Starting phenix.real_space_refine on Thu Feb 22 08:16:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezj_3999/02_2024/6ezj_3999_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezj_3999/02_2024/6ezj_3999.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezj_3999/02_2024/6ezj_3999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezj_3999/02_2024/6ezj_3999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezj_3999/02_2024/6ezj_3999_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ezj_3999/02_2024/6ezj_3999_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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 Symmetric amino acids flipped None Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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, 'ASN:plan1': 1, 'ASP:plan': 5} 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: 16.83, per 1000 atoms: 0.50 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.27 Conformation dependent library (CDL) restraints added in 6.5 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... running ksdssp... Secondary structure from input PDB file: 120 helices and 48 sheets defined 30.3% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.52 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 removed outlier: 3.554A pdb=" N HIS A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 54 No H-bonds generated for 'chain 'A' and resid 51 through 54' Processing helix chain 'A' and resid 74 through 90 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 143 through 154 removed outlier: 3.787A pdb=" N THR A 153 " --> pdb=" O SER A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 183 removed outlier: 3.728A pdb=" N ALA A 180 " --> pdb=" O PHE A 176 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 49 removed outlier: 3.554A pdb=" N HIS B 47 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 54 No H-bonds generated for 'chain 'B' and resid 51 through 54' Processing helix chain 'B' and resid 74 through 90 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 143 through 154 removed outlier: 3.787A pdb=" N THR B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA B 180 " --> pdb=" O PHE B 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS C 47 " --> pdb=" O PRO C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 54 No H-bonds generated for 'chain 'C' and resid 51 through 54' Processing helix chain 'C' and resid 74 through 90 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 143 through 154 removed outlier: 3.787A pdb=" N THR C 153 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 183 removed outlier: 3.727A pdb=" N ALA C 180 " --> pdb=" O PHE C 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 49 removed outlier: 3.554A pdb=" N HIS D 47 " --> pdb=" O PRO D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 54 No H-bonds generated for 'chain 'D' and resid 51 through 54' Processing helix chain 'D' and resid 74 through 90 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 143 through 154 removed outlier: 3.786A pdb=" N THR D 153 " --> pdb=" O SER D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 183 removed outlier: 3.728A pdb=" N ALA D 180 " --> pdb=" O PHE D 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 49 removed outlier: 3.554A pdb=" N HIS E 47 " --> pdb=" O PRO E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 54 No H-bonds generated for 'chain 'E' and resid 51 through 54' Processing helix chain 'E' and resid 74 through 90 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 143 through 154 removed outlier: 3.786A pdb=" N THR E 153 " --> pdb=" O SER E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA E 180 " --> pdb=" O PHE E 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS F 47 " --> pdb=" O PRO F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 54 No H-bonds generated for 'chain 'F' and resid 51 through 54' Processing helix chain 'F' and resid 74 through 90 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 143 through 154 removed outlier: 3.787A pdb=" N THR F 153 " --> pdb=" O SER F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA F 180 " --> pdb=" O PHE F 176 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 49 removed outlier: 3.554A pdb=" N HIS G 47 " --> pdb=" O PRO G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 54 No H-bonds generated for 'chain 'G' and resid 51 through 54' Processing helix chain 'G' and resid 74 through 90 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 143 through 154 removed outlier: 3.788A pdb=" N THR G 153 " --> pdb=" O SER G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA G 180 " --> pdb=" O PHE G 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS H 47 " --> pdb=" O PRO H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 54 No H-bonds generated for 'chain 'H' and resid 51 through 54' Processing helix chain 'H' and resid 74 through 90 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 143 through 154 removed outlier: 3.788A pdb=" N THR H 153 " --> pdb=" O SER H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA H 180 " --> pdb=" O PHE H 176 " (cutoff:3.500A) Processing helix chain 'I' and resid 43 through 49 removed outlier: 3.554A pdb=" N HIS I 47 " --> pdb=" O PRO I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 51 through 54 No H-bonds generated for 'chain 'I' and resid 51 through 54' Processing helix chain 'I' and resid 74 through 90 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 143 through 154 removed outlier: 3.787A pdb=" N THR I 153 " --> pdb=" O SER I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA I 180 " --> pdb=" O PHE I 176 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS J 47 " --> pdb=" O PRO J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 51 through 54 No H-bonds generated for 'chain 'J' and resid 51 through 54' Processing helix chain 'J' and resid 74 through 90 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 143 through 154 removed outlier: 3.787A pdb=" N THR J 153 " --> pdb=" O SER J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 168 through 183 removed outlier: 3.728A pdb=" N ALA J 180 " --> pdb=" O PHE J 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS K 47 " --> pdb=" O PRO K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 54 No H-bonds generated for 'chain 'K' and resid 51 through 54' Processing helix chain 'K' and resid 74 through 90 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 143 through 154 removed outlier: 3.787A pdb=" N THR K 153 " --> pdb=" O SER K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 168 through 183 removed outlier: 3.728A pdb=" N ALA K 180 " --> pdb=" O PHE K 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 43 through 49 removed outlier: 3.554A pdb=" N HIS L 47 " --> pdb=" O PRO L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 51 through 54 No H-bonds generated for 'chain 'L' and resid 51 through 54' Processing helix chain 'L' and resid 74 through 90 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 143 through 154 removed outlier: 3.788A pdb=" N THR L 153 " --> pdb=" O SER L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 183 removed outlier: 3.728A pdb=" N ALA L 180 " --> pdb=" O PHE L 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS M 47 " --> pdb=" O PRO M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 54 No H-bonds generated for 'chain 'M' and resid 51 through 54' Processing helix chain 'M' and resid 74 through 90 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 143 through 154 removed outlier: 3.787A pdb=" N THR M 153 " --> pdb=" O SER M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA M 180 " --> pdb=" O PHE M 176 " (cutoff:3.500A) Processing helix chain 'N' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS N 47 " --> pdb=" O PRO N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 51 through 54 No H-bonds generated for 'chain 'N' and resid 51 through 54' Processing helix chain 'N' and resid 74 through 90 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 143 through 154 removed outlier: 3.787A pdb=" N THR N 153 " --> pdb=" O SER N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA N 180 " --> pdb=" O PHE N 176 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS O 47 " --> pdb=" O PRO O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 51 through 54 No H-bonds generated for 'chain 'O' and resid 51 through 54' Processing helix chain 'O' and resid 74 through 90 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 143 through 154 removed outlier: 3.787A pdb=" N THR O 153 " --> pdb=" O SER O 149 " (cutoff:3.500A) Processing helix chain 'O' and resid 168 through 183 removed outlier: 3.728A pdb=" N ALA O 180 " --> pdb=" O PHE O 176 " (cutoff:3.500A) Processing helix chain 'P' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS P 47 " --> pdb=" O PRO P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 51 through 54 No H-bonds generated for 'chain 'P' and resid 51 through 54' Processing helix chain 'P' and resid 74 through 90 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 143 through 154 removed outlier: 3.787A pdb=" N THR P 153 " --> pdb=" O SER P 149 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 183 removed outlier: 3.728A pdb=" N ALA P 180 " --> pdb=" O PHE P 176 " (cutoff:3.500A) Processing helix chain 'Q' and resid 43 through 49 removed outlier: 3.554A pdb=" N HIS Q 47 " --> pdb=" O PRO Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 51 through 54 No H-bonds generated for 'chain 'Q' and resid 51 through 54' Processing helix chain 'Q' and resid 74 through 90 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 143 through 154 removed outlier: 3.787A pdb=" N THR Q 153 " --> pdb=" O SER Q 149 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 183 removed outlier: 3.728A pdb=" N ALA Q 180 " --> pdb=" O PHE Q 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS R 47 " --> pdb=" O PRO R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 51 through 54 No H-bonds generated for 'chain 'R' and resid 51 through 54' Processing helix chain 'R' and resid 74 through 90 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 143 through 154 removed outlier: 3.787A pdb=" N THR R 153 " --> pdb=" O SER R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA R 180 " --> pdb=" O PHE R 176 " (cutoff:3.500A) Processing helix chain 'S' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS S 47 " --> pdb=" O PRO S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 54 No H-bonds generated for 'chain 'S' and resid 51 through 54' Processing helix chain 'S' and resid 74 through 90 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 143 through 154 removed outlier: 3.787A pdb=" N THR S 153 " --> pdb=" O SER S 149 " (cutoff:3.500A) Processing helix chain 'S' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA S 180 " --> pdb=" O PHE S 176 " (cutoff:3.500A) Processing helix chain 'T' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS T 47 " --> pdb=" O PRO T 43 " (cutoff:3.500A) Processing helix chain 'T' and resid 51 through 54 No H-bonds generated for 'chain 'T' and resid 51 through 54' Processing helix chain 'T' and resid 74 through 90 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 143 through 154 removed outlier: 3.787A pdb=" N THR T 153 " --> pdb=" O SER T 149 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA T 180 " --> pdb=" O PHE T 176 " (cutoff:3.500A) Processing helix chain 'U' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS U 47 " --> pdb=" O PRO U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 51 through 54 No H-bonds generated for 'chain 'U' and resid 51 through 54' Processing helix chain 'U' and resid 74 through 90 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 143 through 154 removed outlier: 3.786A pdb=" N THR U 153 " --> pdb=" O SER U 149 " (cutoff:3.500A) Processing helix chain 'U' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA U 180 " --> pdb=" O PHE U 176 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS V 47 " --> pdb=" O PRO V 43 " (cutoff:3.500A) Processing helix chain 'V' and resid 51 through 54 No H-bonds generated for 'chain 'V' and resid 51 through 54' Processing helix chain 'V' and resid 74 through 90 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 143 through 154 removed outlier: 3.787A pdb=" N THR V 153 " --> pdb=" O SER V 149 " (cutoff:3.500A) Processing helix chain 'V' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA V 180 " --> pdb=" O PHE V 176 " (cutoff:3.500A) Processing helix chain 'W' and resid 43 through 49 removed outlier: 3.553A pdb=" N HIS W 47 " --> pdb=" O PRO W 43 " (cutoff:3.500A) Processing helix chain 'W' and resid 51 through 54 No H-bonds generated for 'chain 'W' and resid 51 through 54' Processing helix chain 'W' and resid 74 through 90 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 143 through 154 removed outlier: 3.787A pdb=" N THR W 153 " --> pdb=" O SER W 149 " (cutoff:3.500A) Processing helix chain 'W' and resid 168 through 183 removed outlier: 3.728A pdb=" N ALA W 180 " --> pdb=" O PHE W 176 " (cutoff:3.500A) Processing helix chain 'X' and resid 43 through 49 removed outlier: 3.554A pdb=" N HIS X 47 " --> pdb=" O PRO X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 51 through 54 No H-bonds generated for 'chain 'X' and resid 51 through 54' Processing helix chain 'X' and resid 74 through 90 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 143 through 154 removed outlier: 3.787A pdb=" N THR X 153 " --> pdb=" O SER X 149 " (cutoff:3.500A) Processing helix chain 'X' and resid 168 through 183 removed outlier: 3.729A pdb=" N ALA X 180 " --> pdb=" O PHE X 176 " (cutoff:3.500A) Processing sheet with id= A, 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= B, 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: 3.761A pdb=" N ALA A 164 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS A 113 " --> pdb=" O GLN A 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN A 162 " --> pdb=" O HIS A 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER A 115 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE A 160 " --> pdb=" O SER A 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR A 123 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE A 160 " --> pdb=" O TYR A 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY A 125 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLN A 162 " --> pdb=" O GLY A 125 " (cutoff:3.500A) Processing sheet with id= C, 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= D, 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: 3.761A pdb=" N ALA B 164 " --> pdb=" O