Starting phenix.real_space_refine on Mon Sep 14 19:21:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6ezj_3999/09_2026/6ezj_3999.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ezj_3999/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/6ezj_3999/09_2026/6ezj_3999.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ezj_3999/09_2026/6ezj_3999.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ezj_3999/09_2026/6ezj_3999.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ezj_3999/09_2026/6ezj_3999.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6ezj_3999/09_2026/6ezj_3999.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6ezj_3999/09_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-2.2.1-6174/lib/python3.11/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: 7.89, per 1000 atoms: 0.23 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: 0.81 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: 8.56 Time building geometry restraints manager: 3.49 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: 240 45.68 - 60.91: 0 60.91 - 76.13: 24 Dihedral angle restraints: 19896 sinusoidal: 7344 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 19893 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: 0.520 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: 0.040 Extract box with map and model: 0.430 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 31.570 Find NCS groups from input model: 1.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 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 : 10.822 76.133 11832 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 : 1.247 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: 0.2560 time to fit residues: 336.1835 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 : 1.153 ------------------------------------------------------------------------------- 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... 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 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.199245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.178693 restraints weight = 33534.006| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 1.20 r_work: 0.3914 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3780 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3780 r_free = 0.3780 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3776 r_free = 0.3776 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3776 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2523 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= 0.246 Angle : 0.855 7.606 46440 Z= 0.448 Chirality : 0.050 0.135 5424 Planarity : 0.008 0.051 6024 Dihedral : 7.803 56.612 4824 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 3.24 % Allowed : 7.43 % Favored : 89.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.28 % 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: -3.43 (0.11), residues: 4392 helix: -2.66 (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 K 138 PHE 0.008 0.002 PHE L 100 HIS 0.007 0.002 HIS S 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00569 / 0.25 (34200) covalent geometry : angle 0.85450 / 0.45 (46440) hydrogen bonds : bond 0.05475 / 3.72 ( 1608) hydrogen bonds : angle 5.13418 / 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 : 1.239 Fit side-chains REVERT: A 133 GLN cc_start: 0.8356 (mt0) cc_final: 0.8086 (mt0) REVERT: C 133 GLN cc_start: 0.8411 (mt0) cc_final: 0.8139 (mt0) REVERT: O 99 ARG cc_start: 0.7808 (ttt180) cc_final: 0.7599 (ttt180) REVERT: R 133 GLN cc_start: 0.8364 (mt0) cc_final: 0.8034 (mt0) REVERT: S 26 VAL cc_start: 0.8105 (p) cc_final: 0.7853 (p) REVERT: S 133 GLN cc_start: 0.8397 (mt0) cc_final: 0.8160 (mt0) REVERT: W 133 GLN cc_start: 0.8435 (mt0) cc_final: 0.8127 (mt0) outliers start: 108 outliers final: 59 residues processed: 673 average time/residue: 0.2602 time to fit residues: 261.7660 Evaluate side-chains 552 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 493 time to evaluate : 1.259 ------------------------------------------------------------------------------- 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 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: 4.9990 chunk 85 optimal weight: 6.9990 chunk 368 optimal weight: 3.9990 chunk 423 optimal weight: 9.9990 chunk 141 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 173 optimal weight: 7.9990 chunk 108 optimal weight: 40.0000 chunk 89 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... P 133 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.200936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.179599 restraints weight = 35566.483| |-----------------------------------------------------------------------------| r_work (start): 0.4011 rms_B_bonded: 1.34 r_work: 0.3923 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3809 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3800 r_free = 0.3800 target_work(ls_wunit_k1) = 0.160 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (9 function evaluations) r_final: 0.3800 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2885 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= 0.165 Angle : 0.724 7.018 46440 Z= 0.385 Chirality : 0.046 0.130 5424 Planarity : 0.006 0.040 6024 Dihedral : 6.946 44.687 4824 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 4.26 % Allowed : 11.54 % Favored : 84.20 % 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: -2.64 (0.12), residues: 4392 helix: -1.25 (0.11), residues: 1584 sheet: -0.22 (0.15), residues: 1248 loop : -3.56 (0.12), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 63 TYR 0.012 0.002 TYR Q 138 PHE 0.005 0.001 PHE F 176 HIS 0.005 0.001 HIS P 73 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.16 (34200) covalent geometry : angle 0.72427 / 0.39 (46440) hydrogen bonds : bond 0.04398 / 2.98 ( 1608) hydrogen bonds : angle 4.66329 / 3.27 ( 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 719 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 577 time to evaluate : 1.193 Fit side-chains REVERT: A 133 GLN cc_start: 0.8434 (mt0) cc_final: 0.8194 (mt0) REVERT: C 133 GLN cc_start: 0.8409 (mt0) cc_final: 0.8184 (mt0) REVERT: G 166 LYS cc_start: 0.8565 (ptmt) cc_final: 0.8342 (pttp) REVERT: O 26 VAL cc_start: 0.8022 (p) cc_final: 0.7821 (p) REVERT: R 133 GLN cc_start: 0.8412 (mt0) cc_final: 0.8179 (mt0) REVERT: S 26 VAL cc_start: 0.8058 (p) cc_final: 0.7856 (p) REVERT: S 133 GLN cc_start: 0.8477 (mt0) cc_final: 0.8277 (mt0) REVERT: V 133 GLN cc_start: 0.8437 (mt0) cc_final: 0.8199 (mt0) REVERT: W 133 GLN cc_start: 0.8514 (mt0) cc_final: 0.8249 (mt0) outliers start: 142 outliers final: 78 residues processed: 651 average time/residue: 0.2259 time to fit residues: 230.2832 Evaluate side-chains 584 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 506 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 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 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 35 VAL Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain T residue 151 VAL 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 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: 5.9990 chunk 10 optimal weight: 6.9990 chunk 225 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 407 optimal weight: 20.0000 chunk 48 optimal weight: 6.9990 chunk 239 optimal weight: 20.0000 chunk 18 optimal weight: 40.0000 chunk 291 optimal weight: 4.