pttt) cc_final: 0.8191 (pttp) REVERT: S 72 ASP cc_start: 0.7838 (m-30) cc_final: 0.7314 (t0) REVERT: S 109 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.5812 (pm20) REVERT: T 72 ASP cc_start: 0.7869 (m-30) cc_final: 0.7330 (t0) REVERT: T 109 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.5816 (pm20) REVERT: T 166 LYS cc_start: 0.8449 (pttt) cc_final: 0.8148 (pttp) REVERT: U 109 GLU cc_start: 0.6722 (OUTLIER) cc_final: 0.5917 (pm20) REVERT: V 109 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.5900 (pm20) REVERT: V 133 GLN cc_start: 0.8353 (mt0) cc_final: 0.8129 (mt0) REVERT: W 109 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.5817 (pm20) REVERT: W 166 LYS cc_start: 0.8485 (pttt) cc_final: 0.8220 (pttt) REVERT: X 109 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.5876 (pm20) outliers start: 149 outliers final: 70 residues processed: 629 average time/residue: 0.2397 time to fit residues: 234.6850 Evaluate side-chains 598 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 503 time to evaluate : 1.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 109 GLU Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 109 GLU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 109 GLU Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 109 GLU Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain T residue 109 GLU Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 109 GLU Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 109 GLU Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 151 VAL Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 104 THR Chi-restraints excluded: chain X residue 109 GLU Chi-restraints excluded: chain X residue 151 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 288 optimal weight: 40.0000 chunk 329 optimal weight: 20.0000 chunk 343 optimal weight: 20.0000 chunk 379 optimal weight: 10.0000 chunk 263 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 chunk 21 optimal weight: 6.9990 chunk 239 optimal weight: 20.0000 chunk 119 optimal weight: 0.2980 chunk 4 optimal weight: 9.9990 chunk 191 optimal weight: 5.9990 overall best weight: 6.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS D 69 HIS ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 HIS E 185 GLN H 69 HIS ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 69 HIS ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 69 HIS M 185 GLN O 69 HIS Q 69 HIS R 69 HIS T 69 HIS T 185 GLN ** U 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 185 GLN X 69 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.194274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.173656 restraints weight = 36196.314| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 1.31 r_work: 0.3844 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3731 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3722 r_free = 0.3722 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.3401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 34200 Z= 0.255 Angle : 0.830 7.522 46440 Z= 0.433 Chirality : 0.052 0.141 5424 Planarity : 0.007 0.051 6024 Dihedral : 8.592 51.887 4920 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % Rotamer: Outliers : 5.37 % Allowed : 13.31 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.22 (0.12), residues: 4392 helix: -0.60 (0.12), residues: 1584 sheet: -0.20 (0.15), residues: 1248 loop : -3.50 (0.13), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG S 134 TYR 0.009 0.003 TYR N 126 PHE 0.018 0.002 PHE W 146 HIS 0.010 0.002 HIS R 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00604 / 0.26 (34200) covalent geometry : angle 0.83049 / 0.43 (46440) hydrogen bonds : bond 0.04774 / 3.24 ( 1608) hydrogen bonds : angle 4.86480 / 3.40 ( 4680) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 179 poor density : 450 time to evaluate : 1.425 Fit side-chains REVERT: A 30 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8557 (mp) REVERT: A 109 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.5418 (pm20) REVERT: B 30 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8461 (mp) REVERT: B 109 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.5436 (pm20) REVERT: C 30 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8601 (mp) REVERT: C 109 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.5625 (pm20) REVERT: D 30 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8476 (mp) REVERT: D 109 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.5491 (pm20) REVERT: E 109 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.5537 (pm20) REVERT: F 109 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.5425 (pm20) REVERT: G 109 GLU cc_start: 0.6961 (OUTLIER) cc_final: 0.5630 (pm20) REVERT: H 109 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.5412 (pm20) REVERT: I 109 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.5663 (pm20) REVERT: J 109 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.5472 (pm20) REVERT: K 109 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.5560 (pm20) REVERT: L 30 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8484 (mp) REVERT: L 109 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.5441 (pm20) REVERT: M 109 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.5448 (pm20) REVERT: N 109 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.5459 (pm20) REVERT: O 109 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.5533 (pm20) REVERT: P 109 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.5455 (pm20) REVERT: Q 30 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8487 (mp) REVERT: Q 109 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.5459 (pm20) REVERT: R 109 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.5512 (pm20) REVERT: S 109 GLU cc_start: 0.6824 (OUTLIER) cc_final: 0.5690 (pm20) REVERT: T 30 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8534 (mp) REVERT: T 109 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.5436 (pm20) REVERT: U 30 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8553 (mp) REVERT: U 109 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.5527 (pm20) REVERT: V 109 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.5450 (pm20) REVERT: W 30 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8506 (mp) REVERT: W 37 ASP cc_start: 0.7455 (t0) cc_final: 0.7251 (t70) REVERT: W 109 GLU cc_start: 0.6664 (OUTLIER) cc_final: 0.5485 (pm20) REVERT: X 30 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8492 (mp) REVERT: X 109 GLU cc_start: 0.6723 (OUTLIER) cc_final: 0.5442 (pm20) outliers start: 179 outliers final: 121 residues processed: 569 average time/residue: 0.2518 time to fit residues: 221.8201 Evaluate side-chains 599 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 155 poor density : 444 time to evaluate : 1.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 109 GLU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 109 GLU Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 109 GLU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain P residue 19 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 109 GLU Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 30 LEU Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain T residue 109 GLU Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain U residue 26 VAL Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 109 GLU Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 109 GLU Chi-restraints excluded: chain V residue 137 THR Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 151 VAL Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 104 THR Chi-restraints excluded: chain X residue 109 GLU Chi-restraints excluded: chain X residue 151 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 245 optimal weight: 7.9990 chunk 267 optimal weight: 4.9990 chunk 237 optimal weight: 0.9990 chunk 246 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 402 optimal weight: 9.9990 chunk 1 optimal weight: 8.9990 chunk 387 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 398 optimal weight: 30.0000 chunk 221 optimal weight: 20.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.196973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.176162 restraints weight = 35938.964| |-----------------------------------------------------------------------------| r_work (start): 0.3975 rms_B_bonded: 1.32 r_work: 0.3893 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3779 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34200 Z= 0.176 Angle : 0.723 7.242 46440 Z= 0.383 Chirality : 0.048 0.138 5424 Planarity : 0.006 0.036 6024 Dihedral : 8.171 49.580 4920 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 5.43 % Allowed : 15.02 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.94 (0.12), residues: 4392 helix: -0.28 (0.12), residues: 1584 sheet: -0.27 (0.16), residues: 1272 loop : -3.26 (0.14), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 134 TYR 0.008 0.002 TYR S 138 PHE 0.018 0.002 PHE T 146 HIS 0.006 0.001 HIS G 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (34200) covalent geometry : angle 0.72271 / 0.38 (46440) hydrogen bonds : bond 0.04116 / 2.79 ( 1608) hydrogen bonds : angle 4.74869 / 3.32 ( 4680) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 481 time to evaluate : 1.350 Fit side-chains REVERT: A 109 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.5514 (pm20) REVERT: B 30 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8516 (mp) REVERT: B 109 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.5578 (pm20) REVERT: C 30 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8617 (mp) REVERT: C 109 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.5611 (pm20) REVERT: D 109 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.5634 (pm20) REVERT: E 109 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.5543 (pm20) REVERT: F 30 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8503 (mp) REVERT: F 109 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.5563 (pm20) REVERT: G 109 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.5558 (pm20) REVERT: H 109 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.5548 (pm20) REVERT: I 109 GLU cc_start: 0.6781 (OUTLIER) cc_final: 0.5688 (pm20) REVERT: J 30 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8582 (mp) REVERT: J 109 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.5569 (pm20) REVERT: K 37 ASP cc_start: 0.6313 (p0) cc_final: 0.6112 (p0) REVERT: K 109 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.5669 (pm20) REVERT: L 109 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.5600 (pm20) REVERT: M 109 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.5631 (pm20) REVERT: N 30 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8508 (mp) REVERT: N 109 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.5566 (pm20) REVERT: O 30 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8474 (mp) REVERT: O 109 GLU cc_start: 0.6770 (OUTLIER) cc_final: 0.5641 (pm20) REVERT: P 30 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8509 (mp) REVERT: P 109 GLU cc_start: 0.6778 (OUTLIER) cc_final: 0.5553 (pm20) REVERT: Q 30 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8601 (mp) REVERT: Q 109 GLU cc_start: 0.6855 (OUTLIER) cc_final: 0.5609 (pm20) REVERT: R 109 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.5713 (pm20) REVERT: S 30 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8591 (mp) REVERT: S 109 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.5665 (pm20) REVERT: T 30 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8572 (mp) REVERT: T 109 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.5654 (pm20) REVERT: U 30 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8555 (mp) REVERT: U 109 GLU cc_start: 0.6804 (OUTLIER) cc_final: 0.5623 (pm20) REVERT: V 30 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8532 (mp) REVERT: V 109 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.5554 (pm20) REVERT: W 30 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8529 (mp) REVERT: W 109 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.5583 (pm20) REVERT: X 109 GLU cc_start: 0.6766 (OUTLIER) cc_final: 0.5557 (pm20) outliers start: 181 outliers final: 119 residues processed: 600 average time/residue: 0.2558 time to fit residues: 238.4633 Evaluate side-chains 618 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 462 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 109 GLU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 109 GLU Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 109 GLU Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 109 GLU Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 30 LEU Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain T residue 109 GLU Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 109 GLU Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain V residue 30 LEU Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 109 GLU Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 151 VAL Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 104 THR Chi-restraints excluded: chain X residue 109 GLU Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain X residue 151 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 158 optimal weight: 10.0000 chunk 144 optimal weight: 40.0000 chunk 249 optimal weight: 9.9990 chunk 99 optimal weight: 0.0980 chunk 419 optimal weight: 10.0000 chunk 140 optimal weight: 0.3980 chunk 276 optimal weight: 8.9990 chunk 207 optimal weight: 9.9990 chunk 290 optimal weight: 40.0000 chunk 349 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 overall best weight: 5.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 169 HIS ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 169 HIS ** U 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.194299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.173955 restraints weight = 36181.072| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 1.30 r_work: 0.3834 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3721 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 34200 Z= 0.227 Angle : 0.798 7.499 46440 Z= 0.418 Chirality : 0.051 0.150 5424 Planarity : 0.006 0.045 6024 Dihedral : 8.360 53.601 4920 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 6.18 % Allowed : 15.44 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.12), residues: 4392 helix: -0.33 (0.12), residues: 1584 sheet: -0.14 (0.15), residues: 1248 loop : -3.38 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG P 134 TYR 0.009 0.003 TYR O 126 PHE 0.015 0.002 PHE W 146 HIS 0.006 0.001 HIS G 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.23 (34200) covalent geometry : angle 0.79838 / 0.42 (46440) hydrogen bonds : bond 0.04516 / 3.06 ( 1608) hydrogen bonds : angle 4.91437 / 3.44 ( 4680) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 463 time to evaluate : 1.301 Fit side-chains REVERT: A 30 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8606 (mp) REVERT: A 109 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.5591 (pm20) REVERT: B 30 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8588 (mp) REVERT: B 109 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.5631 (pm20) REVERT: C 30 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8625 (mp) REVERT: C 109 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.5663 (pm20) REVERT: D 30 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8574 (mp) REVERT: D 109 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.5577 (pm20) REVERT: E 109 GLU cc_start: 0.6929 (OUTLIER) cc_final: 0.5609 (pm20) REVERT: E 166 LYS cc_start: 0.8667 (pttt) cc_final: 0.8329 (pttt) REVERT: F 30 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8518 (mp) REVERT: F 109 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.5580 (pm20) REVERT: G 109 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.5633 (pm20) REVERT: H 30 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8490 (mp) REVERT: H 109 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.5560 (pm20) REVERT: I 109 GLU cc_start: 0.6866 (OUTLIER) cc_final: 0.5584 (pm20) REVERT: J 30 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8622 (mp) REVERT: J 109 GLU cc_start: 0.6922 (OUTLIER) cc_final: 