LEU B 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS B 113 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN B 162 " --> pdb=" O HIS B 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER B 115 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE B 160 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR B 123 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE B 160 " --> pdb=" O TYR B 123 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY B 125 " --> pdb=" O ILE B 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN B 162 " --> pdb=" O GLY B 125 " (cutoff:3.500A) Processing sheet with id= E, 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= F, 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: 3.761A pdb=" N ALA C 164 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS C 113 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N GLN C 162 " --> pdb=" O HIS C 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER C 115 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE C 160 " --> pdb=" O SER C 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR C 123 " --> pdb=" O LEU C 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE C 160 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY C 125 " --> pdb=" O ILE C 160 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLN C 162 " --> pdb=" O GLY C 125 " (cutoff:3.500A) Processing sheet with id= G, 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= H, 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: 3.760A pdb=" N ALA D 164 " --> pdb=" O LEU D 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS D 113 " --> pdb=" O GLN D 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN D 162 " --> pdb=" O HIS D 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER D 115 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE D 160 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR D 123 " --> pdb=" O LEU D 158 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE D 160 " --> pdb=" O TYR D 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY D 125 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN D 162 " --> pdb=" O GLY D 125 " (cutoff:3.500A) Processing sheet with id= I, 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= J, 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: 3.761A pdb=" N ALA E 164 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS E 113 " --> pdb=" O GLN E 162 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN E 162 " --> pdb=" O HIS E 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER E 115 " --> pdb=" O ILE E 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE E 160 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR E 123 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE E 160 " --> pdb=" O TYR E 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY E 125 " --> pdb=" O ILE E 160 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLN E 162 " --> pdb=" O GLY E 125 " (cutoff:3.500A) Processing sheet with id= K, 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= L, 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: 3.761A pdb=" N ALA F 164 " --> pdb=" O LEU F 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS F 113 " --> pdb=" O GLN F 162 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN F 162 " --> pdb=" O HIS F 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER F 115 " --> pdb=" O ILE F 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE F 160 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR F 123 " --> pdb=" O LEU F 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE F 160 " --> pdb=" O TYR F 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY F 125 " --> pdb=" O ILE F 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN F 162 " --> pdb=" O GLY F 125 " (cutoff:3.500A) Processing sheet with id= M, 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= N, 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: 3.761A pdb=" N ALA G 164 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS G 113 " --> pdb=" O GLN G 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN G 162 " --> pdb=" O HIS G 113 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N SER G 115 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE G 160 " --> pdb=" O SER G 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR G 123 " --> pdb=" O LEU G 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE G 160 " --> pdb=" O TYR G 123 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY G 125 " --> pdb=" O ILE G 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN G 162 " --> pdb=" O GLY G 125 " (cutoff:3.500A) Processing sheet with id= O, 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= P, 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: 3.761A pdb=" N ALA H 164 " --> pdb=" O LEU H 111 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS H 113 " --> pdb=" O GLN H 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN H 162 " --> pdb=" O HIS H 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER H 115 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE H 160 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR H 123 " --> pdb=" O LEU H 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE H 160 " --> pdb=" O TYR H 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY H 125 " --> pdb=" O ILE H 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN H 162 " --> pdb=" O GLY H 125 " (cutoff:3.500A) Processing sheet with id= Q, 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= R, 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: 3.761A pdb=" N ALA I 164 " --> pdb=" O LEU I 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS I 113 " --> pdb=" O GLN I 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN I 162 " --> pdb=" O HIS I 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER I 115 " --> pdb=" O ILE I 160 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N ILE I 160 " --> pdb=" O SER I 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR I 123 " --> pdb=" O LEU I 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE I 160 " --> pdb=" O TYR I 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY I 125 " --> pdb=" O ILE I 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN I 162 " --> pdb=" O GLY I 125 " (cutoff:3.500A) Processing sheet with id= S, 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= T, 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: 3.761A pdb=" N ALA J 164 " --> pdb=" O LEU J 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS J 113 " --> pdb=" O GLN J 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN J 162 " --> pdb=" O HIS J 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER J 115 " --> pdb=" O ILE J 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE J 160 " --> pdb=" O SER J 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR J 123 " --> pdb=" O LEU J 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE J 160 " --> pdb=" O TYR J 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY J 125 " --> pdb=" O ILE J 160 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLN J 162 " --> pdb=" O GLY J 125 " (cutoff:3.500A) Processing sheet with id= U, 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= V, 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: 3.761A pdb=" N ALA K 164 " --> pdb=" O LEU K 111 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS K 113 " --> pdb=" O GLN K 162 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN K 162 " --> pdb=" O HIS K 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER K 115 " --> pdb=" O ILE K 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE K 160 " --> pdb=" O SER K 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR K 123 " --> pdb=" O LEU K 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE K 160 " --> pdb=" O TYR K 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY K 125 " --> pdb=" O ILE K 160 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLN K 162 " --> pdb=" O GLY K 125 " (cutoff:3.500A) Processing sheet with id= W, 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= X, 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: 3.761A pdb=" N ALA L 164 " --> pdb=" O LEU L 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS L 113 " --> pdb=" O GLN L 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN L 162 " --> pdb=" O HIS L 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER L 115 " --> pdb=" O ILE L 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE L 160 " --> pdb=" O SER L 115 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR L 123 " --> pdb=" O LEU L 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE L 160 " --> pdb=" O TYR L 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY L 125 " --> pdb=" O ILE L 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN L 162 " --> pdb=" O GLY L 125 " (cutoff:3.500A) Processing sheet with id= Y, 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= Z, 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: 3.760A pdb=" N ALA M 164 " --> pdb=" O LEU M 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS M 113 " --> pdb=" O GLN M 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN M 162 " --> pdb=" O HIS M 113 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N SER M 115 " --> pdb=" O ILE M 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE M 160 " --> pdb=" O SER M 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR M 123 " --> pdb=" O LEU M 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE M 160 " --> pdb=" O TYR M 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY M 125 " --> pdb=" O ILE M 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN M 162 " --> pdb=" O GLY M 125 " (cutoff:3.500A) Processing sheet with id= AA, 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= AB, 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: 3.761A pdb=" N ALA N 164 " --> pdb=" O LEU N 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS N 113 " --> pdb=" O GLN N 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN N 162 " --> pdb=" O HIS N 113 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N SER N 115 " --> pdb=" O ILE N 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE N 160 " --> pdb=" O SER N 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR N 123 " --> pdb=" O LEU N 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE N 160 " --> pdb=" O TYR N 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY N 125 " --> pdb=" O ILE N 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN N 162 " --> pdb=" O GLY N 125 " (cutoff:3.500A) Processing sheet with id= AC, 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= AD, 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: 3.761A pdb=" N ALA O 164 " --> pdb=" O LEU O 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS O 113 " --> pdb=" O GLN O 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN O 162 " --> pdb=" O HIS O 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER O 115 " --> pdb=" O ILE O 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE O 160 " --> pdb=" O SER O 115 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR O 123 " --> pdb=" O LEU O 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE O 160 " --> pdb=" O TYR O 123 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY O 125 " --> pdb=" O ILE O 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN O 162 " --> pdb=" O GLY O 125 " (cutoff:3.500A) Processing sheet with id= AE, 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= AF, 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: 3.761A pdb=" N ALA P 164 " --> pdb=" O LEU P 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS P 113 " --> pdb=" O GLN P 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN P 162 " --> pdb=" O HIS P 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER P 115 " --> pdb=" O ILE P 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE P 160 " --> pdb=" O SER P 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR P 123 " --> pdb=" O LEU P 158 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE P 160 " --> pdb=" O TYR P 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY P 125 " --> pdb=" O ILE P 160 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLN P 162 " --> pdb=" O GLY P 125 " (cutoff:3.500A) Processing sheet with id= AG, 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= AH, 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: 3.761A pdb=" N ALA Q 164 " --> pdb=" O LEU Q 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS Q 113 " --> pdb=" O GLN Q 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN Q 162 " --> pdb=" O HIS Q 113 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N SER Q 115 " --> pdb=" O ILE Q 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE Q 160 " --> pdb=" O SER Q 115 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR Q 123 " --> pdb=" O LEU Q 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE Q 160 " --> pdb=" O TYR Q 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY Q 125 " --> pdb=" O ILE Q 160 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N GLN Q 162 " --> pdb=" O GLY Q 125 " (cutoff:3.500A) Processing sheet with id= AI, 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= AJ, 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: 3.761A pdb=" N ALA R 164 " --> pdb=" O LEU R 111 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS R 113 " --> pdb=" O GLN R 162 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN R 162 " --> pdb=" O HIS R 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER R 115 " --> pdb=" O ILE R 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE R 160 " --> pdb=" O SER R 115 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR R 123 " --> pdb=" O LEU R 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE R 160 " --> pdb=" O TYR R 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY R 125 " --> pdb=" O ILE R 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN R 162 " --> pdb=" O GLY R 125 " (cutoff:3.500A) Processing sheet with id= AK, 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= AL, 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: 3.761A pdb=" N ALA S 164 " --> pdb=" O LEU S 111 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS S 113 " --> pdb=" O GLN S 162 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN S 162 " --> pdb=" O HIS S 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER S 115 " --> pdb=" O ILE S 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE S 160 " --> pdb=" O SER S 115 