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.196743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.175637 restraints weight = 35861.574| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 1.33 r_work: 0.3872 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.3239 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= 0.205 Angle : 0.778 7.292 46440 Z= 0.409 Chirality : 0.049 0.141 5424 Planarity : 0.006 0.042 6024 Dihedral : 6.805 31.251 4824 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 5.55 % Allowed : 12.98 % Favored : 81.47 % 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: -2.38 (0.12), residues: 4392 helix: -0.77 (0.12), residues: 1584 sheet: -0.22 (0.15), residues: 1248 loop : -3.60 (0.12), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG S 134 TYR 0.011 0.003 TYR A 138 PHE 0.007 0.002 PHE F 176 HIS 0.004 0.001 HIS W 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.20 (34200) covalent geometry : angle 0.77799 / 0.41 (46440) hydrogen bonds : bond 0.04504 / 3.06 ( 1608) hydrogen bonds : angle 4.77351 / 3.34 ( 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 664 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 479 time to evaluate : 1.269 Fit side-chains REVERT: A 109 GLU cc_start: 0.7057 (OUTLIER) cc_final: 0.5711 (pm20) REVERT: B 109 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.5703 (pm20) REVERT: C 30 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8559 (mp) REVERT: C 109 GLU cc_start: 0.6939 (OUTLIER) cc_final: 0.5699 (pm20) REVERT: C 133 GLN cc_start: 0.8420 (mt0) cc_final: 0.8209 (mt0) REVERT: D 109 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.5689 (pm20) REVERT: D 166 LYS cc_start: 0.8415 (pttt) cc_final: 0.8159 (pttp) REVERT: E 109 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.5723 (pm20) REVERT: F 109 GLU cc_start: 0.7034 (OUTLIER) cc_final: 0.5668 (pm20) REVERT: G 109 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.5692 (pm20) REVERT: H 109 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.5686 (pm20) REVERT: I 109 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.5690 (pm20) REVERT: J 109 GLU cc_start: 0.7017 (OUTLIER) cc_final: 0.5723 (pm20) REVERT: K 109 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.5667 (pm20) REVERT: L 109 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.5701 (pm20) REVERT: M 109 GLU cc_start: 0.7007 (OUTLIER) cc_final: 0.5715 (pm20) REVERT: N 109 GLU cc_start: 0.7025 (OUTLIER) cc_final: 0.5718 (pm20) REVERT: O 109 GLU cc_start: 0.6994 (OUTLIER) cc_final: 0.5768 (pm20) REVERT: O 166 LYS cc_start: 0.8534 (pttt) cc_final: 0.8289 (pttt) REVERT: P 109 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.5718 (pm20) REVERT: Q 109 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.5727 (pm20) REVERT: R 109 GLU cc_start: 0.7093 (OUTLIER) cc_final: 0.5766 (pm20) REVERT: S 109 GLU cc_start: 0.7006 (OUTLIER) cc_final: 0.5765 (pm20) REVERT: T 109 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.5683 (pm20) REVERT: U 109 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.5809 (pm20) REVERT: V 109 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.5716 (pm20) REVERT: W 109 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.5725 (pm20) REVERT: W 133 GLN cc_start: 0.8463 (mt0) cc_final: 0.8219 (mt0) REVERT: X 109 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.5673 (pm20) outliers start: 185 outliers final: 104 residues processed: 601 average time/residue: 0.2197 time to fit residues: 206.9944 Evaluate side-chains 598 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 469 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 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 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 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 35 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 109 GLU 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 151 VAL 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 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 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 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 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 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 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 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: 30.0000 chunk 343 optimal weight: 20.0000 chunk 379 optimal weight: 9.9990 chunk 263 optimal weight: 8.9990 chunk 150 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 239 optimal weight: 20.0000 chunk 119 optimal weight: 0.0010 chunk 4 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 overall best weight: 5.