0.5627 (pm20) REVERT: J 166 LYS cc_start: 0.8526 (pttt) cc_final: 0.8288 (pttt) REVERT: K 109 GLU cc_start: 0.6948 (OUTLIER) cc_final: 0.5560 (pm20) REVERT: L 30 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8526 (mp) REVERT: L 109 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.5611 (pm20) REVERT: M 109 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.5610 (pm20) REVERT: N 30 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8566 (mp) REVERT: N 109 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.5608 (pm20) REVERT: O 30 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8541 (mp) REVERT: O 109 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.5592 (pm20) REVERT: O 166 LYS cc_start: 0.8587 (pttt) cc_final: 0.8351 (pttt) REVERT: P 30 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8499 (mp) REVERT: P 109 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.5606 (pm20) REVERT: Q 30 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8570 (mp) REVERT: Q 109 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.5623 (pm20) REVERT: R 30 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8592 (mp) REVERT: R 109 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.5605 (pm20) REVERT: R 166 LYS cc_start: 0.8610 (pttt) cc_final: 0.8373 (pttt) REVERT: S 30 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8629 (mp) REVERT: S 109 GLU cc_start: 0.6881 (OUTLIER) cc_final: 0.5690 (pm20) REVERT: T 30 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8530 (mp) REVERT: T 109 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.5592 (pm20) REVERT: T 166 LYS cc_start: 0.8559 (pttt) cc_final: 0.8335 (pttt) REVERT: U 30 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8584 (mp) REVERT: U 109 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.5525 (pm20) REVERT: V 30 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8588 (mp) REVERT: V 109 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.5561 (pm20) REVERT: W 30 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8577 (mp) REVERT: W 109 GLU cc_start: 0.6848 (OUTLIER) cc_final: 0.5556 (pm20) REVERT: X 30 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8587 (mp) REVERT: X 109 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.5606 (pm20) outliers start: 206 outliers final: 138 residues processed: 604 average time/residue: 0.2491 time to fit residues: 235.0068 Evaluate side-chains 642 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 461 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 109 GLU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 109 GLU Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 109 GLU Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain P residue 19 THR Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 109 GLU Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 30 LEU Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain T residue 109 GLU Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 137 THR Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain U residue 26 VAL Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 109 GLU Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 30 LEU Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 109 GLU Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 116 LEU Chi-restraints excluded: chain W residue 151 VAL Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 104 THR Chi-restraints excluded: chain X residue 109 GLU Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain X residue 151 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 282 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 126 optimal weight: 40.0000 chunk 413 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 419 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.200197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.180747 restraints weight = 35689.138| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.27 r_work: 0.3880 rms_B_bonded: 2.05 restraints_weight: 0.5000 r_work: 0.3769 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3752 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3752 r_free = 0.3752 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3752 r_free = 0.3752 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3752 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.3671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34200 Z= 0.182 Angle : 0.731 7.261 46440 Z= 0.388 Chirality : 0.048 0.190 5424 Planarity : 0.006 0.037 6024 Dihedral : 8.020 51.825 4920 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 6.29 % Allowed : 16.52 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.12), residues: 4392 helix: 0.01 (0.12), residues: 1584 sheet: -0.24 (0.15), residues: 1272 loop : -3.24 (0.14), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 134 TYR 0.008 0.002 TYR M 138 PHE 0.016 0.002 PHE T 146 HIS 0.007 0.001 HIS G 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (34200) covalent geometry : angle 0.73119 / 0.39 (46440) hydrogen bonds : bond 0.04121 / 2.79 ( 1608) hydrogen bonds : angle 4.80555 / 3.36 ( 4680) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 691 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 210 poor density : 481 time to evaluate : 1.396 Fit side-chains REVERT: A 109 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.5505 (pm20) REVERT: B 30 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8568 (mp) REVERT: B 109 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.5517 (pm20) REVERT: C 30 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8627 (mp) REVERT: C 109 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.5627 (pm20) REVERT: C 166 LYS cc_start: 0.8536 (pttt) cc_final: 0.8330 (pttt) REVERT: D 30 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8609 (mp) REVERT: D 109 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.5643 (pm20) REVERT: E 109 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.5494 (pm20) REVERT: E 166 LYS cc_start: 0.8625 (pttt) cc_final: 0.8280 (pttt) REVERT: F 30 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8557 (mp) REVERT: F 109 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.5505 (pm20) REVERT: G 109 GLU cc_start: 0.6721 (OUTLIER) cc_final: 0.5488 (pm20) REVERT: H 30 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8579 (mp) REVERT: H 109 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.5478 (pm20) REVERT: I 109 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.5615 (pm20) REVERT: J 30 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8615 (mp) REVERT: J 109 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.5681 (pm20) REVERT: K 109 GLU cc_start: 0.6895 (OUTLIER) cc_final: 0.5659 (pm20) REVERT: L 30 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8617 (mp) REVERT: L 109 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.5530 (pm20) REVERT: M 109 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.5659 (pm20) REVERT: N 30 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8567 (mp) REVERT: N 109 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.5640 (pm20) REVERT: O 30 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8572 (mp) REVERT: O 109 GLU cc_start: 0.6769 (OUTLIER) cc_final: 0.5636 (pm20) REVERT: P 30 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8554 (mp) REVERT: P 109 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.5559 (pm20) REVERT: Q 30 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8618 (mp) REVERT: Q 109 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.5538 (pm20) REVERT: R 109 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.5663 (pm20) REVERT: R 166 LYS cc_start: 0.8531 (pttt) cc_final: 0.8299 (pttt) REVERT: S 30 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8628 (mp) REVERT: S 109 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.5636 (pm20) REVERT: S 166 LYS cc_start: 0.8550 (pttt) cc_final: 0.8307 (pttt) REVERT: T 30 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8589 (mp) REVERT: T 109 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.5659 (pm20) REVERT: T 166 LYS cc_start: 0.8472 (pttt) cc_final: 0.8241 (pttt) REVERT: U 30 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8571 (mp) REVERT: U 109 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.5672 (pm20) REVERT: V 30 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8624 (mp) REVERT: V 109 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.5574 (pm20) REVERT: W 30 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8596 (mp) REVERT: W 109 GLU cc_start: 0.6709 (OUTLIER) cc_final: 0.5563 (pm20) REVERT: W 166 LYS cc_start: 0.8517 (pttt) cc_final: 0.8309 (pttt) REVERT: X 30 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8583 (mp) REVERT: X 109 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.5566 (pm20) outliers start: 210 outliers final: 144 residues processed: 621 average time/residue: 0.2429 time to fit residues: 236.3020 Evaluate side-chains 656 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 471 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 109 GLU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 109 GLU Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 109 GLU Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain P residue 19 THR Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 109 GLU Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 30 LEU Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain T residue 109 GLU Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain U residue 26 VAL Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 109 GLU Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 30 LEU Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 109 GLU Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 116 LEU Chi-restraints excluded: chain W residue 151 VAL Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 104 THR Chi-restraints excluded: chain X residue 109 GLU Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain X residue 151 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 115 optimal weight: 10.0000 chunk 209 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 321 optimal weight: 3.9990 chunk 346 optimal weight: 20.0000 chunk 61 optimal weight: 9.9990 chunk 295 optimal weight: 9.9990 chunk 329 optimal weight: 20.0000 chunk 431 optimal weight: 9.9990 chunk 101 optimal weight: 0.0970 chunk 298 optimal weight: 5.9990 overall best weight: 5.