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR S 123 " --> pdb=" O LEU S 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE S 160 " --> pdb=" O TYR S 123 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY S 125 " --> pdb=" O ILE S 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN S 162 " --> pdb=" O GLY S 125 " (cutoff:3.500A) Processing sheet with id= AM, 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= AN, 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: 3.761A pdb=" N ALA T 164 " --> pdb=" O LEU T 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS T 113 " --> pdb=" O GLN T 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN T 162 " --> pdb=" O HIS T 113 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N SER T 115 " --> pdb=" O ILE T 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE T 160 " --> pdb=" O SER T 115 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR T 123 " --> pdb=" O LEU T 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE T 160 " --> pdb=" O TYR T 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY T 125 " --> pdb=" O ILE T 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN T 162 " --> pdb=" O GLY T 125 " (cutoff:3.500A) Processing sheet with id= AO, 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= AP, 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: 3.761A pdb=" N ALA U 164 " --> pdb=" O LEU U 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS U 113 " --> pdb=" O GLN U 162 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N GLN U 162 " --> pdb=" O HIS U 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER U 115 " --> pdb=" O ILE U 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE U 160 " --> pdb=" O SER U 115 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR U 123 " --> pdb=" O LEU U 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE U 160 " --> pdb=" O TYR U 123 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY U 125 " --> pdb=" O ILE U 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN U 162 " --> pdb=" O GLY U 125 " (cutoff:3.500A) Processing sheet with id= AQ, 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= AR, 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: 3.760A pdb=" N ALA V 164 " --> pdb=" O LEU V 111 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N HIS V 113 " --> pdb=" O GLN V 162 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN V 162 " --> pdb=" O HIS V 113 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N SER V 115 " --> pdb=" O ILE V 160 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ILE V 160 " --> pdb=" O SER V 115 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR V 123 " --> pdb=" O LEU V 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE V 160 " --> pdb=" O TYR V 123 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY V 125 " --> pdb=" O ILE V 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN V 162 " --> pdb=" O GLY V 125 " (cutoff:3.500A) Processing sheet with id= AS, 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= AT, 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: 3.761A pdb=" N ALA W 164 " --> pdb=" O LEU W 111 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS W 113 " --> pdb=" O GLN W 162 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN W 162 " --> pdb=" O HIS W 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER W 115 " --> pdb=" O ILE W 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE W 160 " --> pdb=" O SER W 115 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N TYR W 123 " --> pdb=" O LEU W 158 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ILE W 160 " --> pdb=" O TYR W 123 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N GLY W 125 " --> pdb=" O ILE W 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN W 162 " --> pdb=" O GLY W 125 " (cutoff:3.500A) Processing sheet with id= AU, 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= AV, 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: 3.761A pdb=" N ALA X 164 " --> pdb=" O LEU X 111 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N HIS X 113 " --> pdb=" O GLN X 162 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N GLN X 162 " --> pdb=" O HIS X 113 " (cutoff:3.500A) removed outlier: 7.529A pdb=" N SER X 115 " --> pdb=" O ILE X 160 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ILE X 160 " --> pdb=" O SER X 115 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR X 123 " --> pdb=" O LEU X 158 " (cutoff:3.500A) removed outlier: 7.813A pdb=" N ILE X 160 " --> pdb=" O TYR X 123 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLY X 125 " --> pdb=" O ILE X 160 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N GLN X 162 " --> pdb=" O GLY X 125 " (cutoff:3.500A) 1224 hydrogen bonds defined for protein. 3384 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: 11.03 Time building geometry restraints manager: 14.23 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: 99.56 - 106.26: 816 106.26 - 112.97: 19024 112.97 - 119.67: 9513 119.67 - 126.38: 16607 126.38 - 133.08: 480 Bond angle restraints: 46440 Sorted by residual: angle pdb=" C ASP V 108 " pdb=" N GLU V 109 " pdb=" CA GLU V 109 " ideal model delta sigma weight residual 121.54 130.29 -8.75 1.91e+00 2.74e-01 2.10e+01 angle pdb=" C ASP R 108 " pdb=" N GLU R 109 " pdb=" CA GLU R 109 " ideal model delta sigma weight residual 121.54 130.28 -8.74 1.91e+00 2.74e-01 2.10e+01 angle pdb=" C ASP U 108 " pdb=" N GLU U 109 " pdb=" CA GLU U 109 " ideal model delta sigma weight residual 121.54 130.28 -8.74 1.91e+00 2.74e-01 2.09e+01 angle pdb=" C ASP Q 108 " pdb=" N GLU Q 109 " pdb=" CA GLU Q 109 " ideal model delta sigma weight residual 121.54 130.27 -8.73 1.91e+00 2.74e-01 2.09e+01 angle pdb=" C ASP B 108 " pdb=" N GLU B 109 " pdb=" CA GLU B 109 " ideal model delta sigma weight residual 121.54 130.26 -8.72 1.91e+00 2.74e-01 2.09e+01 ... (remaining 46435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.23: 18596 15.23 - 30.45: 1036 30.45 - 45.68: 264 45.68 - 60.91: 72 60.91 - 76.13: 24 Dihedral angle restraints: 19992 sinusoidal: 7440 harmonic: 12552 Sorted by residual: dihedral pdb=" CA PRO K 106 " pdb=" C PRO K 106 " pdb=" N LEU K 107 " pdb=" CA LEU K 107 " ideal model delta harmonic sigma weight residual 180.00 150.72 29.28 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA PRO G 106 " pdb=" C PRO G 106 " pdb=" N LEU G 107 " pdb=" CA LEU G 107 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA PRO E 106 " pdb=" C PRO E 106 " pdb=" N LEU E 107 " pdb=" CA LEU E 107 " ideal model delta harmonic sigma weight residual 180.00 150.74 29.26 0 5.00e+00 4.00e-02 3.42e+01 ... (remaining 19989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3644 0.047 - 0.094: 1264 0.094 - 0.142: 354 0.142 - 0.189: 138 0.189 - 0.236: 24 Chirality restraints: 5424 Sorted by residual: chirality pdb=" C7 5LD L 303 " pdb=" C6 5LD L 303 " pdb=" C8 5LD L 303 " pdb=" O13 5LD L 303 " both_signs ideal model delta sigma weight residual False 2.41 2.64 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C7 5LD M 402 " pdb=" C6 5LD M 402 " pdb=" C8 5LD M 402 " pdb=" O13 5LD M 402 " both_signs ideal model delta sigma weight residual False 2.41 2.64 -0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" C7 5LD O 402 " pdb=" C6 5LD O 402 " pdb=" C8 5LD O 402 " pdb=" O13 5LD O 402 " both_signs ideal model delta sigma weight residual False 2.41 2.64 -0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 5421 not shown) Planarity restraints: 6024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP N 108 " 0.014 2.00e-02 2.50e+03 2.79e-02 7.76e+00 pdb=" C ASP N 108 " -0.048 2.00e-02 2.50e+03 pdb=" O ASP N 108 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU N 109 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP Q 108 " 0.014 2.00e-02 2.50e+03 2.78e-02 7.74e+00 pdb=" C ASP Q 108 " -0.048 2.00e-02 2.50e+03 pdb=" O ASP Q 108 " 0.018 2.00e-02 2.50e+03 pdb=" N GLU Q 109 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP I 108 " -0.014 2.00e-02 2.50e+03 2.78e-02 7.73e+00 pdb=" C ASP I 108 " 0.048 2.00e-02 2.50e+03 pdb=" O ASP I 108 " -0.018 2.00e-02 2.50e+03 pdb=" N GLU I 109 " -0.016 2.00e-02 2.50e+03 ... (remaining 6021 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 846 2.67 - 3.23: 28357 3.23 - 3.78: 51930 3.78 - 4.34: 71786 4.34 - 4.90: 118843 Nonbonded interactions: 271762 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 271757 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 195 or resid 401)) selection = (chain 'B' and (resid 11 through 195 or resid 401)) selection = (chain 'C' and (resid 11 through 195 or resid 401)) selection = (chain 'D' and (resid 11 through 195 or resid 401)) selection = (chain 'E' and (resid 11 through 195 or resid 401)) selection = (chain 'F' and (resid 11 through 195 or resid 401)) selection = (chain 'G' and (resid 11 through 195 or resid 401)) selection = (chain 'H' and (resid 11 through 195 or resid 301)) selection = (chain 'I' and (resid 11 through 195 or resid 401)) selection = (chain 'J' and (resid 11 through 195 or resid 401)) selection = (chain 'K' and (resid 11 through 195 or resid 401)) selection = (chain 'L' and (resid 11 through 195 or resid 301)) selection = (chain 'M' and (resid 11 through 195 or resid 401)) selection = (chain 'N' and (resid 11 through 195 or resid 301)) selection = (chain 'O' and (resid 11 through 195 or resid 401)) selection = (chain 'P' and (resid 11 through 195 or resid 301)) selection = (chain 'Q' and (resid 11 through 195 or resid 301)) selection = (chain 'R' and (resid 11 through 195 or resid 301)) selection = (chain 'S' and (resid 11 through 195 or resid 301)) selection = (chain 'T' and (resid 11 through 195 or resid 301)) selection = (chain 'U' and (resid 11 through 195 or resid 301)) selection = (chain 'V' and (resid 11 through 195 or resid 301)) selection = (chain 'W' and (resid 11 through 195 or resid 301)) selection = (chain 'X' and (resid 11 through 195 or resid 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: 0.330 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: 0.030 Extract box with map and model: 3.460 Check model and map are aligned: 0.500 Set scattering table: 0.310 Process input model: 87.230 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.490 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 97.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 34200 Z= 0.446 Angle : 1.124 8.754 46440 Z= 0.605 Chirality : 0.057 0.236 5424 Planarity : 0.007 0.051 6024 Dihedral : 11.613 76.133 11928 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 3.79 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.010 0.003 HIS J 47 PHE 0.008 0.002 PHE B 176 TYR 0.021 0.004 TYR E 138 ARG 0.005 0.001 ARG J 17 *********************** 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 fitting. rotamer outliers: 0 poor density : 882 time to evaluate : 3.592 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: 0.7793 (ptpt) cc_final: 0.7573 (pttp) outliers start: 0 outliers final: 0 residues processed: 882 average time/residue: 0.5729 time to fit residues: 742.6010 Evaluate side-chains 625 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 625 time to evaluate : 3.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 364 optimal weight: 6.9990 chunk 327 optimal weight: 5.9990 chunk 181 optimal weight: 7.9990 chunk 111 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 174 optimal weight: 0.8980 chunk 338 optimal weight: 10.0000 chunk 131 optimal weight: 30.0000 chunk 205 optimal weight: 5.9990 chunk 252 optimal weight: 40.0000 chunk 392 optimal weight: 10.0000 overall best weight: 5.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 185 GLN B 185 GLN C 185 GLN ** D 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 185 GLN E 185 GLN ** F 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 185 GLN G 185 GLN ** H 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 GLN I 185 GLN J 185 GLN ** K 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 185 GLN ** L 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 185 GLN M 185 GLN N 185 GLN O 185 GLN P 185 GLN ** Q 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 185 GLN R 185 GLN S 185 GLN ** T 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 185 GLN U 185 GLN V 185 GLN ** W 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 185 GLN ** X 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 185 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 34200 Z= 0.367 Angle : 0.802 7.265 46440 Z= 0.421 Chirality : 0.049 0.135 5424 Planarity : 0.008 0.047 6024 Dihedral : 9.275 49.291 4920 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 3.42 % Allowed : 7.49 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.11), residues: 4392 helix: -2.79 (0.09), residues: 1584 sheet: -0.65 (0.14), residues: 1440 loop : -3.69 (0.14), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS S 47 PHE 0.008 0.002 PHE N 100 TYR 0.018 0.003 TYR E 138 ARG 0.005 0.001 ARG I 134 *********************** 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 768 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 654 time to evaluate : 4.092 Fit side-chains REVERT: C 133 GLN cc_start: 0.8210 (mt0) cc_final: 0.7931 (mt0) REVERT: H 133 GLN cc_start: 0.8188 (mt0) cc_final: 0.7937 (mt0) REVERT: L 133 GLN cc_start: 0.8193 (mt0) cc_final: 0.7884 (mt0) REVERT: Q 133 GLN cc_start: 0.8212 (mt0) cc_final: 0.7920 (mt0) REVERT: S 26 VAL cc_start: 0.7886 (p) cc_final: 0.7630 (p) REVERT: S 133 GLN cc_start: 0.8212 (mt0) cc_final: 0.7968 (mt0) REVERT: T 26 VAL cc_start: 0.7930 (p) cc_final: 0.7703 (p) REVERT: W 133 GLN cc_start: 0.8243 (mt0) cc_final: 0.7924 (mt0) outliers start: 114 outliers final: 88 residues processed: 735 average time/residue: 0.5992 time to fit residues: 667.0732 Evaluate side-chains 644 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 556 time to evaluate : 3.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 72 ASP 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 42 ILE Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 72 ASP 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 72 ASP Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 137 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 72 ASP 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 72 ASP Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 28 ILE Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 72 ASP Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 72 ASP Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 72 ASP 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 72 ASP Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 72 ASP Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 72 ASP 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 218 optimal weight: 40.0000 chunk 121 optimal weight: 6.9990 chunk 326 optimal weight: 40.0000 chunk 267 optimal weight: 2.9990 chunk 108 optimal weight: 40.0000 chunk 393 optimal weight: 3.9990 chunk 424 optimal weight: 6.9990 chunk 350 optimal weight: 2.9990 chunk 389 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 315 optimal weight: 5.