Starting phenix.real_space_refine on Mon Mar 18 21:16:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejl_28186/03_2024/8ejl_28186.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejl_28186/03_2024/8ejl_28186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejl_28186/03_2024/8ejl_28186.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejl_28186/03_2024/8ejl_28186.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejl_28186/03_2024/8ejl_28186.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ejl_28186/03_2024/8ejl_28186.pdb" } resolution = 3.9 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= 0.009 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 150 5.16 5 C 14220 2.51 5 N 3740 2.21 5 O 4045 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "L PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22155 Number of models: 1 Model: "" Number of chains: 30 Chain: "L" Number of atoms: 1450 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 202, 1450 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 13, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 97 Chain: "M" Number of atoms: 831 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 120, 831 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 77 Chain: "N" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 535 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "Y" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 84 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 8} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "Z" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 94 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1437 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 73 Chain: "B" Number of atoms: 1450 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 202, 1450 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 13, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 97 Chain: "C" Number of atoms: 831 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 120, 831 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 77 Chain: "D" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 535 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "E" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 84 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 8} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 94 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1437 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 73 Chain: "H" Number of atoms: 1450 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 202, 1450 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 13, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 97 Chain: "I" Number of atoms: 831 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 120, 831 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 77 Chain: "J" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 535 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "K" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 84 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 8} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "O" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 94 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "P" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1437 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 73 Chain: "Q" Number of atoms: 1450 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 202, 1450 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 13, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 97 Chain: "R" Number of atoms: 831 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 120, 831 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 77 Chain: "S" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 535 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "T" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 84 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 8} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "U" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 94 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "V" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1437 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 73 Chain: "W" Number of atoms: 1450 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 202, 1450 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 187} Chain breaks: 2 Unresolved non-hydrogen bonds: 135 Unresolved non-hydrogen angles: 163 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 13, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 97 Chain: "X" Number of atoms: 831 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 120, 831 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 111} Chain breaks: 1 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 140 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 77 Chain: "0" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 535 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "1" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 84 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 8} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 14 Chain: "2" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 94 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 8} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "3" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1437 Classifications: {'peptide': 197} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 183} Chain breaks: 2 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 6, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 73 Time building chain proxies: 11.21, per 1000 atoms: 0.51 Number of scatterers: 22155 At special positions: 0 Unit cell: (177.12, 179.28, 90.