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 61 HIS K 152 ASN M 152 ASN M 185 GLN U 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.195766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.174813 restraints weight = 35991.348| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 1.33 r_work: 0.3849 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3736 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3730 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3730 r_free = 0.3730 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3730 r_free = 0.3730 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3730 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.3418 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= 0.211 Angle : 0.773 7.088 46440 Z= 0.407 Chirality : 0.050 0.131 5424 Planarity : 0.006 0.040 6024 Dihedral : 6.800 30.551 4824 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 5.43 % Allowed : 14.51 % Favored : 80.07 % 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: -2.21 (0.12), residues: 4392 helix: -0.54 (0.12), residues: 1584 sheet: -0.27 (0.16), residues: 1272 loop : -3.52 (0.12), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 134 TYR 0.009 0.002 TYR D 138 PHE 0.007 0.002 PHE U 176 HIS 0.004 0.001 HIS G 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 (34200) covalent geometry : angle 0.77341 / 0.41 (46440) hydrogen bonds : bond 0.04425 / 3.00 ( 1608) hydrogen bonds : angle 4.84726 / 3.39 ( 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 658 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 477 time to evaluate : 1.362 Fit side-chains REVERT: A 30 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8545 (mp) REVERT: A 109 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.5491 (pm20) REVERT: B 30 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8486 (mp) REVERT: B 109 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.5526 (pm20) REVERT: C 30 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8620 (mp) REVERT: C 109 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.5572 (pm20) REVERT: D 30 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8551 (mp) REVERT: D 109 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.5572 (pm20) REVERT: E 109 GLU cc_start: 0.6953 (OUTLIER) cc_final: 0.5622 (pm20) REVERT: F 30 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8525 (mp) REVERT: F 109 GLU cc_start: 0.6875 (OUTLIER) cc_final: 0.5531 (pm20) REVERT: G 109 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.5684 (pm20) REVERT: H 37 ASP cc_start: 0.6414 (p0) cc_final: 0.6182 (p0) REVERT: H 109 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.5516 (pm20) REVERT: I 109 GLU cc_start: 0.6823 (OUTLIER) cc_final: 0.5593 (pm20) REVERT: J 30 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8533 (mp) REVERT: J 109 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.5564 (pm20) REVERT: K 109 GLU cc_start: 0.7004 (OUTLIER) cc_final: 0.5678 (pm20) REVERT: L 30 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8563 (mp) REVERT: L 109 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.5530 (pm20) REVERT: M 109 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.5648 (pm20) REVERT: N 30 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8528 (mp) REVERT: N 109 GLU cc_start: 0.6945 (OUTLIER) cc_final: 0.5680 (pm20) REVERT: O 30 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8484 (mp) REVERT: O 109 GLU cc_start: 0.6863 (OUTLIER) cc_final: 0.5644 (pm20) REVERT: P 30 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8546 (mp) REVERT: P 109 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.5553 (pm20) REVERT: Q 30 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8558 (mp) REVERT: Q 109 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.5559 (pm20) REVERT: R 109 GLU cc_start: 0.6919 (OUTLIER) cc_final: 0.5597 (pm20) REVERT: S 30 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8560 (mp) REVERT: S 109 GLU cc_start: 0.7002 (OUTLIER) cc_final: 0.5791 (pm20) REVERT: T 30 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8582 (mp) REVERT: T 109 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.5633 (pm20) REVERT: U 30 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8542 (mp) REVERT: U 109 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.5643 (pm20) REVERT: V 109 GLU cc_start: 0.6876 (OUTLIER) cc_final: 0.5558 (pm20) REVERT: W 30 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8572 (mp) REVERT: W 109 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.5603 (pm20) REVERT: W 133 GLN cc_start: 0.8483 (mt0) cc_final: 0.8249 (mt0) REVERT: X 30 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8554 (mp) REVERT: X 109 GLU cc_start: 0.6862 (OUTLIER) cc_final: 0.5539 (pm20) outliers start: 181 outliers final: 112 residues processed: 587 average time/residue: 0.2262 time to fit residues: 207.8889 Evaluate side-chains 627 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 475 time to evaluate : 1.052 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 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 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 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 104 THR Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain K residue 152 ASN 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 151 VAL Chi-restraints excluded: chain M residue 152 ASN 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 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 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 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 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 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 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 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: 0.0370 chunk 267 optimal weight: 7.9990 chunk 237 optimal weight: 2.9990 chunk 246 optimal weight: 7.9990 chunk 80 optimal weight: 6.9990 chunk 402 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 387 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 398 optimal weight: 30.0000 chunk 221 optimal weight: 7.9990 overall best weight: 4.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 76 ASN ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 76 ASN ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 ASN R 76 ASN V 76 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.196635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.175836 restraints weight = 35838.359| |-----------------------------------------------------------------------------| r_work (start): 0.3951 rms_B_bonded: 1.33 r_work: 0.3866 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3754 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3754 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 34200 Z= 0.187 Angle : 0.738 6.969 46440 Z= 0.390 Chirality : 0.049 0.133 5424 Planarity : 0.006 0.036 6024 Dihedral : 6.669 30.889 4824 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Rotamer: Outliers : 5.88 % Allowed : 15.53 % Favored : 78.60 % 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: -2.14 (0.12), residues: 4392 helix: -0.28 (0.12), residues: 1584 sheet: -0.82 (0.14), residues: 1512 loop : -3.47 (0.14), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG W 134 TYR 0.008 0.002 TYR W 138 PHE 