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 HIS ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 169 HIS ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.198515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.179145 restraints weight = 35724.487| |-----------------------------------------------------------------------------| r_work (start): 0.3934 rms_B_bonded: 1.26 r_work: 0.3850 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3740 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3742 r_free = 0.3742 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 34200 Z= 0.207 Angle : 0.768 7.355 46440 Z= 0.405 Chirality : 0.050 0.205 5424 Planarity : 0.006 0.037 6024 Dihedral : 8.055 53.015 4920 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 6.38 % Allowed : 17.06 % Favored : 76.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.12), residues: 4392 helix: -0.04 (0.12), residues: 1584 sheet: -0.76 (0.14), residues: 1512 loop : -3.21 (0.15), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG T 134 TYR 0.008 0.002 TYR O 126 PHE 0.015 0.002 PHE W 146 HIS 0.007 0.001 HIS G 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (34200) covalent geometry : angle 0.76802 / 0.41 (46440) hydrogen bonds : bond 0.04341 / 2.94 ( 1608) hydrogen bonds : angle 4.86097 / 3.40 ( 4680) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 213 poor density : 476 time to evaluate : 1.224 Fit side-chains REVERT: A 109 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.5569 (pm20) REVERT: B 30 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8601 (mp) REVERT: B 109 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.5609 (pm20) REVERT: C 30 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8634 (mp) REVERT: C 109 GLU cc_start: 0.6772 (OUTLIER) cc_final: 0.5608 (pm20) REVERT: D 30 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8601 (mp) REVERT: D 109 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.5586 (pm20) REVERT: E 109 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.5575 (pm20) REVERT: F 30 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8594 (mp) REVERT: F 109 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.5593 (pm20) REVERT: G 109 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.5594 (pm20) REVERT: H 30 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8579 (mp) REVERT: H 109 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.5562 (pm20) REVERT: I 109 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.5561 (pm20) REVERT: J 30 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8616 (mp) REVERT: J 109 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.5594 (pm20) REVERT: K 109 GLU cc_start: 0.6936 (OUTLIER) cc_final: 0.5605 (pm20) REVERT: L 30 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8616 (mp) REVERT: L 109 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.5521 (pm20) REVERT: M 109 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.5580 (pm20) REVERT: N 30 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8575 (mp) REVERT: N 109 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.5606 (pm20) REVERT: O 30 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8531 (mp) REVERT: O 109 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.5600 (pm20) REVERT: P 30 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8591 (mp) REVERT: P 109 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.5613 (pm20) REVERT: Q 30 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8608 (mp) REVERT: Q 109 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.5517 (pm20) REVERT: R 30 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8625 (mp) REVERT: R 109 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.5650 (pm20) REVERT: R 166 LYS cc_start: 0.8585 (pttt) cc_final: 0.8370 (pttt) REVERT: S 30 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8617 (mp) REVERT: S 109 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.5660 (pm20) REVERT: T 30 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8631 (mp) REVERT: T 109 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.5604 (pm20) REVERT: T 166 LYS cc_start: 0.8514 (pttt) cc_final: 0.8298 (pttt) REVERT: U 30 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8567 (mp) REVERT: U 109 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.5604 (pm20) REVERT: V 30 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8617 (mp) REVERT: V 109 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.5587 (pm20) REVERT: W 30 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8592 (mp) REVERT: W 109 GLU cc_start: 0.6798 (OUTLIER) cc_final: 0.5542 (pm20) REVERT: X 30 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8615 (mp) REVERT: X 109 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.5616 (pm20) outliers start: 213 outliers final: 147 residues processed: 613 average time/residue: 0.2397 time to fit residues: 229.6664 Evaluate side-chains 663 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 189 poor density : 474 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 109 GLU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 109 GLU Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 109 GLU Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain P residue 19 THR Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 109 GLU Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 30 LEU Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain T residue 109 GLU Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain U residue 26 VAL Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 109 GLU Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 30 LEU Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 109 GLU Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 116 LEU Chi-restraints excluded: chain W residue 151 VAL Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 104 THR Chi-restraints excluded: chain X residue 109 GLU Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain X residue 151 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 355 optimal weight: 8.9990 chunk 282 optimal weight: 0.4980 chunk 31 optimal weight: 6.9990 chunk 140 optimal weight: 9.9990 chunk 421 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 233 optimal weight: 9.9990 chunk 399 optimal weight: 2.9990 chunk 183 optimal weight: 0.9980 chunk 244 optimal weight: 9.9990 chunk 271 optimal weight: 20.0000 overall best weight: 4.