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 133 GLN K 76 ASN O 133 GLN T 133 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2849 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= 0.307 Angle : 0.741 7.813 46440 Z= 0.388 Chirality : 0.048 0.128 5424 Planarity : 0.006 0.038 6024 Dihedral : 8.941 55.416 4920 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.24 % Favored : 90.76 % Rotamer: Outliers : 6.53 % Allowed : 9.02 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.88 (0.12), residues: 4392 helix: -1.36 (0.11), residues: 1560 sheet: -0.71 (0.14), residues: 1464 loop : -3.77 (0.13), residues: 1368 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS S 47 PHE 0.006 0.001 PHE F 176 TYR 0.013 0.003 TYR Q 138 ARG 0.004 0.001 ARG I 134 *********************** 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 832 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 614 time to evaluate : 3.823 Fit side-chains REVERT: F 42 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.6772 (tp) REVERT: G 42 ILE cc_start: 0.8172 (OUTLIER) cc_final: 0.6826 (tp) REVERT: I 42 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.6842 (tp) REVERT: J 42 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.6795 (tp) REVERT: K 166 LYS cc_start: 0.8190 (pttt) cc_final: 0.7765 (pttt) REVERT: M 42 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.6786 (tp) REVERT: N 42 ILE cc_start: 0.8209 (OUTLIER) cc_final: 0.6865 (tp) REVERT: N 133 GLN cc_start: 0.8202 (mt0) cc_final: 0.7952 (mt0) REVERT: S 26 VAL cc_start: 0.8015 (p) cc_final: 0.7815 (p) REVERT: V 42 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.6787 (tp) REVERT: W 42 ILE cc_start: 0.8148 (OUTLIER) cc_final: 0.6805 (tp) REVERT: W 133 GLN cc_start: 0.8269 (mt0) cc_final: 0.8053 (mt0) outliers start: 218 outliers final: 127 residues processed: 733 average time/residue: 0.5138 time to fit residues: 578.1832 Evaluate side-chains 704 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 569 time to evaluate : 4.164 ------------------------------------------------------------------------------- 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 137 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 137 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 137 THR 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 35 VAL Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 151 VAL Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 137 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 42 ILE Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 137 THR 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 137 THR Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 137 THR Chi-restraints excluded: chain I residue 151 VAL Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 42 ILE Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 137 THR 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 137 THR 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 137 THR Chi-restraints excluded: chain L residue 151 VAL Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 137 THR 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 137 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 137 THR 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 137 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 137 THR 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 137 THR Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain T residue 137 THR Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain U residue 26 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 137 THR Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 42 ILE Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 137 THR Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 42 ILE Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 137 THR 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 137 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 388 optimal weight: 3.9990 chunk 295 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 187 optimal weight: 3.9990 chunk 263 optimal weight: 1.9990 chunk 394 optimal weight: 2.9990 chunk 417 optimal weight: 7.9990 chunk 206 optimal weight: 6.9990 chunk 373 optimal weight: 6.9990 chunk 112 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN D 76 ASN D 133 GLN E 76 ASN F 76 ASN G 76 ASN H 76 ASN H 133 GLN I 76 ASN J 76 ASN J 133 GLN L 76 ASN L 133 GLN M 76 ASN M 133 GLN N 76 ASN N 133 GLN O 76 ASN P 133 GLN Q 76 ASN Q 133 GLN R 76 ASN T 76 ASN U 76 ASN X 76 ASN X 133 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34200 Z= 0.272 Angle : 0.697 7.411 46440 Z= 0.366 Chirality : 0.047 0.133 5424 Planarity : 0.006 0.039 6024 Dihedral : 8.774 59.217 4920 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 6.86 % Allowed : 11.30 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.12), residues: 4392 helix: -0.70 (0.12), residues: 1560 sheet: -0.81 (0.14), residues: 1488 loop : -3.65 (0.13), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 145 PHE 0.006 0.001 PHE U 176 TYR 0.018 0.002 TYR I 126 ARG 0.003 0.000 ARG I 134 *********************** 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 808 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 579 time to evaluate : 3.861 Fit side-chains REVERT: A 30 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8467 (mp) REVERT: A 109 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.5193 (pm20) REVERT: B 42 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.6810 (tp) REVERT: B 109 GLU cc_start: 0.6665 (OUTLIER) cc_final: 0.5211 (pm20) REVERT: C 30 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8517 (mp) REVERT: C 109 GLU cc_start: 0.6574 (OUTLIER) cc_final: 0.5197 (pm20) REVERT: C 166 LYS cc_start: 0.8196 (pttt) cc_final: 0.7856 (pttt) REVERT: D 42 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.6765 (tp) REVERT: D 109 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.5193 (pm20) REVERT: E 109 GLU cc_start: 0.6744 (OUTLIER) cc_final: 0.5305 (pm20) REVERT: F 42 ILE cc_start: 0.8155 (OUTLIER) cc_final: 0.6809 (tp) REVERT: F 109 GLU cc_start: 0.6659 (OUTLIER) cc_final: 0.5230 (pm20) REVERT: G 42 ILE cc_start: 0.8226 (OUTLIER) cc_final: 0.6880 (tp) REVERT: G 109 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.5255 (pm20) REVERT: H 42 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.6725 (tp) REVERT: H 109 GLU cc_start: 0.6677 (OUTLIER) cc_final: 0.5240 (pm20) REVERT: I 42 ILE cc_start: 0.8244 (OUTLIER) cc_final: 0.6902 (tp) REVERT: I 109 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.5244 (pm20) REVERT: J 42 ILE cc_start: 0.8173 (OUTLIER) cc_final: 0.6812 (tp) REVERT: J 109 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.5270 (pm20) REVERT: J 166 LYS cc_start: 0.8187 (pttt) cc_final: 0.7863 (pttt) REVERT: K 109 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.5272 (pm20) REVERT: L 42 ILE cc_start: 0.8235 (OUTLIER) cc_final: 0.6785 (tp) REVERT: L 109 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.5206 (pm20) REVERT: M 42 ILE cc_start: 0.8161 (OUTLIER) cc_final: 0.6813 (tp) REVERT: M 109 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.5205 (pm20) REVERT: N 42 ILE cc_start: 0.8247 (OUTLIER) cc_final: 0.6899 (tp) REVERT: N 109 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.5206 (pm20) REVERT: O 109 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.5199 (pm20) REVERT: O 166 LYS cc_start: 0.8210 (pttt) cc_final: 0.7875 (pttt) REVERT: P 42 ILE cc_start: 0.8249 (OUTLIER) cc_final: 0.6802 (tp) REVERT: P 109 GLU cc_start: 0.6656 (OUTLIER) cc_final: 0.5232 (pm20) REVERT: Q 109 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.5252 (pm20) REVERT: R 109 GLU cc_start: 0.6655 (OUTLIER) cc_final: 0.5231 (pm20) REVERT: S 109 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.5260 (pm20) REVERT: T 42 ILE cc_start: 0.8147 (OUTLIER) cc_final: 0.6686 (tp) REVERT: T 109 GLU cc_start: 0.6641 (OUTLIER) cc_final: 0.5217 (pm20) REVERT: T 166 LYS cc_start: 0.8181 (pttt) cc_final: 0.7848 (pttt) REVERT: U 37 ASP cc_start: 0.5859 (p0) cc_final: 0.5651 (p0) REVERT: U 109 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.5251 (pm20) REVERT: V 42 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.6840 (tp) REVERT: V 109 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.5215 (pm20) REVERT: W 42 ILE cc_start: 0.8214 (OUTLIER) cc_final: 0.6861 (tp) REVERT: W 109 GLU cc_start: 0.6621 (OUTLIER) cc_final: 0.5189 (pm20) REVERT: W 133 GLN cc_start: 0.8250 (mt0) cc_final: 0.8047 (mt0) REVERT: W 166 LYS cc_start: 0.8201 (pttt) cc_final: 0.7856 (pttt) REVERT: X 109 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.5225 (pm20) outliers start: 229 outliers final: 151 residues processed: 727 average time/residue: 0.4928 time to fit residues: 560.2584 Evaluate side-chains 745 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 554 time to evaluate : 3.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 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 42 ILE Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 137 THR 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 42 ILE Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 137 THR 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 42 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 42 ILE 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 137 THR 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 42 ILE Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 109 GLU Chi-restraints excluded: chain J residue 137 THR 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 72 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 137 THR 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 42 ILE Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 137 THR 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 42 ILE Chi-restraints excluded: chain M residue 72 ASP Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 109 GLU Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 109 GLU Chi-restraints excluded: chain N residue 137 THR 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 72 ASP Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 109 GLU Chi-restraints excluded: chain P residue 137 THR 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 72 ASP Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 109 GLU 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 35 VAL Chi-restraints excluded: chain S residue 72 ASP Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 137 THR Chi-restraints excluded: chain S residue 151 VAL Chi-restraints excluded: chain T residue 19 THR Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 72 ASP Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain T residue 109 GLU Chi-restraints excluded: chain T residue 137 THR Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain U residue 26 VAL Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 109 GLU Chi-restraints excluded: chain U residue 137 THR Chi-restraints excluded: chain U residue 151 VAL Chi-restraints excluded: chain V residue 35 VAL Chi-restraints excluded: chain V residue 42 ILE Chi-restraints excluded: chain V residue 72 ASP Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 109 GLU Chi-restraints excluded: chain V residue 137 THR Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 42 ILE Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 137 THR 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 72 ASP Chi-restraints excluded: chain X residue 104 THR Chi-restraints excluded: chain X residue 109 GLU Chi-restraints excluded: chain X residue 137 THR 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 347 optimal weight: 20.0000 chunk 237 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 310 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 356 optimal weight: 9.9990 chunk 288 optimal weight: 40.0000 chunk 0 optimal weight: 40.0000 chunk 213 optimal weight: 6.9990 chunk 374 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 185 GLN H 185 GLN N 61 HIS N 76 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 34200 Z= 0.468 Angle : 0.857 7.847 46440 Z= 0.444 Chirality : 0.054 0.142 5424 Planarity : 0.007 0.057 6024 Dihedral : 9.127 59.801 4920 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 7.25 % Allowed : 12.77 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.12), residues: 4392 helix: -0.69 (0.12), residues: 1560 sheet: -0.70 (0.14), residues: 1488 loop : -3.74 (0.13), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS V 47 PHE 0.009 0.002 PHE W 147 TYR 0.022 0.003 TYR C 126 ARG 0.005 0.001 ARG P 134 *********************** 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 726 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 484 time to evaluate : 3.986 Fit side-chains REVERT: A 30 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8574 (mp) REVERT: A 109 GLU cc_start: 0.6586 (OUTLIER) cc_final: 0.5032 (pm20) REVERT: A 166 LYS cc_start: 0.8276 (pttt) cc_final: 0.7931 (pttt) REVERT: B 30 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8469 (mp) REVERT: B 109 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.5095 (pm20) REVERT: C 30 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8579 (mp) REVERT: C 109 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.5069 (pm20) REVERT: D 30 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8529 (mp) REVERT: D 109 GLU cc_start: 0.6607 (OUTLIER) cc_final: 0.5016 (pm20) REVERT: E 109 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.5102 (pm20) REVERT: F 30 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8507 (mp) REVERT: F 109 GLU cc_start: 0.6652 (OUTLIER) cc_final: 0.4965 (pm20) REVERT: G 109 GLU cc_start: 0.6660 (OUTLIER) cc_final: 0.5094 (pm20) REVERT: H 30 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8472 (mp) REVERT: H 37 ASP cc_start: 0.5905 (p0) cc_final: 0.5692 (p0) REVERT: H 109 GLU cc_start: 0.6669 (OUTLIER) cc_final: 0.4971 (pm20) REVERT: H 166 LYS cc_start: 0.8222 (pttt) cc_final: 0.7882 (pttt) REVERT: I 109 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.5065 (pm20) REVERT: J 30 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8523 (mp) REVERT: J 109 GLU cc_start: 0.6613 (OUTLIER) cc_final: 0.5051 (pm20) REVERT: K 109 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.5098 (pm20) REVERT: L 30 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8517 (mp) REVERT: L 109 GLU cc_start: 0.6566 (OUTLIER) cc_final: 0.5032 (pm20) REVERT: M 109 GLU cc_start: 0.6568 (OUTLIER) cc_final: 0.5040 (pm20) REVERT: N 30 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8509 (mp) REVERT: N 109 GLU cc_start: 0.6619 (OUTLIER) cc_final: 0.5014 (pm20) REVERT: N 166 LYS cc_start: 0.8195 (pttt) cc_final: 0.7993 (pttt) REVERT: O 30 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8469 (mp) REVERT: O 37 ASP cc_start: 0.5883 (p0) cc_final: 0.5676 (p0) REVERT: O 109 GLU cc_start: 0.6580 (OUTLIER) cc_final: 0.5105 (pm20) REVERT: P 30 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8511 (mp) REVERT: P 109 GLU cc_start: 0.6612 (OUTLIER) cc_final: 0.5055 (pm20) REVERT: Q 30 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8501 (mp) REVERT: Q 109 GLU cc_start: 0.6610 (OUTLIER) cc_final: 0.5062 (pm20) REVERT: Q 166 LYS cc_start: 0.8204 (pttt) cc_final: 0.7875 (pttt) REVERT: R 109 GLU cc_start: 0.6609 (OUTLIER) cc_final: 0.5041 (pm20) REVERT: S 30 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8524 (mp) REVERT: S 109 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.5279 (pm20) REVERT: T 30 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8502 (mp) REVERT: T 109 GLU cc_start: 0.6593 (OUTLIER) cc_final: 0.5031 (pm20) REVERT: U 30 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8548 (mp) REVERT: U 109 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.5096 (pm20) REVERT: V 30 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8452 (mp) REVERT: V 109 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.5045 (pm20) REVERT: W 30 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8435 (mp) REVERT: W 109 GLU cc_start: 0.6535 (OUTLIER) cc_final: 0.5058 (pm20) REVERT: X 30 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8467 (mp) REVERT: X 109 GLU cc_start: 0.6608 (OUTLIER) cc_final: 0.5048 (pm20) REVERT: X 166 LYS cc_start: 0.8355 (pttt) cc_final: 0.8037 (pttt) outliers start: 242 outliers final: 175 residues processed: 661 average time/residue: 0.5222 time to fit residues: 537.0139 Evaluate side-chains 693 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 217 poor density : 476 time to evaluate : 3.808 ------------------------------------------------------------------------------- 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 72 ASP Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 72 ASP 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 137 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 72 ASP 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 137 THR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 154 SER 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 42 ILE Chi-restraints excluded: chain E residue 72 ASP 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 137 THR 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 72 ASP 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 137 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 48 MET Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 137 THR 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 72 ASP 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 137 THR Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain I residue 137 THR 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 72 ASP 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 137 THR 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 72 ASP 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 137 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 137 THR 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 72 ASP Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 109 GLU Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 109 GLU Chi-restraints excluded: chain N residue 137 THR 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 72 ASP Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain O residue 137 THR Chi-restraints excluded: chain O residue 151 VAL Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 109 GLU Chi-restraints excluded: chain P residue 137 THR 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 52 LEU Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain Q residue 137 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 72 ASP 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 72 ASP Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 137 THR 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 72 ASP Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain T residue 109 GLU Chi-restraints excluded: chain T residue 137 THR Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain U residue 26 VAL Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 72 ASP 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 137 THR 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 72 ASP 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 137 THR Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain V residue 154 SER Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 137 THR 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 72 ASP Chi-restraints excluded: chain X residue 104 THR Chi-restraints excluded: chain X residue 109 GLU Chi-restraints excluded: chain X residue 137 THR 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 140 optimal weight: 8.9990 chunk 376 optimal weight: 4.9990 chunk 82 optimal weight: 8.9990 chunk 245 optimal weight: 1.9990 chunk 103 optimal weight: 0.8980 chunk 417 optimal weight: 3.9990 chunk 346 optimal weight: 10.0000 chunk 193 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 138 optimal weight: 6.9990 chunk 219 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN ** A 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 ASN B 133 GLN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 HIS C 76 ASN D 76 ASN ** D 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 76 ASN ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 76 ASN ** F 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN ** G 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 76 ASN ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN J 76 ASN K 76 ASN ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 76 ASN M 61 HIS M 76 ASN ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 76 ASN P 76 ASN ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 76 ASN ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN S 76 ASN ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 ASN ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 76 ASN V 76 ASN ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 ASN X 61 HIS X 76 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 34200 Z= 0.162 Angle : 0.597 7.555 46440 Z= 0.318 Chirality : 0.044 0.136 5424 Planarity : 0.005 0.043 6024 Dihedral : 7.953 55.178 4920 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 4.71 % Allowed : 16.37 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.12), residues: 4392 helix: 0.13 (0.13), residues: 1560 sheet: -0.88 (0.13), residues: 1512 loop : -3.55 (0.13), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 69 PHE 0.009 0.001 PHE U 146 TYR 0.012 0.002 TYR S 126 ARG 0.003 0.000 ARG S 63 *********************** 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 792 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 635 time to evaluate : 3.578 Fit side-chains REVERT: A 37 ASP cc_start: 0.5913 (p0) cc_final: 0.5634 (p0) REVERT: A 72 ASP cc_start: 0.7433 (OUTLIER) cc_final: 0.7211 (t0) REVERT: A 109 GLU cc_start: 0.6264 (OUTLIER) cc_final: 0.5409 (pm20) REVERT: B 30 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8520 (mp) REVERT: B 42 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.6762 (tp) REVERT: B 72 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.7082 (t0) REVERT: B 109 GLU cc_start: 0.6340 (OUTLIER) cc_final: 0.5503 (pm20) REVERT: C 30 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8508 (mp) REVERT: C 72 ASP cc_start: 0.7268 (OUTLIER) cc_final: 0.7035 (t0) REVERT: C 109 GLU cc_start: 0.6207 (OUTLIER) cc_final: 0.5364 (pm20) REVERT: D 30 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8476 (mp) REVERT: D 37 ASP cc_start: 0.5950 (p0) cc_final: 0.5667 (p0) REVERT: D 42 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.6729 (tp) REVERT: D 72 ASP cc_start: 0.7554 (OUTLIER) cc_final: 0.7161 (t0) REVERT: D 109 GLU cc_start: 0.6314 (OUTLIER) cc_final: 0.5472 (pm20) REVERT: E 72 ASP cc_start: 0.7226 (OUTLIER) cc_final: 0.6966 (t0) REVERT: E 109 GLU cc_start: 0.6376 (OUTLIER) cc_final: 0.5495 (pm20) REVERT: F 42 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.6711 (tp) REVERT: F 72 ASP cc_start: 0.7453 (OUTLIER) cc_final: 0.7109 (t0) REVERT: F 109 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.5481 (pm20) REVERT: G 42 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.6731 (tp) REVERT: G 72 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6992 (t0) REVERT: G 109 GLU cc_start: 0.6259 (OUTLIER) cc_final: 0.5420 (pm20) REVERT: H 42 ILE cc_start: 0.8208 (OUTLIER) cc_final: 0.6777 (tp) REVERT: H 72 ASP cc_start: 0.7590 (OUTLIER) cc_final: 0.7190 (t0) REVERT: H 109 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.5482 (pm20) REVERT: I 42 ILE cc_start: 0.8320 (OUTLIER) cc_final: 0.6732 (tp) REVERT: I 72 ASP cc_start: 0.7299 (OUTLIER) cc_final: 0.7053 (t0) REVERT: I 109 GLU cc_start: 0.6215 (OUTLIER) cc_final: 0.5360 (pm20) REVERT: J 42 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.6709 (tp) REVERT: J 72 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7054 (t0) REVERT: J 109 GLU cc_start: 0.6301 (OUTLIER) cc_final: 0.5439 (pm20) REVERT: K 72 ASP cc_start: 0.7394 (OUTLIER) cc_final: 0.7120 (t0) REVERT: K 109 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.5492 (pm20) REVERT: L 30 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8546 (mp) REVERT: L 42 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.6727 (tp) REVERT: L 72 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7175 (t0) REVERT: L 109 GLU cc_start: 0.6257 (OUTLIER) cc_final: 0.5434 (pm20) REVERT: M 42 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.6698 (tp) REVERT: M 72 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7101 (t0) REVERT: M 109 GLU cc_start: 0.6224 (OUTLIER) cc_final: 0.5380 (pm20) REVERT: N 42 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.6750 (tp) REVERT: N 72 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.7058 (t0) REVERT: N 109 GLU cc_start: 0.6336 (OUTLIER) cc_final: 0.5462 (pm20) REVERT: O 30 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8515 (mp) REVERT: O 37 ASP cc_start: 0.6088 (p0) cc_final: 0.5783 (p0) REVERT: O 72 ASP cc_start: 0.7543 (OUTLIER) cc_final: 0.7142 (t0) REVERT: O 109 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5393 (pm20) REVERT: P 42 ILE cc_start: 0.8310 (OUTLIER) cc_final: 0.6738 (tp) REVERT: P 72 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.7066 (t0) REVERT: P 109 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.5447 (pm20) REVERT: Q 30 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8575 (mp) REVERT: Q 42 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.6660 (tp) REVERT: Q 72 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.7126 (t0) REVERT: Q 109 GLU cc_start: 0.6291 (OUTLIER) cc_final: 0.5438 (pm20) REVERT: R 37 ASP cc_start: 0.5902 (p0) cc_final: 0.5679 (p0) REVERT: R 42 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.6647 (tp) REVERT: R 72 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7147 (t0) REVERT: R 109 GLU cc_start: 0.6300 (OUTLIER) cc_final: 0.5437 (pm20) REVERT: S 72 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.7077 (t0) REVERT: S 109 GLU cc_start: 0.6234 (OUTLIER) cc_final: 0.5391 (pm20) REVERT: T 30 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8507 (mp) REVERT: T 37 ASP cc_start: 0.6003 (p0) cc_final: 0.5767 (p0) REVERT: T 42 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.6688 (tp) REVERT: T 72 ASP cc_start: 0.7586 (OUTLIER) cc_final: 0.7185 (t0) REVERT: T 109 GLU cc_start: 0.6277 (OUTLIER) cc_final: 0.5402 (pm20) REVERT: U 37 ASP cc_start: 0.5829 (p0) cc_final: 0.5612 (p0) REVERT: U 109 GLU cc_start: 0.6375 (OUTLIER) cc_final: 0.5543 (pm20) REVERT: V 42 ILE cc_start: 0.8240 (OUTLIER) cc_final: 0.6694 (tp) REVERT: V 72 ASP cc_start: 0.7451 (OUTLIER) cc_final: 0.7050 (t0) REVERT: V 109 GLU cc_start: 0.6251 (OUTLIER) cc_final: 0.5412 (pm20) REVERT: W 30 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8529 (mp) REVERT: W 42 ILE cc_start: 0.8330 (OUTLIER) cc_final: 0.6686 (tp) REVERT: W 72 ASP cc_start: 0.7256 (OUTLIER) cc_final: 0.7040 (t0) REVERT: W 109 GLU cc_start: 0.6240 (OUTLIER) cc_final: 0.5384 (pm20) REVERT: X 42 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.6754 (tp) REVERT: X 72 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7138 (t0) REVERT: X 109 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5419 (pm20) REVERT: X 166 LYS cc_start: 0.8260 (pttt) cc_final: 0.7961 (pttt) outliers start: 157 outliers final: 75 residues processed: 706 average time/residue: 0.4874 time to fit residues: 537.3290 Evaluate side-chains 754 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 607 time to evaluate : 4.