0.008 0.002 PHE M 146 HIS 0.006 0.001 HIS G 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.19 (34200) covalent geometry : angle 0.73820 / 0.39 (46440) hydrogen bonds : bond 0.04232 / 2.87 ( 1608) hydrogen bonds : angle 4.80803 / 3.36 ( 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 701 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 505 time to evaluate : 1.252 Fit side-chains REVERT: A 30 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8620 (mp) REVERT: A 109 GLU cc_start: 0.6834 (OUTLIER) cc_final: 0.5576 (pm20) REVERT: B 30 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8554 (mp) REVERT: B 109 GLU cc_start: 0.6827 (OUTLIER) cc_final: 0.5578 (pm20) REVERT: C 30 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8620 (mp) REVERT: C 109 GLU cc_start: 0.6745 (OUTLIER) cc_final: 0.5603 (pm20) REVERT: D 30 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8580 (mp) REVERT: D 109 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.5628 (pm20) REVERT: E 109 GLU cc_start: 0.6905 (OUTLIER) cc_final: 0.5644 (pm20) REVERT: F 109 GLU cc_start: 0.6826 (OUTLIER) cc_final: 0.5582 (pm20) REVERT: G 109 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.5658 (pm20) REVERT: H 30 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8519 (mp) REVERT: H 72 ASP cc_start: 0.7877 (m-30) cc_final: 0.7249 (t0) REVERT: H 109 GLU cc_start: 0.6831 (OUTLIER) cc_final: 0.5567 (pm20) REVERT: I 109 GLU cc_start: 0.6754 (OUTLIER) cc_final: 0.5618 (pm20) REVERT: J 30 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8588 (mp) REVERT: J 109 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.5625 (pm20) REVERT: K 109 GLU cc_start: 0.6913 (OUTLIER) cc_final: 0.5644 (pm20) REVERT: L 30 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8588 (mp) REVERT: L 72 ASP cc_start: 0.7907 (m-30) cc_final: 0.7301 (t0) REVERT: L 109 GLU cc_start: 0.6814 (OUTLIER) cc_final: 0.5545 (pm20) REVERT: M 109 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.5551 (pm20) REVERT: N 30 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8555 (mp) REVERT: N 109 GLU cc_start: 0.6796 (OUTLIER) cc_final: 0.5582 (pm20) REVERT: O 30 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8585 (mp) REVERT: O 109 GLU cc_start: 0.6818 (OUTLIER) cc_final: 0.5682 (pm20) REVERT: P 30 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8566 (mp) REVERT: P 109 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.5567 (pm20) REVERT: Q 30 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8573 (mp) REVERT: Q 109 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.5586 (pm20) REVERT: R 109 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.5622 (pm20) REVERT: S 72 ASP cc_start: 0.7838 (m-30) cc_final: 0.7202 (t0) REVERT: S 109 GLU cc_start: 0.6911 (OUTLIER) cc_final: 0.5764 (pm20) REVERT: T 30 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8603 (mp) REVERT: T 72 ASP cc_start: 0.7914 (m-30) cc_final: 0.7268 (t0) REVERT: T 109 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.5596 (pm20) REVERT: U 30 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8553 (mp) REVERT: U 109 GLU cc_start: 0.6846 (OUTLIER) cc_final: 0.5662 (pm20) REVERT: V 30 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8567 (mp) REVERT: V 109 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.5575 (pm20) REVERT: W 30 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8602 (mp) REVERT: W 109 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.5617 (pm20) REVERT: W 133 GLN cc_start: 0.8509 (mt0) cc_final: 0.8286 (mt0) REVERT: X 30 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8587 (mp) REVERT: X 109 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.5566 (pm20) outliers start: 196 outliers final: 131 residues processed: 635 average time/residue: 0.2207 time to fit residues: 222.1933 Evaluate side-chains 652 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 481 time to evaluate : 1.278 ------------------------------------------------------------------------------- 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 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 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 104 THR Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 116 LEU 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 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 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 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 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: 9.9990 chunk 144 optimal weight: 40.0000 chunk 249 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 419 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 276 optimal weight: 4.9990 chunk 207 optimal weight: 10.0000 chunk 290 optimal weight: 2.9990 chunk 349 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 ASN A 133 GLN B 76 ASN C 76 ASN C 133 GLN ** C 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 185 GLN F 76 ASN ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 152 ASN L 76 ASN M 152 ASN N 76 ASN O 76 ASN Q 76 ASN ** 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** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 ASN ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.198343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.177893 restraints weight = 35912.127| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 1.31 r_work: 0.3877 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3767 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3767 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3759 r_free = 0.3759 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3565 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= 0.176 Angle : 0.721 6.919 46440 Z= 0.382 Chirality : 0.048 0.156 5424 Planarity : 0.006 0.036 6024 Dihedral : 6.513 30.937 4824 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 6.00 % Allowed : 17.00 % Favored : 77.01 % 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: -1.83 (0.12), residues: 4392 helix: 0.02 (0.12), residues: 1584 sheet: -0.27 (0.15), residues: 1272 loop : -3.40 (0.12), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 134 TYR 0.008 0.002 TYR N 138 PHE 0.008 0.001 PHE W 146 HIS 0.007 0.001 HIS G 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.18 (34200) covalent geometry : angle 0.72063 / 0.38 (46440) hydrogen bonds : bond 0.04089 / 2.78 ( 1608) hydrogen bonds : angle 4.76613 / 3.34 ( 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 700 