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 150 16.00 O 4045 8.00 N 3740 7.00 C 14220 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: 8.91 Conformation dependent library (CDL) restraints added in 4.2 seconds 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5790 Finding SS restraints... Secondary structure from input PDB file: 185 helices and 0 sheets defined 74.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.04 Creating SS restraints... Processing helix chain 'L' and resid 16 through 30 Processing helix chain 'L' and resid 35 through 44 Processing helix chain 'L' and resid 48 through 58 removed outlier: 3.740A pdb=" N THR L 58 " --> pdb=" O THR L 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 84 Processing helix chain 'L' and resid 100 through 105 removed outlier: 3.670A pdb=" N ALA L 105 " --> pdb=" O GLY L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 110 through 120 Processing helix chain 'L' and resid 125 through 146 removed outlier: 3.608A pdb=" N LYS L 140 " --> pdb=" O LEU L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 153 removed outlier: 3.590A pdb=" N ILE L 153 " --> pdb=" O ILE L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 160 through 175 Processing helix chain 'L' and resid 178 through 193 removed outlier: 4.605A pdb=" N LEU L 190 " --> pdb=" O THR L 186 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL L 191 " --> pdb=" O GLU L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 195 through 206 removed outlier: 3.683A pdb=" N THR L 200 " --> pdb=" O PRO L 196 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE L 201 " --> pdb=" O ASP L 197 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY L 206 " --> pdb=" O LEU L 202 " (cutoff:3.500A) Processing helix chain 'L' and resid 210 through 218 removed outlier: 3.569A pdb=" N CYS L 218 " --> pdb=" O MET L 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 30 Processing helix chain 'M' and resid 35 through 43 Processing helix chain 'M' and resid 48 through 58 Processing helix chain 'M' and resid 62 through 84 Processing helix chain 'M' and resid 110 through 120 Processing helix chain 'M' and resid 125 through 145 Processing helix chain 'N' and resid 149 through 153 Processing helix chain 'N' and resid 160 through 175 Processing helix chain 'N' and resid 178 through 193 removed outlier: 4.424A pdb=" N LEU N 190 " --> pdb=" O THR N 186 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL N 191 " --> pdb=" O GLU N 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 195 through 206 removed outlier: 3.539A pdb=" N THR N 200 " --> pdb=" O PRO N 196 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE N 201 " --> pdb=" O ASP N 197 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY N 206 " --> pdb=" O LEU N 202 " (cutoff:3.500A) Processing helix chain 'N' and resid 210 through 218 Processing helix chain 'A' and resid 16 through 31 removed outlier: 3.724A pdb=" N LEU A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 21 " --> pdb=" O PRO A 17 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA A 31 " --> pdb=" O VAL A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 44 removed outlier: 3.726A pdb=" N MET A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER A 44 " --> pdb=" O PHE A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 57 removed outlier: 3.567A pdb=" N ASN A 53 " --> pdb=" O PRO A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 61 removed outlier: 3.980A pdb=" N GLY A 61 " --> pdb=" O THR A 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 58 through 61' Processing helix chain 'A' and resid 62 through 81 removed outlier: 3.551A pdb=" N MET A 68 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP A 81 " --> pdb=" O ALA A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 105 Processing helix chain 'A' and resid 110 through 119 Processing helix chain 'A' and resid 125 through 146 removed outlier: 3.755A pdb=" N ILE A 129 " --> pdb=" O PRO A 125 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 153 Processing helix chain 'A' and resid 160 through 176 removed outlier: 3.880A pdb=" N ASP A 166 " --> pdb=" O ARG A 162 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A 176 " --> pdb=" O LEU A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 188 removed outlier: 3.553A pdb=" N LYS A 182 " --> pdb=" O SER A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 Processing helix chain 'A' and resid 195 through 206 removed outlier: 4.144A pdb=" N ILE A 201 " --> pdb=" O ASP A 197 