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 104 THR Chi-restraints excluded: chain C residue 109 GLU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 42 ILE Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 154 SER 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 42 ILE Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 72 ASP Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 104 THR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain I residue 72 ASP Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain I residue 109 GLU Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 42 ILE Chi-restraints excluded: chain J residue 72 ASP Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 109 GLU Chi-restraints excluded: chain J residue 137 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 72 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain L residue 72 ASP Chi-restraints excluded: chain L residue 104 THR Chi-restraints excluded: chain L residue 109 GLU Chi-restraints excluded: chain L residue 137 THR Chi-restraints excluded: chain M residue 30 LEU Chi-restraints excluded: chain M residue 35 VAL Chi-restraints excluded: chain M residue 42 ILE Chi-restraints excluded: chain M residue 72 ASP Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain M residue 109 GLU Chi-restraints excluded: chain M residue 137 THR Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 109 GLU Chi-restraints excluded: chain N residue 137 THR Chi-restraints excluded: chain O residue 30 LEU Chi-restraints excluded: chain O residue 35 VAL Chi-restraints excluded: chain O residue 72 ASP Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 109 GLU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 72 ASP Chi-restraints excluded: chain P residue 104 THR Chi-restraints excluded: chain P residue 109 GLU Chi-restraints excluded: chain Q residue 30 LEU Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 42 ILE Chi-restraints excluded: chain Q residue 72 ASP Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain Q residue 109 GLU Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 42 ILE Chi-restraints excluded: chain R residue 72 ASP Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 109 GLU Chi-restraints excluded: chain S residue 35 VAL Chi-restraints excluded: chain S residue 72 ASP Chi-restraints excluded: chain S residue 104 THR Chi-restraints excluded: chain S residue 109 GLU Chi-restraints excluded: chain S residue 154 SER Chi-restraints excluded: chain T residue 30 LEU Chi-restraints excluded: chain T residue 35 VAL Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 72 ASP Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain T residue 109 GLU Chi-restraints excluded: chain T residue 154 SER 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 V residue 35 VAL Chi-restraints excluded: chain V residue 42 ILE Chi-restraints excluded: chain V residue 72 ASP Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 109 GLU Chi-restraints excluded: chain V residue 154 SER 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 52 LEU Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 137 THR Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 42 ILE Chi-restraints excluded: chain X residue 72 ASP Chi-restraints excluded: chain X residue 104 THR Chi-restraints excluded: chain X residue 109 GLU Chi-restraints excluded: chain X residue 137 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 402 optimal weight: 20.0000 chunk 47 optimal weight: 0.7980 chunk 238 optimal weight: 20.0000 chunk 305 optimal weight: 7.9990 chunk 236 optimal weight: 1.9990 chunk 351 optimal weight: 9.9990 chunk 233 optimal weight: 9.9990 chunk 416 optimal weight: 30.0000 chunk 260 optimal weight: 9.9990 chunk 253 optimal weight: 6.9990 chunk 192 optimal weight: 7.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 76 ASN ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 GLN E 69 HIS E 185 GLN G 185 GLN H 76 ASN ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 GLN I 185 GLN K 69 HIS K 185 GLN N 185 GLN O 76 ASN ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 HIS ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 185 GLN ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 34200 Z= 0.328 Angle : 0.757 10.617 46440 Z= 0.388 Chirality : 0.050 0.155 5424 Planarity : 0.006 0.038 6024 Dihedral : 8.484 59.924 4920 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 7.10 % Allowed : 15.56 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.12), residues: 4392 helix: 0.01 (0.13), residues: 1560 sheet: -0.65 (0.14), residues: 1488 loop : -3.39 (0.14), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS R 69 PHE 0.008 0.002 PHE K 176 TYR 0.020 0.003 TYR S 126 ARG 0.003 0.000 ARG R 184 *********************** 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 808 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 571 time to evaluate : 4.048 Fit side-chains REVERT: A 30 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8584 (mp) REVERT: A 37 ASP cc_start: 0.5862 (p0) cc_final: 0.5514 (p0) REVERT: A 109 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.5252 (pm20) REVERT: B 30 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8573 (mp) REVERT: B 109 GLU cc_start: 0.6727 (OUTLIER) cc_final: 0.5173 (pm20) REVERT: C 30 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8578 (mp) REVERT: C 109 GLU cc_start: 0.6616 (OUTLIER) cc_final: 0.5133 (pm20) REVERT: D 30 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8572 (mp) REVERT: D 37 ASP cc_start: 0.5888 (p0) cc_final: 0.5658 (p0) REVERT: D 109 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.5122 (pm20) REVERT: E 109 GLU cc_start: 0.6624 (OUTLIER) cc_final: 0.5114 (pm20) REVERT: F 30 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8566 (mp) REVERT: F 109 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.5154 (pm20) REVERT: G 109 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.5067 (pm20) REVERT: H 30 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8583 (mp) REVERT: H 42 ILE cc_start: 0.8278 (OUTLIER) cc_final: 0.6763 (tp) REVERT: H 109 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.5117 (pm20) REVERT: I 109 GLU cc_start: 0.6679 (OUTLIER) cc_final: 0.5212 (pm20) REVERT: J 30 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8567 (mp) REVERT: J 109 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.5109 (pm20) REVERT: K 109 GLU cc_start: 0.6661 (OUTLIER) cc_final: 0.5145 (pm20) REVERT: K 166 LYS cc_start: 0.8330 (pttt) cc_final: 0.8061 (pttt) REVERT: L 30 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8564 (mp) REVERT: L 109 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.5186 (pm20) REVERT: M 109 GLU cc_start: 0.6680 (OUTLIER) cc_final: 0.5248 (pm20) REVERT: N 30 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8566 (mp) REVERT: N 109 GLU cc_start: 0.6738 (OUTLIER) cc_final: 0.5271 (pm20) REVERT: O 30 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8567 (mp) REVERT: O 109 GLU cc_start: 0.6628 (OUTLIER) cc_final: 0.5204 (pm20) REVERT: P 30 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8557 (mp) REVERT: P 109 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.5070 (pm20) REVERT: Q 30 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8590 (mp) REVERT: Q 109 GLU cc_start: 0.6614 (OUTLIER) cc_final: 0.5110 (pm20) REVERT: R 30 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8529 (mp) REVERT: R 37 ASP cc_start: 0.5948 (p0) cc_final: 0.5625 (p0) REVERT: R 109 GLU cc_start: 0.6674 (OUTLIER) cc_final: 0.5219 (pm20) REVERT: S 30 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8585 (mp) REVERT: S 109 GLU cc_start: 0.6720 (OUTLIER) cc_final: 0.5530 (pm20) REVERT: T 30 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8560 (mp) REVERT: T 42 ILE cc_start: 0.8326 (OUTLIER) cc_final: 0.6757 (tp) REVERT: T 109 GLU cc_start: 0.6557 (OUTLIER) cc_final: 0.5127 (pm20) REVERT: U 37 ASP cc_start: 0.5943 (p0) cc_final: 0.5725 (p0) REVERT: U 109 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.5099 (pm20) REVERT: V 30 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8565 (mp) REVERT: V 42 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.6803 (tp) REVERT: V 109 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.5218 (pm20) REVERT: W 30 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8559 (mp) REVERT: W 42 ILE cc_start: 0.8345 (OUTLIER) cc_final: 0.6712 (tp) REVERT: W 109 GLU cc_start: 0.6668 (OUTLIER) cc_final: 0.5218 (pm20) REVERT: X 30 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8572 (mp) REVERT: X 109 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.5132 (pm20) REVERT: X 166 LYS cc_start: 0.8315 (pttt) cc_final: 0.7980 (pttt) outliers start: 237 outliers final: 173 residues processed: 720 average time/residue: 0.5150 time to fit residues: 589.2485 Evaluate side-chains 785 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 566 time to evaluate : 3.999 ------------------------------------------------------------------------------- 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 68 THR Chi-restraints excluded: chain A residue 72 ASP 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 137 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 72 ASP 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 137 THR 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 72 ASP Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 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 42 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 137 THR 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 72 ASP Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 72 ASP 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 137 THR 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 42 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 72 ASP 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 137 THR 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 72 ASP Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain J residue 109 GLU Chi-restraints excluded: chain J residue 137 THR 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 72 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 72 ASP 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 137 THR 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 72 ASP 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 137 THR Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 72 ASP 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 137 THR 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 72 ASP 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 137 THR 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 72 ASP 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 137 THR 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 52 LEU Chi-restraints excluded: chain Q residue 72 ASP 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 137 THR 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 72 ASP Chi-restraints excluded: chain R residue 104 THR Chi-restraints excluded: chain R residue 109 GLU 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 72 ASP 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 137 THR 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 42 ILE Chi-restraints excluded: chain T residue 72 ASP Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain T residue 109 GLU Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 137 THR Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain U residue 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 137 THR 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 42 ILE Chi-restraints excluded: chain V residue 72 ASP Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 109 GLU Chi-restraints excluded: chain V residue 137 THR Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 42 ILE Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 72 ASP 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 137 THR 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 72 ASP 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 137 THR 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 257 optimal weight: 7.9990 chunk 166 optimal weight: 20.0000 chunk 248 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 264 optimal weight: 9.9990 chunk 283 optimal weight: 7.9990 chunk 205 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 327 optimal weight: 0.4980 overall best weight: 5.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 ASN D 76 ASN ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 76 ASN ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 76 ASN J 76 ASN L 76 ASN M 76 ASN ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 76 ASN ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 76 ASN ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.3737 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= 0.366 Angle : 0.787 10.007 46440 Z= 0.405 Chirality : 0.051 0.140 5424 Planarity : 0.006 0.044 6024 Dihedral : 8.689 59.997 4920 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 7.58 % Allowed : 16.82 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.12), residues: 4392 helix: -0.07 (0.13), residues: 1560 sheet: -0.69 (0.14), residues: 1488 loop : -3.39 (0.14), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS U 145 PHE 0.008 0.002 PHE K 176 TYR 0.025 0.003 TYR J 126 ARG 0.004 0.000 ARG R 184 *********************** 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 788 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 535 time to evaluate : 3.991 Fit side-chains REVERT: A 30 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8581 (mp) REVERT: A 37 ASP cc_start: 0.5892 (p0) cc_final: 0.5589 (p0) REVERT: A 109 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.4945 (pm20) REVERT: A 166 LYS cc_start: 0.8248 (pttt) cc_final: 0.7988 (pttt) REVERT: B 30 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8584 (mp) REVERT: B 109 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.5311 (pm20) REVERT: B 166 LYS cc_start: 0.8273 (pttt) cc_final: 0.8059 (pttt) REVERT: C 30 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8583 (mp) REVERT: C 109 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.5052 (pm20) REVERT: D 30 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8577 (mp) REVERT: D 37 ASP cc_start: 0.5837 (p0) cc_final: 0.5569 (p0) REVERT: D 109 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.5383 (pm20) REVERT: E 42 ILE cc_start: 0.8059 (OUTLIER) cc_final: 0.6487 (tp) REVERT: E 109 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.4995 (pm20) REVERT: F 30 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8588 (mp) REVERT: F 109 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.5304 (pm20) REVERT: F 166 LYS cc_start: 0.8273 (pttt) cc_final: 0.8062 (pttt) REVERT: G 109 GLU cc_start: 0.6472 (OUTLIER) cc_final: 0.5046 (pm20) REVERT: H 30 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8589 (mp) REVERT: H 42 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.6738 (tp) REVERT: H 109 GLU cc_start: 0.6571 (OUTLIER) cc_final: 0.5305 (pm20) REVERT: H 166 LYS cc_start: 0.8263 (pttt) cc_final: 0.8046 (pttt) REVERT: I 109 GLU cc_start: 0.6591 (OUTLIER) cc_final: 0.5389 (pm20) REVERT: J 30 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8586 (mp) REVERT: J 109 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.4989 (pm20) REVERT: J 166 LYS cc_start: 0.8276 (pttt) cc_final: 0.8040 (pttt) REVERT: K 109 GLU cc_start: 0.6520 (OUTLIER) cc_final: 0.5019 (pm20) REVERT: K 166 LYS cc_start: 0.8270 (pttt) cc_final: 0.7994 (pttt) REVERT: L 30 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8575 (mp) REVERT: L 109 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.5079 (pm20) REVERT: M 109 GLU cc_start: 0.6464 (OUTLIER) cc_final: 0.5045 (pm20) REVERT: N 30 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8544 (mp) REVERT: N 109 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.5424 (pm20) REVERT: N 166 LYS cc_start: 0.8269 (pttt) cc_final: 0.8063 (pttt) REVERT: O 30 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8573 (mp) REVERT: O 109 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.5072 (pm20) REVERT: O 166 LYS cc_start: 0.8281 (pttt) cc_final: 0.8067 (pttt) REVERT: P 30 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8566 (mp) REVERT: P 109 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.5024 (pm20) REVERT: Q 30 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8602 (mp) REVERT: Q 109 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.5058 (pm20) REVERT: Q 166 LYS cc_start: 0.8272 (pttt) cc_final: 0.8057 (pttt) REVERT: R 30 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8541 (mp) REVERT: R 37 ASP cc_start: 0.5944 (p0) cc_final: 0.5646 (p0) REVERT: R 109 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.5098 (pm20) REVERT: R 166 LYS cc_start: 0.8314 (pttt) cc_final: 0.8103 (pttt) REVERT: S 30 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8578 (mp) REVERT: S 109 GLU cc_start: 0.6653 (OUTLIER) cc_final: 0.5498 (pm20) REVERT: T 30 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8563 (mp) REVERT: T 37 ASP cc_start: 0.5902 (p0) cc_final: 0.5688 (p0) REVERT: T 109 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.4951 (pm20) REVERT: T 166 LYS cc_start: 0.8267 (pttt) cc_final: 0.8045 (pttt) REVERT: U 109 GLU cc_start: 0.6494 (OUTLIER) cc_final: 0.5083 (pm20) REVERT: V 30 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8577 (mp) REVERT: V 42 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.6571 (tp) REVERT: V 109 GLU cc_start: 0.6426 (OUTLIER) cc_final: 0.5014 (pm20) REVERT: W 30 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8573 (mp) REVERT: W 42 ILE cc_start: 0.8280 (OUTLIER) cc_final: 0.6594 (tp) REVERT: W 109 GLU cc_start: 0.6512 (OUTLIER) cc_final: 0.5095 (pm20) REVERT: X 30 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8556 (mp) REVERT: X 109 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.4947 (pm20) REVERT: X 166 LYS cc_start: 0.8305 (pttt) cc_final: 0.8008 (pttt) outliers start: 253 outliers final: 184 residues processed: 701 average time/residue: 0.4853 time to fit residues: 534.1161 Evaluate side-chains 754 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 524 time to evaluate : 3.870 ------------------------------------------------------------------------------- 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 68 THR Chi-restraints excluded: chain A residue 72 ASP 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 137 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 72 ASP 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 137 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 72 ASP 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 137 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 72 ASP Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain D residue 109 GLU Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 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 42 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 72 ASP 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 137 THR 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 72 ASP 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 137 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 72 ASP 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 137 THR 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 42 ILE Chi-restraints excluded: chain H residue 72 ASP 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 137 THR Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain I residue 19 THR Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 28 ILE Chi-restraints excluded: chain I residue 30 LEU Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 72 ASP 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 137 THR 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 72 ASP 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 137 THR 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 72 ASP 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 137 THR Chi-restraints excluded: chain K residue 151 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 72 ASP 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 137 THR 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 72 ASP 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 137 THR Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 72 ASP 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 137 THR 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 72 ASP 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 137 THR 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 72 ASP 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 137 THR 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 52 LEU Chi-restraints excluded: chain Q residue 72 ASP 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 137 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 72 ASP 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 72 ASP 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 137 THR 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 72 ASP Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain T residue 109 GLU Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 137 THR Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain U residue 19 THR Chi-restraints excluded: chain U residue 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 137 THR 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 42 ILE Chi-restraints excluded: chain V residue 72 ASP Chi-restraints excluded: chain V residue 104 THR Chi-restraints excluded: chain V residue 109 GLU Chi-restraints excluded: chain V residue 137 THR Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 42 ILE Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 72 ASP 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 137 THR 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 72 ASP 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 137 THR 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 378 optimal weight: 40.0000 chunk 398 optimal weight: 9.9990 chunk 363 optimal weight: 0.9990 chunk 388 optimal weight: 10.0000 chunk 233 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 304 optimal weight: 1.9990 chunk 119 optimal weight: 0.3980 chunk 350 optimal weight: 9.9990 chunk 366 optimal weight: 5.9990 chunk 386 optimal weight: 5.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 34200 Z= 0.231 Angle : 0.679 9.736 46440 Z= 0.352 Chirality : 0.046 0.159 5424 Planarity : 0.005 0.039 6024 Dihedral : 8.117 59.167 4920 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 6.56 % Allowed : 18.59 % Favored : 74.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.12), residues: 4392 helix: 0.35 (0.13), residues: 1560 sheet: -0.63 (0.14), residues: 1488 loop : -3.39 (0.14), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS U 145 PHE 0.006 0.001 PHE K 176 TYR 0.019 0.002 TYR C 126 ARG 0.002 0.000 ARG S 63 *********************** 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 774 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 555 time to evaluate : 3.934 Fit side-chains REVERT: A 37 ASP cc_start: 0.5797 (p0) cc_final: 0.5573 (p0) REVERT: A 109 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.5446 (pm20) REVERT: B 30 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8564 (mp) REVERT: B 42 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.6786 (tp) REVERT: B 109 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.5425 (pm20) REVERT: C 30 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8579 (mp) REVERT: C 72 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.6891 (t0) REVERT: C 109 GLU cc_start: 0.6430 (OUTLIER) cc_final: 0.5422 (pm20) REVERT: D 30 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8592 (mp) REVERT: D 37 ASP cc_start: 0.5809 (p0) cc_final: 0.5583 (p0) REVERT: D 109 GLU cc_start: 0.6489 (OUTLIER) cc_final: 0.5425 (pm20) REVERT: E 42 ILE cc_start: 0.7988 (OUTLIER) cc_final: 0.6456 (tp) REVERT: E 109 GLU cc_start: 0.6548 (OUTLIER) cc_final: 0.5443 (pm20) REVERT: F 30 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8593 (mp) REVERT: F 42 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.6744 (tp) REVERT: F 109 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.5430 (pm20) REVERT: G 42 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.6770 (tp) REVERT: G 109 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.5394 (pm20) REVERT: H 42 ILE cc_start: 0.8238 (OUTLIER) cc_final: 0.6659 (tp) REVERT: H 109 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.5434 (pm20) REVERT: I 42 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.6735 (tp) REVERT: I 109 GLU cc_start: 0.6462 (OUTLIER) cc_final: 0.5442 (pm20) REVERT: J 30 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8588 (mp) REVERT: J 42 ILE cc_start: 0.8178 (OUTLIER) cc_final: 0.6688 (tp) REVERT: J 109 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.5420 (pm20) REVERT: K 109 GLU cc_start: 0.6534 (OUTLIER) cc_final: 0.5439 (pm20) REVERT: K 166 LYS cc_start: 0.8275 (pttt) cc_final: 0.7958 (pttt) REVERT: L 30 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8583 (mp) REVERT: L 42 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.6718 (tp) REVERT: L 109 GLU cc_start: 0.6482 (OUTLIER) cc_final: 0.5394 (pm20) REVERT: M 42 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.6711 (tp) REVERT: M 109 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.5425 (pm20) REVERT: N 30 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8559 (mp) REVERT: N 42 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.6804 (tp) REVERT: N 109 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.5473 (pm20) REVERT: N 166 LYS cc_start: 0.8181 (pttt) cc_final: 0.7968 (pttt) REVERT: O 30 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8592 (mp) REVERT: O 109 GLU cc_start: 0.6468 (OUTLIER) cc_final: 0.5420 (pm20) REVERT: P 30 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8540 (mp) REVERT: P 42 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.6794 (tp) REVERT: P 109 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.5452 (pm20) REVERT: Q 30 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8608 (mp) REVERT: Q 109 GLU cc_start: 0.6506 (OUTLIER) cc_final: 0.5410 (pm20) REVERT: R 30 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8550 (mp) REVERT: R 37 ASP cc_start: 0.5886 (p0) cc_final: 0.5683 (p0) REVERT: R 109 GLU cc_start: 0.6511 (OUTLIER) cc_final: 0.5462 (pm20) REVERT: R 166 LYS cc_start: 0.8288 (pttt) cc_final: 0.8049 (pttt) REVERT: S 30 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8590 (mp) REVERT: S 109 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.5470 (pm20) REVERT: T 30 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8573 (mp) REVERT: T 42 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.6855 (tp) REVERT: T 109 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.5439 (pm20) REVERT: U 109 GLU cc_start: 0.6422 (OUTLIER) cc_final: 0.5122 (pm20) REVERT: V 30 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8587 (mp) REVERT: V 42 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.6624 (tp) REVERT: V 109 GLU cc_start: 0.6473 (OUTLIER) cc_final: 0.5428 (pm20) REVERT: W 30 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8569 (mp) REVERT: W 42 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.6607 (tp) REVERT: W 109 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.5410 (pm20) REVERT: X 30 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8561 (mp) REVERT: X 37 ASP cc_start: 0.6409 (t70) cc_final: 0.6163 (t0) REVERT: X 109 GLU cc_start: 0.6499 (OUTLIER) cc_final: 0.5397 (pm20) REVERT: X 166 LYS cc_start: 0.8277 (pttt) cc_final: 0.7958 (pttt) outliers start: 219 outliers final: 140 residues processed: 682 average time/residue: 0.4876 time to fit residues: 521.6833 Evaluate side-chains 743 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 548 time to evaluate : 4.073 ------------------------------------------------------------------------------- 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 116 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain 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 72 ASP 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 137 THR Chi-restraints excluded: chain C residue 151 VAL 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 137 THR Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 30 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 42 ILE Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 137 THR 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 42 ILE Chi-restraints excluded: chain F residue 104 THR Chi-restraints excluded: chain F residue 109 GLU Chi-restraints excluded: chain F residue 137 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 42 ILE 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 137 THR Chi-restraints excluded: chain G residue 151 VAL Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain 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 42 ILE 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 137 THR 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 42 ILE Chi-restraints excluded: chain J residue 72 ASP 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 137 THR 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 137 THR Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain L residue 52 LEU 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 137 THR 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 42 ILE 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 137 THR 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 42 ILE 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 137 THR 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 137 THR Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 72 ASP 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 137 THR Chi-restraints excluded: chain Q residue 30 LEU Chi-restraints excluded: chain Q residue 35 VAL Chi-restraints excluded: chain Q residue 52 LEU 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 137 THR Chi-restraints excluded: chain Q residue 151 VAL Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 35 VAL Chi-restraints excluded: chain R residue 72 ASP 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 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 137 THR 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 42 ILE Chi-restraints excluded: chain T residue 72 ASP Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain T residue 109 GLU Chi-restraints excluded: chain T residue 137 THR Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain U residue 30 LEU Chi-restraints excluded: chain U residue 35 VAL Chi-restraints excluded: chain U residue 104 THR Chi-restraints excluded: chain U residue 109 GLU Chi-restraints excluded: chain U residue 137 THR 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 42 ILE Chi-restraints excluded: chain V residue 72 ASP 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 137 THR Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 42 ILE Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 137 THR 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 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 254 optimal weight: 7.9990 chunk 410 optimal weight: 9.9990 chunk 250 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 285 optimal weight: 0.0870 chunk 430 optimal weight: 1.9990 chunk 396 optimal weight: 40.0000 chunk 342 optimal weight: 40.0000 chunk 35 optimal weight: 20.0000 chunk 264 optimal weight: 9.9990 chunk 210 optimal weight: 0.0060 overall best weight: 2.