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 200 poor density : 500 time to evaluate : 1.265 Fit side-chains REVERT: A 30 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8617 (mp) REVERT: A 109 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.5566 (pm20) REVERT: B 30 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8577 (mp) REVERT: B 72 ASP cc_start: 0.7820 (m-30) cc_final: 0.7255 (t0) REVERT: B 109 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.5524 (pm20) REVERT: C 30 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8646 (mp) REVERT: C 109 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.5578 (pm20) REVERT: D 30 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8618 (mp) REVERT: D 72 ASP cc_start: 0.7828 (m-30) cc_final: 0.7261 (t0) REVERT: D 109 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.5571 (pm20) REVERT: E 109 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.5635 (pm20) REVERT: F 30 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8591 (mp) REVERT: F 72 ASP cc_start: 0.7830 (m-30) cc_final: 0.7265 (t0) REVERT: F 109 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.5541 (pm20) REVERT: G 109 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.5578 (pm20) REVERT: H 30 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8555 (mp) REVERT: H 72 ASP cc_start: 0.7829 (m-30) cc_final: 0.7259 (t0) REVERT: H 109 GLU cc_start: 0.6743 (OUTLIER) cc_final: 0.5533 (pm20) REVERT: I 109 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.5604 (pm20) REVERT: J 30 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8618 (mp) REVERT: J 109 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.5583 (pm20) REVERT: K 109 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.5630 (pm20) REVERT: L 30 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8606 (mp) REVERT: L 72 ASP cc_start: 0.7843 (m-30) cc_final: 0.7293 (t0) REVERT: L 109 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.5529 (pm20) REVERT: M 72 ASP cc_start: 0.7847 (m-30) cc_final: 0.7247 (t0) REVERT: M 109 GLU cc_start: 0.6711 (OUTLIER) cc_final: 0.5515 (pm20) REVERT: N 30 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8553 (mp) REVERT: N 109 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.5564 (pm20) REVERT: O 30 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8603 (mp) REVERT: O 72 ASP cc_start: 0.7917 (m-30) cc_final: 0.7353 (t0) REVERT: O 109 GLU cc_start: 0.6733 (OUTLIER) cc_final: 0.5643 (pm20) REVERT: P 30 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8590 (mp) REVERT: P 109 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.5537 (pm20) REVERT: Q 30 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8628 (mp) REVERT: Q 72 ASP cc_start: 0.7923 (m-30) cc_final: 0.7295 (t0) REVERT: Q 109 GLU cc_start: 0.6752 (OUTLIER) cc_final: 0.5561 (pm20) REVERT: R 30 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8613 (mp) REVERT: R 109 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.5615 (pm20) REVERT: S 30 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8603 (mp) REVERT: S 72 ASP cc_start: 0.7794 (m-30) cc_final: 0.7225 (t0) REVERT: S 109 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.5676 (pm20) REVERT: T 30 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8592 (mp) REVERT: T 72 ASP cc_start: 0.7871 (m-30) cc_final: 0.7279 (t0) REVERT: T 109 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.5542 (pm20) REVERT: U 30 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8548 (mp) REVERT: U 72 ASP cc_start: 0.7836 (m-30) cc_final: 0.7277 (t0) REVERT: U 109 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.5691 (pm20) REVERT: V 30 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8617 (mp) REVERT: V 109 GLU cc_start: 0.6741 (OUTLIER) cc_final: 0.5553 (pm20) REVERT: W 30 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8602 (mp) REVERT: W 109 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.5602 (pm20) REVERT: W 133 GLN cc_start: 0.8477 (mt0) cc_final: 0.8258 (mt0) REVERT: X 30 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8599 (mp) REVERT: X 109 GLU cc_start: 0.6739 (OUTLIER) cc_final: 0.5542 (pm20) outliers start: 200 outliers final: 133 residues processed: 628 average time/residue: 0.2130 time to fit residues: 211.1921 Evaluate side-chains 665 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 176 poor density : 489 time to evaluate : 1.199 ------------------------------------------------------------------------------- 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 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 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 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 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 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 K residue 152 ASN 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 M residue 152 ASN 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 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 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: 1.9990 chunk 207 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 126 optimal weight: 40.0000 chunk 413 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 83 optimal weight: 0.2980 chunk 419 optimal weight: 20.0000 chunk 9 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 overall best weight: 4.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 HIS ** 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 ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN ** 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 69 HIS ** 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 69 HIS ** X 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.197333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.177139 restraints weight = 35907.429| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 1.29 r_work: 0.3858 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3737 r_free = 0.3737 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3737 r_free = 0.3737 target_work(ls_wunit_k1) = 0.155 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (11 function evaluations) r_final: 0.3737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3636 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= 0.201 Angle : 0.759 7.037 46440 Z= 0.401 Chirality : 0.050 0.192 5424 Planarity : 0.006 0.038 6024 Dihedral : 6.614 31.217 4824 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 6.12 % Allowed : 17.12 % Favored : 76.77 % 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: -1.88 (0.12), residues: 4392 helix: 0.02 (0.12), residues: 1584 sheet: -0.77 (0.14), residues: 1512 loop : -3.33 (0.15), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 134 TYR 0.008 0.002 TYR M 126 PHE 0.010 0.002 PHE K 146 HIS 0.009 0.001 HIS X 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (34200) covalent geometry : angle 0.75950 / 0.40 (46440) hydrogen bonds : bond 0.04286 / 2.91 ( 1608) hydrogen bonds : angle 4.83428 / 3.38 ( 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 689 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 204 poor density : 485 time to evaluate : 1.304 Fit side-chains REVERT: A 30 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8630 (mp) REVERT: A 109 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.5553 (pm20) REVERT: B 30 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8573 (mp) REVERT: B 109 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.5524 (pm20) REVERT: C 30 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8627 (mp) REVERT: C 109 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.5570 (pm20) REVERT: D 30 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8622 (mp) REVERT: D 109 GLU cc_start: 0.6857 (OUTLIER) cc_final: 0.5556 (pm20) REVERT: E 109 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.5538 (pm20) REVERT: F 30 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8600 (mp) REVERT: F 109 GLU cc_start: 0.6838 (OUTLIER) cc_final: 0.5522 (pm20) REVERT: G 109 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.5530 (pm20) REVERT: H 30 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8556 (mp) REVERT: H 72 ASP cc_start: 0.7862 (m-30) cc_final: 0.7213 (t0) REVERT: H 109 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.5507 (pm20) REVERT: I 109 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.5589 (pm20) REVERT: J 30 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8620 (mp) REVERT: J 109 GLU cc_start: 0.6867 (OUTLIER) cc_final: 0.5568 (pm20) REVERT: K 109 GLU cc_start: 0.6910 (OUTLIER) cc_final: 0.5592 (pm20) REVERT: L 30 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8611 (mp) REVERT: L 109 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.5515 (pm20) REVERT: M 109 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.5626 (pm20) REVERT: N 30 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8579 (mp) REVERT: N 109 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.5642 (pm20) REVERT: O 30 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8605 (mp) REVERT: O 109 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.5631 (pm20) REVERT: P 30 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8592 (mp) REVERT: P 109 GLU cc_start: 0.6840 (OUTLIER) cc_final: 0.5529 (pm20) REVERT: Q 30 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8561 (mp) REVERT: Q 109 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.5553 (pm20) REVERT: R 30 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8622 (mp) REVERT: R 109 GLU cc_start: 0.6886 (OUTLIER) cc_final: 0.5682 (pm20) REVERT: R 166 LYS cc_start: 0.8568 (pttt) cc_final: 0.8363 (pttt) REVERT: S 30 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8610 (mp) REVERT: S 109 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.5651 (pm20) REVERT: T 30 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8610 (mp) REVERT: T 109 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.5627 (pm20) REVERT: U 30 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8574 (mp) REVERT: U 109 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.5583 (pm20) REVERT: V 30 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8627 (mp) REVERT: V 109 GLU cc_start: 0.6845 (OUTLIER) cc_final: 0.5539 (pm20) REVERT: W 30 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8588 (mp) REVERT: W 109 GLU cc_start: 0.6776 (OUTLIER) cc_final: 0.5588 (pm20) REVERT: X 30 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8624 (mp) REVERT: X 109 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.5528 (pm20) outliers start: 204 outliers final: 137 residues processed: 617 average time/residue: 0.2232 time to fit residues: 218.2881 Evaluate side-chains 655 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 475 time to evaluate : 1.290 ------------------------------------------------------------------------------- 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 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 68 THR 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 152 ASN 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 152 ASN 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 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 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: 9.9990 chunk 209 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 321 optimal weight: 10.0000 chunk 346 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 295 optimal weight: 9.9990 chunk 329 optimal weight: 20.0000 chunk 431 optimal weight: 7.9990 chunk 101 optimal weight: 0.6980 chunk 298 optimal weight: 5.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 145 HIS ** 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 ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN ** 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** ** U 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 145 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.194122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.174474 restraints weight = 36064.029| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 1.21 r_work: 0.3854 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3747 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3741 r_free = 0.3741 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 34200 Z= 0.221 Angle : 0.788 7.008 46440 Z= 0.414 Chirality : 0.051 0.189 5424 Planarity : 0.006 0.041 6024 Dihedral : 6.726 31.964 4824 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 6.18 % Allowed : 17.75 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.95 (0.12), residues: 4392 helix: -0.09 (0.12), residues: 1584 sheet: -0.77 (0.14), residues: 1512 loop : -3.33 (0.15), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG T 134 TYR 0.009 0.002 TYR G 126 PHE 0.012 0.002 PHE M 146 HIS 0.006 0.001 HIS G 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00519 / 0.22 (34200) covalent geometry : angle 0.78769 / 0.41 (46440) hydrogen bonds : bond 0.04435 / 3.01 ( 