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 217 Processing helix chain 'B' and resid 16 through 30 Processing helix chain 'B' and resid 35 through 44 Processing helix chain 'B' and resid 48 through 58 removed outlier: 3.739A pdb=" N THR B 58 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 84 Processing helix chain 'B' and resid 100 through 105 removed outlier: 3.670A pdb=" N ALA B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 120 Processing helix chain 'B' and resid 125 through 146 removed outlier: 3.607A pdb=" N LYS B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 149 through 153 removed outlier: 3.590A pdb=" N ILE B 153 " --> pdb=" O ILE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 175 Processing helix chain 'B' and resid 178 through 193 removed outlier: 4.605A pdb=" N LEU B 190 " --> pdb=" O THR B 186 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL B 191 " --> pdb=" O GLU B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 removed outlier: 3.683A pdb=" N THR B 200 " --> pdb=" O PRO B 196 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE B 201 " --> pdb=" O ASP B 197 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY B 206 " --> pdb=" O LEU B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 218 removed outlier: 3.569A pdb=" N CYS B 218 " --> pdb=" O MET B 214 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 30 Processing helix chain 'C' and resid 35 through 43 Processing helix chain 'C' and resid 48 through 58 Processing helix chain 'C' and resid 62 through 84 Processing helix chain 'C' and resid 110 through 120 Processing helix chain 'C' and resid 125 through 145 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 160 through 175 Processing helix chain 'D' and resid 178 through 193 removed outlier: 4.424A pdb=" N LEU D 190 " --> pdb=" O THR D 186 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 206 removed outlier: 3.539A pdb=" N THR D 200 " --> pdb=" O PRO D 196 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE D 201 " --> pdb=" O ASP D 197 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY D 206 " --> pdb=" O LEU D 202 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 218 Processing helix chain 'G' and resid 16 through 31 removed outlier: 3.725A pdb=" N LEU G 20 " --> pdb=" O SER G 16 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN G 21 " --> pdb=" O PRO G 17 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU G 29 " --> pdb=" O LYS G 25 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA G 31 " --> pdb=" O VAL G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 44 removed outlier: 3.726A pdb=" N MET G 39 " --> pdb=" O GLU G 35 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER G 44 " --> pdb=" O PHE G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.567A pdb=" N ASN G 53 " --> pdb=" O PRO G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 61 removed outlier: 3.980A pdb=" N GLY G 61 " --> pdb=" O THR G 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 58 through 61' Processing helix chain 'G' and resid 62 through 81 removed outlier: 3.551A pdb=" N MET G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP G 81 " --> pdb=" O ALA G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 105 Processing helix chain 'G' and resid 110 through 119 Processing helix chain 'G' and resid 125 through 146 removed outlier: 3.755A pdb=" N ILE G 129 " --> pdb=" O PRO G 125 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU G 136 " --> pdb=" O ARG G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 153 Processing helix chain 'G' and resid 160 through 176 removed outlier: 3.879A pdb=" N ASP G 166 " --> pdb=" O ARG G 162 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN G 176 " --> pdb=" O LEU G 172 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 188 removed outlier: 3.553A pdb=" N LYS G 182 " --> pdb=" O SER G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 193 Processing helix chain 'G' and resid 195 through 206 removed outlier: 4.144A pdb=" N ILE G 201 " --> pdb=" O ASP G 197 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY G 206 " --> pdb=" O LEU G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 210 through 217 Processing helix chain 'H' and resid 16 through 30 Processing helix chain 'H' and resid 35 through 44 Processing helix chain 'H' and resid 48 through 58 removed outlier: 3.739A pdb=" N THR H 58 " --> pdb=" O THR H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 84 Processing helix chain 'H' and resid 100 through 105 removed outlier: 3.670A pdb=" N ALA H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 110 through 120 Processing helix chain 'H' and resid 125 through 146 removed outlier: 3.608A pdb=" N LYS H 140 " --> pdb=" O LEU H 136 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 153 removed outlier: 3.590A pdb=" N ILE H 153 " --> pdb=" O ILE H 150 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 175 Processing helix chain 'H' and resid 178 through 193 removed outlier: 4.606A pdb=" N LEU H 190 " --> pdb=" O THR H 186 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL H 191 " --> pdb=" O GLU H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 