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN O 185 GLN ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 185 GLN Q 76 ASN R 133 GLN ** S 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 69 HIS ** V 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 76 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34200 Z= 0.220 Angle : 0.662 9.559 46440 Z= 0.342 Chirality : 0.046 0.170 5424 Planarity : 0.005 0.040 6024 Dihedral : 7.846 59.821 4920 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.65 % Favored : 91.35 % Rotamer: Outliers : 6.29 % Allowed : 19.06 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.12), residues: 4392 helix: 0.63 (0.13), residues: 1560 sheet: -0.69 (0.14), residues: 1512 loop : -3.37 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS U 145 PHE 0.007 0.001 PHE N 146 TYR 0.019 0.002 TYR R 126 ARG 0.002 0.000 ARG J 63 ********************** 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 760 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 550 time to evaluate : 3.976 Fit side-chains REVERT: A 109 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.5432 (pm20) REVERT: B 30 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8573 (mp) REVERT: B 42 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.6497 (tp) REVERT: B 72 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.7120 (t0) REVERT: B 109 GLU cc_start: 0.6516 (OUTLIER) cc_final: 0.5412 (pm20) REVERT: C 30 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8577 (mp) REVERT: C 72 ASP cc_start: 0.7260 (OUTLIER) cc_final: 0.6968 (t0) REVERT: C 109 GLU cc_start: 0.6406 (OUTLIER) cc_final: 0.5399 (pm20) REVERT: D 30 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8583 (mp) REVERT: D 37 ASP cc_start: 0.5824 (p0) cc_final: 0.5612 (p0) REVERT: D 72 ASP cc_start: 0.7450 (OUTLIER) cc_final: 0.7162 (t0) REVERT: D 109 GLU cc_start: 0.6469 (OUTLIER) cc_final: 0.5440 (pm20) REVERT: E 42 ILE cc_start: 0.7956 (OUTLIER) cc_final: 0.6389 (tp) REVERT: E 72 ASP cc_start: 0.7236 (OUTLIER) cc_final: 0.6835 (t0) REVERT: E 109 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.5482 (pm20) REVERT: F 30 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8576 (mp) REVERT: F 37 ASP cc_start: 0.6502 (t70) cc_final: 0.6249 (t70) REVERT: F 42 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.6527 (tp) REVERT: F 72 ASP cc_start: 0.7381 (OUTLIER) cc_final: 0.7102 (t0) REVERT: F 109 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.5387 (pm20) REVERT: G 37 ASP cc_start: 0.6352 (t0) cc_final: 0.6072 (t70) REVERT: G 42 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.6482 (tp) REVERT: G 72 ASP cc_start: 0.7380 (OUTLIER) cc_final: 0.7111 (t0) REVERT: G 109 GLU cc_start: 0.6480 (OUTLIER) cc_final: 0.5431 (pm20) REVERT: H 42 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.6625 (tp) REVERT: H 109 GLU cc_start: 0.6523 (OUTLIER) cc_final: 0.5412 (pm20) REVERT: I 42 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.6513 (tp) REVERT: I 72 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.7098 (t0) REVERT: I 109 GLU cc_start: 0.6445 (OUTLIER) cc_final: 0.5445 (pm20) REVERT: J 30 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8575 (mp) REVERT: J 42 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.6646 (tp) REVERT: J 109 GLU cc_start: 0.6510 (OUTLIER) cc_final: 0.5471 (pm20) REVERT: K 72 ASP cc_start: 0.7366 (OUTLIER) cc_final: 0.7038 (t0) REVERT: K 109 GLU cc_start: 0.6495 (OUTLIER) cc_final: 0.5384 (pm20) REVERT: K 166 LYS cc_start: 0.8269 (pttt) cc_final: 0.7946 (pttt) REVERT: L 30 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8585 (mp) REVERT: L 42 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.6531 (tp) REVERT: L 72 ASP cc_start: 0.7417 (OUTLIER) cc_final: 0.7136 (t0) REVERT: L 109 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.5439 (pm20) REVERT: M 42 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.6524 (tp) REVERT: M 72 ASP cc_start: 0.7432 (OUTLIER) cc_final: 0.7142 (t0) REVERT: M 109 GLU cc_start: 0.6444 (OUTLIER) cc_final: 0.5410 (pm20) REVERT: N 30 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8565 (mp) REVERT: N 42 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.6525 (tp) REVERT: N 72 ASP cc_start: 0.7404 (OUTLIER) cc_final: 0.7152 (t0) REVERT: N 109 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.5452 (pm20) REVERT: N 166 LYS cc_start: 0.8227 (pttt) cc_final: 0.8013 (pttt) REVERT: O 30 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8563 (mp) REVERT: O 72 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.7175 (t0) REVERT: O 109 GLU cc_start: 0.6456 (OUTLIER) cc_final: 0.5421 (pm20) REVERT: P 30 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8556 (mp) REVERT: P 42 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.6753 (tp) REVERT: P 109 GLU cc_start: 0.6491 (OUTLIER) cc_final: 0.5443 (pm20) REVERT: Q 30 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8602 (mp) REVERT: Q 72 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7228 (t0) REVERT: Q 109 GLU cc_start: 0.6484 (OUTLIER) cc_final: 0.5460 (pm20) REVERT: R 30 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8546 (mp) REVERT: R 109 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.5458 (pm20) REVERT: R 166 LYS cc_start: 0.8299 (pttt) cc_final: 0.8053 (pttt) REVERT: S 30 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8589 (mp) REVERT: S 72 ASP cc_start: 0.7368 (m-30) cc_final: 0.7164 (t0) REVERT: S 109 GLU cc_start: 0.6490 (OUTLIER) cc_final: 0.5448 (pm20) REVERT: T 30 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8574 (mp) REVERT: T 42 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.6679 (tp) REVERT: T 109 GLU cc_start: 0.6464 (OUTLIER) cc_final: 0.5431 (pm20) REVERT: T 166 LYS cc_start: 0.8254 (pttt) cc_final: 0.8024 (pttt) REVERT: U 109 GLU cc_start: 0.6416 (OUTLIER) cc_final: 0.5113 (pm20) REVERT: V 42 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.6622 (tp) REVERT: V 109 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.5424 (pm20) REVERT: W 30 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8552 (mp) REVERT: W 42 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.6438 (tp) REVERT: W 72 ASP cc_start: 0.7249 (OUTLIER) cc_final: 0.7002 (t0) REVERT: W 109 GLU cc_start: 0.6441 (OUTLIER) cc_final: 0.5447 (pm20) REVERT: X 37 ASP cc_start: 0.6318 (t70) cc_final: 0.6073 (t0) REVERT: X 72 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7171 (t0) REVERT: X 109 GLU cc_start: 0.6485 (OUTLIER) cc_final: 0.5438 (pm20) REVERT: X 166 LYS cc_start: 0.8277 (pttt) cc_final: 0.7964 (pttt) outliers start: 210 outliers final: 137 residues processed: 689 average time/residue: 0.5279 time to fit residues: 578.7620 Evaluate side-chains 743 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 539 time to evaluate : 3.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 35 VAL Chi-restraints excluded: chain B residue 42 ILE Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 109 GLU Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 30 LEU Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 72 ASP 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 137 THR Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 72 ASP 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 137 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 42 ILE Chi-restraints excluded: chain E residue 72 ASP Chi-restraints excluded: chain E residue 104 THR Chi-restraints excluded: chain E residue 109 GLU Chi-restraints excluded: chain E residue 137 THR 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 42 ILE Chi-restraints excluded: chain F residue 72 ASP 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 137 THR Chi-restraints excluded: chain F residue 151 VAL Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 26 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 72 ASP 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 137 THR Chi-restraints excluded: chain H residue 35 VAL Chi-restraints excluded: chain H residue 42 ILE Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 104 THR Chi-restraints excluded: chain H residue 109 GLU Chi-restraints excluded: chain H residue 137 THR Chi-restraints excluded: chain H residue 151 VAL Chi-restraints excluded: chain I residue 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 42 ILE Chi-restraints excluded: chain I residue 72 ASP 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 137 THR 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 42 ILE 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 137 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 30 LEU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 72 ASP Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 GLU Chi-restraints excluded: chain K residue 137 THR Chi-restraints excluded: chain L residue 30 LEU Chi-restraints excluded: chain L residue 35 VAL Chi-restraints excluded: chain L residue 42 ILE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 72 ASP 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 137 THR 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 42 ILE Chi-restraints excluded: chain M residue 72 ASP 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 137 THR Chi-restraints excluded: chain M residue 151 VAL Chi-restraints excluded: chain N residue 19 THR Chi-restraints excluded: chain N residue 30 LEU Chi-restraints excluded: chain N residue 35 VAL Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 72 ASP 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 137 THR 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 72 ASP 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 137 THR Chi-restraints excluded: chain P residue 30 LEU Chi-restraints excluded: chain P residue 35 VAL Chi-restraints excluded: chain P residue 42 ILE 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 137 THR 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 52 LEU Chi-restraints excluded: chain Q residue 72 ASP 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 137 THR 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 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 137 THR 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 42 ILE Chi-restraints excluded: chain T residue 72 ASP Chi-restraints excluded: chain T residue 104 THR Chi-restraints excluded: chain T residue 109 GLU Chi-restraints excluded: chain T residue 116 LEU Chi-restraints excluded: chain T residue 137 THR Chi-restraints excluded: chain T residue 151 VAL Chi-restraints excluded: chain U residue 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 137 THR 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 42 ILE 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 137 THR Chi-restraints excluded: chain V residue 151 VAL Chi-restraints excluded: chain W residue 30 LEU Chi-restraints excluded: chain W residue 35 VAL Chi-restraints excluded: chain W residue 42 ILE Chi-restraints excluded: chain W residue 52 LEU Chi-restraints excluded: chain W residue 72 ASP Chi-restraints excluded: chain W residue 104 THR Chi-restraints excluded: chain W residue 109 GLU Chi-restraints excluded: chain W residue 137 THR Chi-restraints excluded: chain W residue 151 VAL Chi-restraints excluded: chain X residue 35 VAL Chi-restraints excluded: chain X residue 72 ASP 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 137 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 272 optimal weight: 30.0000 chunk 365 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 316 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 95 optimal weight: 30.0000 chunk 343 optimal weight: 20.0000 chunk 143 optimal weight: 10.0000 chunk 352 optimal weight: 5.9990 chunk 43 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 HIS D 69 HIS ** H 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 76 ASN O 69 HIS ** P 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 69 HIS Q 76 ASN ** 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 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 = 0.4125 r_free = 0.4125 target = 0.190794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.170584 restraints weight = 34541.537| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 1.18 r_work: 0.3817 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3706 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3696 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3696 r_free = 0.3696 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3693 r_free = 0.3693 target_work(ls_wunit_k1) = 0.151 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3693 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.3870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 34200 Z= 0.487 Angle : 0.881 9.906 46440 Z= 0.450 Chirality : 0.055 0.166 5424 Planarity : 0.007 0.053 6024 Dihedral : 8.670 59.666 4920 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 7.46 % Allowed : 18.59 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.12), residues: 4392 helix: -0.15 (0.12), residues: 1560 sheet: -0.66 (0.13), residues: 1488 loop : -3.55 (0.14), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS I 145 PHE 0.010 0.002 PHE A 176 TYR 0.025 0.003 TYR R 126 ARG 0.005 0.001 ARG V 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9262.57 seconds wall clock time: 166 minutes 44.33 seconds (10004.33 seconds total)