1608) hydrogen bonds : angle 4.90368 / 3.43 ( 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 682 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 206 poor density : 476 time to evaluate : 1.180 Fit side-chains REVERT: A 30 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8626 (mp) REVERT: A 109 GLU cc_start: 0.6736 (OUTLIER) cc_final: 0.5471 (pm20) REVERT: B 30 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8594 (mp) REVERT: B 109 GLU cc_start: 0.6879 (OUTLIER) cc_final: 0.5530 (pm20) REVERT: C 30 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8630 (mp) REVERT: C 109 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.5539 (pm20) REVERT: D 30 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.8609 (mp) REVERT: D 109 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.5523 (pm20) REVERT: E 109 GLU cc_start: 0.6959 (OUTLIER) cc_final: 0.5590 (pm20) REVERT: F 30 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8602 (mp) REVERT: F 109 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.5526 (pm20) REVERT: G 109 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.5544 (pm20) REVERT: H 30 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8603 (mp) REVERT: H 109 GLU cc_start: 0.6891 (OUTLIER) cc_final: 0.5517 (pm20) REVERT: I 37 ASP cc_start: 0.6723 (t70) cc_final: 0.6476 (t70) REVERT: I 109 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.5558 (pm20) REVERT: J 30 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8610 (mp) REVERT: J 109 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.5533 (pm20) REVERT: K 30 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8580 (mp) REVERT: K 109 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.5598 (pm20) REVERT: L 30 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8612 (mp) REVERT: L 109 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.5525 (pm20) REVERT: M 109 GLU cc_start: 0.6806 (OUTLIER) cc_final: 0.5600 (pm20) REVERT: N 30 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8582 (mp) REVERT: N 109 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.5640 (pm20) REVERT: O 30 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8612 (mp) REVERT: O 109 GLU cc_start: 0.6839 (OUTLIER) cc_final: 0.5610 (pm20) REVERT: P 30 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8594 (mp) REVERT: P 109 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.5544 (pm20) REVERT: Q 30 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8566 (mp) REVERT: Q 109 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.5555 (pm20) REVERT: R 30 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8629 (mp) REVERT: R 109 GLU cc_start: 0.6890 (OUTLIER) cc_final: 0.5661 (pm20) REVERT: R 166 LYS cc_start: 0.8545 (pttt) cc_final: 0.8333 (pttt) REVERT: S 30 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8629 (mp) REVERT: S 109 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.5609 (pm20) REVERT: T 30 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8578 (mp) REVERT: T 109 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.5552 (pm20) REVERT: U 30 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8572 (mp) REVERT: U 109 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.5540 (pm20) REVERT: V 30 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8622 (mp) REVERT: V 109 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.5534 (pm20) REVERT: W 30 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8598 (mp) REVERT: W 109 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.5595 (pm20) REVERT: X 30 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8620 (mp) REVERT: X 109 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.5491 (pm20) outliers start: 206 outliers final: 137 residues processed: 608 average time/residue: 0.2165 time to fit residues: 206.8526 Evaluate side-chains 653 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 181 poor density : 472 time to evaluate : 1.208 ------------------------------------------------------------------------------- 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 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 68 THR 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 152 ASN 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 152 ASN 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 137 THR 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 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: 7.9990 chunk 282 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 421 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 chunk 233 optimal weight: 9.9990 chunk 399 optimal weight: 0.8980 chunk 183 optimal weight: 5.9990 chunk 244 optimal weight: 8.9990 chunk 271 optimal weight: 20.0000 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 76 ASN ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN ** I 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 76 ASN K 152 ASN ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN ** 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 76 ASN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.204169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.185192 restraints weight = 35524.095| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 1.25 r_work: 0.3903 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3795 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3784 r_free = 0.3784 target_work(ls_wunit_k1) = 0.159 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 34200 Z= 0.156 Angle : 0.691 6.894 46440 Z= 0.370 Chirality : 0.047 0.204 5424 Planarity : 0.005 0.039 6024 Dihedral : 6.377 31.888 4824 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.95 % Allowed : 19.30 % Favored : 75.75 % 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: -1.63 (0.13), residues: 4392 helix: 0.33 (0.13), residues: 1584 sheet: -0.71 (0.14), residues: 1512 loop : -3.25 (0.15), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 63 TYR 0.008 0.002 TYR W 138 PHE 0.010 0.001 PHE K 146 HIS 0.009 0.001 HIS G 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (34200) covalent geometry : angle 0.69148 / 0.37 (46440) hydrogen bonds : bond 0.03877 / 2.63 ( 1608) hydrogen bonds : angle 4.73797 / 3.32 ( 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 674 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 509 time to evaluate : 1.011 Fit side-chains REVERT: A 30 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8621 (mp) REVERT: A 109 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.5589 (pm20) REVERT: B 30 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8567 (mp) REVERT: B 72 ASP cc_start: 0.7660 (m-30) cc_final: 0.7220 (t0) REVERT: B 109 GLU cc_start: 0.6725 (OUTLIER) cc_final: 0.5634 (pm20) REVERT: C 30 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8630 (mp) REVERT: C 109 GLU cc_start: 0.6639 (OUTLIER) cc_final: 0.5657 (pm20) REVERT: D 72 ASP cc_start: 0.7702 (m-30) cc_final: 0.7237 (t0) REVERT: D 109 GLU cc_start: 0.6643 (OUTLIER) cc_final: 0.5618 (pm20) REVERT: E 109 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.5635 (pm20) REVERT: F 30 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8567 (mp) REVERT: F 72 ASP cc_start: 0.7763 (m-30) cc_final: 0.7301 (t0) REVERT: F 109 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.5652 (pm20) REVERT: G 37 ASP cc_start: 0.6737 (t70) cc_final: 0.6501 (t70) REVERT: G 109 GLU cc_start: 0.6764 (OUTLIER) cc_final: 0.5728 (pm20) REVERT: H 30 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8586 (mp) REVERT: H 72 ASP cc_start: 0.7655 (m-30) cc_final: 0.7226 (t0) REVERT: H 109 GLU cc_start: 0.6813 (OUTLIER) cc_final: 0.5694 (pm20) REVERT: I 37 ASP cc_start: 0.6983 (t70) cc_final: 0.6757 (t70) REVERT: I 109 GLU cc_start: 0.6645 (OUTLIER) cc_final: 0.5640 (pm20) REVERT: J 30 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8619 (mp) REVERT: J 109 GLU cc_start: 0.6705 (OUTLIER) cc_final: 0.5672 (pm20) REVERT: K 72 ASP cc_start: 0.7809 (m-30) cc_final: 0.7233 (t0) REVERT: K 109 GLU cc_start: 0.6747 (OUTLIER) cc_final: 0.5676 (pm20) REVERT: L 72 ASP cc_start: 0.7717 (m-30) cc_final: 0.7301 (t0) REVERT: L 109 GLU cc_start: 0.6732 (OUTLIER) cc_final: 0.5637 (pm20) REVERT: M 72 ASP cc_start: 0.7726 (m-30) cc_final: 0.7241 (t0) REVERT: M 109 GLU cc_start: 0.6651 (OUTLIER) cc_final: 0.5621 (pm20) REVERT: N 30 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8570 (mp) REVERT: N 72 ASP cc_start: 0.7782 (m-30) cc_final: 0.7166 (t0) REVERT: N 109 GLU cc_start: 0.6699 (OUTLIER) cc_final: 0.5657 (pm20) REVERT: O 72 ASP cc_start: 0.7701 (m-30) cc_final: 0.7286 (t0) REVERT: O 109 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.5573 (pm20) REVERT: P 30 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8571 (mp) REVERT: P 72 ASP cc_start: 0.7862 (m-30) cc_final: 0.7205 (t0) REVERT: P 109 GLU cc_start: 0.6755 (OUTLIER) cc_final: 0.5687 (pm20) REVERT: Q 30 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8622 (mp) REVERT: Q 109 GLU cc_start: 0.6765 (OUTLIER) cc_final: 0.5681 (pm20) REVERT: R 30 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8630 (mp) REVERT: R 109 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.5618 (pm20) REVERT: R 166 LYS cc_start: 0.8492 (pttt) cc_final: 0.8279 (pttt) REVERT: S 30 LEU cc_start: 0.9012 (OUTLIER) cc_final: 0.8611 (mp) REVERT: S 72 ASP cc_start: 0.7764 (m-30) cc_final: 0.7201 (t0) REVERT: S 109 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.5826 (pm20) REVERT: T 30 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8597 (mp) REVERT: T 72 ASP cc_start: 0.7752 (m-30) cc_final: 0.7170 (t0) REVERT: T 109 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.5625 (pm20) REVERT: U 30 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8550 (mp) REVERT: U 72 ASP cc_start: 0.7710 (m-30) cc_final: 0.7271 (t0) REVERT: U 109 GLU cc_start: 0.6703 (OUTLIER) cc_final: 0.5694 (pm20) REVERT: V 30 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8627 (mp) REVERT: V 109 GLU cc_start: 0.6756 (OUTLIER) cc_final: 0.5680 (pm20) REVERT: W 30 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8588 (mp) REVERT: W 42 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.6764 (tp) REVERT: W 109 GLU cc_start: 0.6601 (OUTLIER) cc_final: 0.5566 (pm20) REVERT: W 133 GLN cc_start: 0.8455 (mt0) cc_final: 0.8236 (mt0) REVERT: X 109 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.5644 (pm20) outliers start: 165 outliers final: 121 residues processed: 621 average time/residue: 0.2189 time to fit residues: 214.6915 Evaluate side-chains 657 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 496 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 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 152 ASN 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 152 ASN 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 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 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 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 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 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 42 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 128 optimal weight: 30.0000 chunk 388 optimal weight: 9.9990 chunk 229 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 322 optimal weight: 0.9990 chunk 244 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 56 optimal weight: 0.0030 chunk 303 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 overall best weight: 3.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 152 ASN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.202571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.183856 restraints weight = 35224.141| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 1.23 r_work: 0.3873 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.3764 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3757 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3757 r_free = 0.3757 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3757 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3732 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= 0.178 Angle : 0.723 6.939 46440 Z= 0.382 Chirality : 0.048 0.185 5424 Planarity : 0.005 0.040 6024 Dihedral : 6.408 31.509 4824 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 5.70 % Allowed : 18.94 % Favored : 75.36 % 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: -1.63 (0.13), residues: 4392 helix: 0.32 (0.13), residues: 1584 sheet: -0.70 (0.14), residues: 1512 loop : -3.23 (0.15), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 17 TYR 0.008 0.002 TYR B 126 PHE 0.010 0.002 PHE M 146 HIS 0.008 0.001 HIS G 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (34200) covalent geometry : angle 0.72291 / 0.38 (46440) hydrogen bonds : bond 0.04081 / 2.77 ( 1608) hydrogen bonds : angle 4.74304 / 3.32 ( 4680) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8023.62 seconds wall clock time: 138 minutes 13.98 seconds (8293.98 seconds total)