195 through 206 removed outlier: 3.683A pdb=" N THR H 200 " --> pdb=" O PRO H 196 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE H 201 " --> pdb=" O ASP H 197 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY H 206 " --> pdb=" O LEU H 202 " (cutoff:3.500A) Processing helix chain 'H' and resid 210 through 218 removed outlier: 3.569A pdb=" N CYS H 218 " --> pdb=" O MET H 214 " (cutoff:3.500A) Processing helix chain 'I' and resid 16 through 30 Processing helix chain 'I' and resid 35 through 43 Processing helix chain 'I' and resid 48 through 58 Processing helix chain 'I' and resid 62 through 84 Processing helix chain 'I' and resid 110 through 120 Processing helix chain 'I' and resid 125 through 145 Processing helix chain 'J' and resid 149 through 153 Processing helix chain 'J' and resid 160 through 175 Processing helix chain 'J' and resid 178 through 193 removed outlier: 4.424A pdb=" N LEU J 190 " --> pdb=" O THR J 186 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL J 191 " --> pdb=" O GLU J 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 195 through 206 removed outlier: 3.539A pdb=" N THR J 200 " --> pdb=" O PRO J 196 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE J 201 " --> pdb=" O ASP J 197 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY J 206 " --> pdb=" O LEU J 202 " (cutoff:3.500A) Processing helix chain 'J' and resid 210 through 218 Processing helix chain 'P' and resid 16 through 31 removed outlier: 3.724A pdb=" N LEU P 20 " --> pdb=" O SER P 16 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN P 21 " --> pdb=" O PRO P 17 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU P 29 " --> pdb=" O LYS P 25 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ALA P 31 " --> pdb=" O VAL P 27 " (cutoff:3.500A) Processing helix chain 'P' and resid 35 through 44 removed outlier: 3.726A pdb=" N MET P 39 " --> pdb=" O GLU P 35 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER P 44 " --> pdb=" O PHE P 40 " (cutoff:3.500A) Processing helix chain 'P' and resid 48 through 57 removed outlier: 3.567A pdb=" N ASN P 53 " --> pdb=" O PRO P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 58 through 61 removed outlier: 3.981A pdb=" N GLY P 61 " --> pdb=" O THR P 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 58 through 61' Processing helix chain 'P' and resid 62 through 81 removed outlier: 3.551A pdb=" N MET P 68 " --> pdb=" O ALA P 64 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU P 69 " --> pdb=" O ALA P 65 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP P 81 " --> pdb=" O ALA P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 105 Processing helix chain 'P' and resid 110 through 119 Processing helix chain 'P' and resid 125 through 146 removed outlier: 3.755A pdb=" N ILE P 129 " --> pdb=" O PRO P 125 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU P 136 " --> pdb=" O ARG P 132 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 153 Processing helix chain 'P' and resid 160 through 176 removed outlier: 3.881A pdb=" N ASP P 166 " --> pdb=" O ARG P 162 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN P 176 " --> pdb=" O LEU P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 178 through 188 removed outlier: 3.553A pdb=" N LYS P 182 " --> pdb=" O SER P 178 " (cutoff:3.500A) Processing helix chain 'P' and resid 188 through 193 Processing helix chain 'P' and resid 195 through 206 removed outlier: 4.144A pdb=" N ILE P 201 " --> pdb=" O ASP P 197 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY P 206 " --> pdb=" O LEU P 202 " (cutoff:3.500A) Processing helix chain 'P' and resid 210 through 217 Processing helix chain 'Q' and resid 16 through 30 Processing helix chain 'Q' and resid 35 through 44 Processing helix chain 'Q' and resid 48 through 58 removed outlier: 3.739A pdb=" N THR Q 58 " --> pdb=" O THR Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 84 Processing helix chain 'Q' and resid 100 through 105 removed outlier: 3.670A pdb=" N ALA Q 105 " --> pdb=" O GLY Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 110 through 120 Processing helix chain 'Q' and resid 125 through 146 removed outlier: 3.608A pdb=" N LYS Q 140 " --> pdb=" O LEU Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 149 through 153 removed outlier: 3.590A pdb=" N ILE Q 153 " --> pdb=" O ILE Q 150 " (cutoff:3.500A) Processing helix chain 'Q' and resid 160 through 175 Processing helix chain 'Q' and resid 178 through 193 removed outlier: 4.606A pdb=" N LEU Q 190 " --> pdb=" O THR Q 186 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL Q 191 " --> pdb=" O GLU Q 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 195 through 206 removed outlier: 3.683A pdb=" N THR Q 200 " --> pdb=" O PRO Q 196 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE Q 201 " --> pdb=" O ASP Q 197 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY Q 206 " --> pdb=" O LEU Q 202 " (cutoff:3.500A) Processing helix chain 'Q' and resid 210 through 218 removed outlier: 3.569A pdb=" N CYS Q 218 " --> pdb=" O MET Q 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 30 Processing helix chain 'R' and resid 35 