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 133 GLN ** R 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.200268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.180890 restraints weight = 35808.457| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 1.26 r_work: 0.3868 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3757 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3757 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3753 r_free = 0.3753 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 34200 Z= 0.180 Angle : 0.726 7.161 46440 Z= 0.386 Chirality : 0.048 0.204 5424 Planarity : 0.006 0.036 6024 Dihedral : 7.745 49.831 4920 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 5.94 % Allowed : 17.93 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.68 (0.13), residues: 4392 helix: 0.19 (0.13), residues: 1584 sheet: -0.71 (0.14), residues: 1512 loop : -3.16 (0.15), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG W 134 TYR 0.008 0.002 TYR W 138 PHE 0.016 0.002 PHE W 146 HIS 0.010 0.001 HIS G 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 (34200) covalent geometry : angle 0.72570 / 0.39 (46440) hydrogen bonds : bond 0.04071 / 2.76 ( 1608) hydrogen bonds : angle 4.77698 / 3.35 ( 4680) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8784 Ramachandran restraints generated. 4392 Oldfield, 0 Emsley, 4392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 484 time to evaluate : 1.262 Fit side-chains REVERT: A 109 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.5549 (pm20) REVERT: B 109 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.5450 (pm20) REVERT: C 30 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8641 (mp) REVERT: C 109 GLU cc_start: 0.6693 (OUTLIER) cc_final: 0.5529 (pm20) REVERT: D 30 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8596 (mp) REVERT: D 109 GLU cc_start: 0.6666 (OUTLIER) cc_final: 0.5549 (pm20) REVERT: E 109 GLU cc_start: 0.6751 (OUTLIER) cc_final: 0.5499 (pm20) REVERT: F 30 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8593 (mp) REVERT: F 109 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.5469 (pm20) REVERT: G 109 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.5531 (pm20) REVERT: H 30 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8579 (mp) REVERT: H 109 GLU cc_start: 0.6758 (OUTLIER) cc_final: 0.5439 (pm20) REVERT: I 37 ASP cc_start: 0.7044 (t70) cc_final: 0.6794 (p0) REVERT: I 109 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.5628 (pm20) REVERT: J 30 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8626 (mp) REVERT: J 109 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.5604 (pm20) REVERT: K 109 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.5648 (pm20) REVERT: L 30 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8616 (mp) REVERT: L 109 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.5476 (pm20) REVERT: M 109 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.5570 (pm20) REVERT: N 30 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8584 (mp) REVERT: N 109 GLU cc_start: 0.6685 (OUTLIER) cc_final: 0.5580 (pm20) REVERT: N 166 LYS cc_start: 0.8544 (pttt) cc_final: 0.8278 (pttt) REVERT: O 30 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8571 (mp) REVERT: O 109 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.5566 (pm20) REVERT: P 30 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8583 (mp) REVERT: P 109 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.5475 (pm20) REVERT: Q 30 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8614 (mp) REVERT: Q 109 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.5484 (pm20) REVERT: R 30 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8624 (mp) REVERT: R 109 GLU cc_start: 0.6777 (OUTLIER) cc_final: 0.5656 (pm20) REVERT: R 166 LYS cc_start: 0.8561 (pttt) cc_final: 0.8360 (pttt) REVERT: S 30 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8628 (mp) REVERT: S 109 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.5543 (pm20) REVERT: T 30 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8645 (mp) REVERT: T 109 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.5559 (pm20) REVERT: T 166 LYS cc_start: 0.8474 (pttt) cc_final: 0.8270 (pttt) REVERT: U 30 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8559 (mp) REVERT: U 109 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.5644 (pm20) REVERT: V 30 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8626 (mp) REVERT: V 109 GLU cc_start: 0.6697 (OUTLIER) cc_final: 0.5483 (pm20) REVERT: W 30 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8592 (mp) REVERT: W 109 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.5539 (pm20) REVERT: X 30 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8612 (mp) REVERT: X 109 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.5455 (pm20) outliers start: 198 outliers final: 146 residues processed: 614 average time/residue: 0.2409 time to fit residues: 230.7336 Evaluate side-chains 666 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 479 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 31 ASP Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 116 LEU Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain F residue 19 THR Chi-restraints excluded: chain F residue 30 LEU Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 116 LEU Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 116 LEU Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 116 LEU Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 30 LEU Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 109 GLU Chi-restraints excluded: chain J residue 116 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain K residue 19 THR Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 30 LEU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 68 THR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 116 LEU Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain M residue 19 THR Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 109 GLU Chi-restraints excluded: chain M residue 116 LEU Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 109 GLU Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 151 VAL Chi-restraints excluded: chain O residue 19 THR Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 68 THR Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain O residue 116 LEU Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain P residue 19 THR Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 109 GLU Chi-restraints excluded: chain P residue 116 LEU Chi-restraints excluded: chain P residue 151 VAL Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 30 LEU Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 68 THR Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain R residue 116 LEU Chi-restraints excluded: chain R residue 151 VAL Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 30 LEU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 116 LEU Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 68 THR Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain T residue 109 GLU Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain U residue 26 VAL Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 109 GLU Chi-restraints excluded: chain U residue 116 LEU Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain V residue 19 THR Chi-restraints excluded: chain V residue 30 LEU Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 109 GLU Chi-restraints excluded: chain V residue 116 LEU Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 116 LEU Chi-restraints excluded: chain W residue 151 VAL Chi-restraints excluded: chain X residue 19 THR Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 68 THR Chi-restraints excluded: chain X residue 104 THR Chi-restraints excluded: chain X residue 109 GLU Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain X residue 151 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 128 optimal weight: 30.0000 chunk 388 optimal weight: 0.0270 chunk 229 optimal weight: 7.9990 chunk 50 optimal weight: 9.9990 chunk 322 optimal weight: 0.9990 chunk 244 optimal weight: 9.9990 chunk 13 optimal weight: 7.9990 chunk 56 optimal weight: 0.0170 chunk 303 optimal weight: 0.6980 chunk 24 optimal weight: 9.9990 chunk 75 optimal weight: 3.9990 overall best weight: 1.1480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 133 GLN A 152 ASN B 152 ASN C 76 ASN C 152 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN H 152 ASN I 76 ASN I 152 ASN J 152 ASN ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 152 ASN P 152 ASN ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 152 ASN ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 ASN ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 152 ASN V 133 GLN ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 ASN ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.211631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.193666 restraints weight = 34899.925| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 1.16 r_work: 0.4063 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3954 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3901 r_free = 0.3901 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3901 r_free = 0.3901 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 34200 Z= 0.116 Angle : 0.619 6.985 46440 Z= 0.334 Chirality : 0.044 0.164 5424 Planarity : 0.005 0.039 6024 Dihedral : 6.822 45.708 4920 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 4.29 % Allowed : 19.54 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.22 (0.13), residues: 4392 helix: 0.81 (0.13), residues: 1584 sheet: -0.27 (0.15), residues: 1272 loop : -3.07 (0.14), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG W 63 TYR 0.006 0.002 TYR L 126 PHE 0.017 0.001 PHE W 146 HIS 0.009 0.001 HIS G 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (34200) covalent geometry : angle 0.61920 / 0.33 (46440) hydrogen bonds : bond 0.03323 / 2.26 ( 1608) hydrogen bonds : angle 4.46481 / 3.13 ( 4680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8705.46 seconds wall clock time: 149 minutes 56.53 seconds (8996.53 seconds total)