through 43 Processing helix chain 'R' and resid 48 through 58 Processing helix chain 'R' and resid 62 through 84 Processing helix chain 'R' and resid 110 through 120 Processing helix chain 'R' and resid 125 through 145 Processing helix chain 'S' and resid 149 through 153 Processing helix chain 'S' and resid 160 through 175 Processing helix chain 'S' and resid 178 through 193 removed outlier: 4.424A pdb=" N LEU S 190 " --> pdb=" O THR S 186 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL S 191 " --> pdb=" O GLU S 187 " (cutoff:3.500A) Processing helix chain 'S' and resid 195 through 206 removed outlier: 3.539A pdb=" N THR S 200 " --> pdb=" O PRO S 196 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE S 201 " --> pdb=" O ASP S 197 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY S 206 " --> pdb=" O LEU S 202 " (cutoff:3.500A) Processing helix chain 'S' and resid 210 through 218 Processing helix chain 'V' and resid 16 through 31 removed outlier: 3.725A pdb=" N LEU V 20 " --> pdb=" O SER V 16 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN V 21 " --> pdb=" O PRO V 17 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU V 29 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA V 31 " --> pdb=" O VAL V 27 " (cutoff:3.500A) Processing helix chain 'V' and resid 35 through 44 removed outlier: 3.726A pdb=" N MET V 39 " --> pdb=" O GLU V 35 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER V 44 " --> pdb=" O PHE V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 48 through 57 removed outlier: 3.567A pdb=" N ASN V 53 " --> pdb=" O PRO V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 58 through 61 removed outlier: 3.980A pdb=" N GLY V 61 " --> pdb=" O THR V 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 58 through 61' Processing helix chain 'V' and resid 62 through 81 removed outlier: 3.551A pdb=" N MET V 68 " --> pdb=" O ALA V 64 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU V 69 " --> pdb=" O ALA V 65 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP V 81 " --> pdb=" O ALA V 77 " (cutoff:3.500A) Processing helix chain 'V' and resid 100 through 105 Processing helix chain 'V' and resid 110 through 119 Processing helix chain 'V' and resid 125 through 146 removed outlier: 3.755A pdb=" N ILE V 129 " --> pdb=" O PRO V 125 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU V 136 " --> pdb=" O ARG V 132 " (cutoff:3.500A) Processing helix chain 'V' and resid 149 through 153 Processing helix chain 'V' and resid 160 through 176 removed outlier: 3.880A pdb=" N ASP V 166 " --> pdb=" O ARG V 162 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN V 176 " --> pdb=" O LEU V 172 " (cutoff:3.500A) Processing helix chain 'V' and resid 178 through 188 removed outlier: 3.553A pdb=" N LYS V 182 " --> pdb=" O SER V 178 " (cutoff:3.500A) Processing helix chain 'V' and resid 188 through 193 Processing helix chain 'V' and resid 195 through 206 removed outlier: 4.144A pdb=" N ILE V 201 " --> pdb=" O ASP V 197 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY V 206 " --> pdb=" O LEU V 202 " (cutoff:3.500A) Processing helix chain 'V' and resid 210 through 217 Processing helix chain 'W' and resid 16 through 30 Processing helix chain 'W' and resid 35 through 44 Processing helix chain 'W' and resid 48 through 58 removed outlier: 3.740A pdb=" N THR W 58 " --> pdb=" O THR W 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 62 through 84 Processing helix chain 'W' and resid 100 through 105 removed outlier: 3.670A pdb=" N ALA W 105 " --> pdb=" O GLY W 101 " (cutoff:3.500A) Processing helix chain 'W' and resid 110 through 120 Processing helix chain 'W' and resid 125 through 146 removed outlier: 3.607A pdb=" N LYS W 140 " --> pdb=" O LEU W 136 " (cutoff:3.500A) Processing helix chain 'W' and resid 149 through 153 removed outlier: 3.590A pdb=" N ILE W 153 " --> pdb=" O ILE W 150 " (cutoff:3.500A) Processing helix chain 'W' and resid 160 through 175 Processing helix chain 'W' and resid 178 through 193 removed outlier: 4.605A pdb=" N LEU W 190 " --> pdb=" O THR W 186 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N VAL W 191 " --> pdb=" O GLU W 187 " (cutoff:3.500A) Processing helix chain 'W' and resid 195 through 206 removed outlier: 3.683A pdb=" N THR W 200 " --> pdb=" O PRO W 196 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE W 201 " --> pdb=" O ASP W 197 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY W 206 " --> pdb=" O LEU W 202 " (cutoff:3.500A) Processing helix chain 'W' and resid 210 through 218 removed outlier: 3.569A pdb=" N CYS W 218 " --> pdb=" O MET W 214 " (cutoff:3.500A) Processing helix chain 'X' and resid 16 through 30 Processing helix chain 'X' and resid 35 through 43 Processing helix chain 'X' and resid 48 through 58 Processing helix chain 'X' and resid 62 through 84 Processing helix chain 'X' and resid 110 through 120 Processing helix chain 'X' and resid 125 through 145 Processing helix chain '0' and resid 149 through 153 Processing helix chain '0' and resid 160 through 175 Processing helix chain '0' and resid 178 through 193 removed outlier: 4.423A pdb=" N LEU 0 190 " --> pdb=" O THR 0 186 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N VAL 0 191 " --> pdb=" O GLU 0 187 " (cutoff:3.500A) Processing helix chain '0' and resid 195 through 206 removed outlier: 3.539A pdb=" N THR 0 200 " --> pdb=" O PRO 0 196 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE 0 201 " --> pdb=" O ASP 0 197 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLY 0 206 " --> pdb=" O LEU 0 202 " (cutoff:3.500A) Processing helix chain '0' and resid 210 through 218 Processing helix chain '3' and resid 16 through 31 removed outlier: 3.724A pdb=" N LEU 3 20 " --> pdb=" O SER 3 16 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASN 3 21 " --> pdb=" O PRO 3 17 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU 3 29 " --> pdb=" O LYS 3 25 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA 3 31 " --> pdb=" O VAL 3 27 " (cutoff:3.500A) Processing helix chain '3' and resid 35 through 44 removed outlier: 3.726A pdb=" N MET 3 39 " --> pdb=" O GLU 3 35 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER 3 44 " --> pdb=" O PHE 3 40 " (cutoff:3.500A) Processing helix chain '3' and resid 48 through 57 removed outlier: 3.567A pdb=" N ASN 3 53 " --> pdb=" O PRO 3 49 " (cutoff:3.500A) Processing helix chain '3' and resid 58 through 61 removed outlier: 3.981A pdb=" N GLY 3 61 " --> pdb=" O THR 3 58 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 58 through 61' Processing helix chain '3' and resid 62 through 81 removed outlier: 3.551A pdb=" N MET 3 68 " --> pdb=" O ALA 3 64 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU 3 69 " --> pdb=" O ALA 3 65 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASP 3 81 " --> pdb=" O ALA 3 77 " (cutoff:3.500A) Processing helix chain '3' and resid 100 through 105 Processing helix chain '3' and resid 110 through 119 Processing helix chain '3' and resid 125 through 146 removed outlier: 3.755A pdb=" N ILE 3 129 " --> pdb=" O PRO 3 125 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU 3 136 " --> pdb=" O ARG 3 132 " (cutoff:3.500A) Processing helix chain '3' and resid 149 through 153 Processing helix chain '3' and resid 160 through 176 removed outlier: 3.880A pdb=" N ASP 3 166 " --> pdb=" O ARG 3 162 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN 3 176 " --> pdb=" O LEU 3 172 " (cutoff:3.500A) Processing helix chain '3' and resid 178 through 188 removed outlier: 3.553A pdb=" N LYS 3 182 " --> pdb=" O SER 3 178 " (cutoff:3.500A) Processing helix chain '3' and resid 188 through 193 Processing helix chain '3' and resid 195 through 206 removed outlier: 4.144A pdb=" N ILE 3 201 " --> pdb=" O ASP 3 197 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLY 3 206 " --> pdb=" O LEU 3 202 " (cutoff:3.500A) Processing helix chain '3' and resid 210 through 217 1420 hydrogen bonds defined for protein. 4185 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: 5.88 Time building geometry restraints manager: 9.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7190 1.34 - 1.46: 3991 1.46 - 1.57: 11234 1.57 - 1.69: 0 1.69 - 1.81: 275 Bond restraints: 22690 Sorted by residual: bond pdb=" C SER V 146 " pdb=" N PRO V 147 " ideal model delta sigma weight residual 1.336 1.319 0.017 1.20e-02 6.94e+03 1.91e+00 bond pdb=" C SER G 146 " pdb=" N PRO G 147 " ideal model delta sigma weight residual 1.336 1.320 0.016 1.20e-02 6.94e+03 1.89e+00 bond pdb=" C SER 3 146 " pdb=" N PRO 3 147 " ideal model delta sigma weight residual 1.336 1.320 0.016 1.20e-02 6.94e+03 1.88e+00 bond pdb=" C SER A 146 " pdb=" N PRO A 147 " ideal model delta sigma weight residual 1.336 1.320 0.016 1.20e-02 6.94e+03 1.86e+00 bond pdb=" C SER P 146 " pdb=" N PRO P 147 " ideal model delta sigma weight residual 1.336 1.320 0.016 1.20e-02 6.94e+03 1.76e+00 ... (remaining 22685 not shown) Histogram of bond angle deviations from ideal: 98.85 - 105.89: 1055 105.89 - 112.94: 12702 112.94 - 119.99: 7332 119.99 - 127.04: 9624 127.04 - 134.08: 427 Bond angle restraints: 31140 Sorted by residual: angle pdb=" C LEU F 315 " pdb=" N PHE F 316 " pdb=" CA PHE F 316 " ideal model delta sigma weight residual 121.48 115.16 6.32 2.04e+00 2.40e-01 9.60e+00 angle pdb=" C LEU Z 315 " pdb=" N PHE Z 316 " pdb=" CA PHE Z 316 " ideal model delta sigma weight residual 121.48 115.17 6.31 2.04e+00 2.40e-01 9.55e+00 angle pdb=" C LEU U 315 " pdb=" N PHE U 316 " pdb=" CA PHE U 316 " ideal model delta sigma weight residual 121.48 115.18 6.30 2.04e+00 2.40e-01 9.54e+00 angle pdb=" C LEU O 315 " pdb=" N PHE O 316 " pdb=" CA PHE O 316 " ideal model delta sigma weight residual 121.48 115.19 6.29 2.04e+00 2.40e-01 9.51e+00 angle pdb=" C LEU 2 315 " pdb=" N PHE 2 316 " pdb=" CA PHE 2 316 " ideal model delta sigma weight residual 121.48 115.23 6.25 2.04e+00 2.40e-01 9.39e+00 ... (remaining 31135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.77: 12435 14.77 - 29.54: 775 29.54 - 44.31: 195 44.31 - 59.08: 75 59.08 - 73.85: 5 Dihedral angle restraints: 13485 sinusoidal: 4600 harmonic: 8885 Sorted by residual: dihedral pdb=" N ARG G 18 " pdb=" CA ARG G 18 " pdb=" CB ARG G 18 " pdb=" CG ARG G 18 " ideal model delta sinusoidal sigma weight residual -60.00 -117.97 57.97 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N ARG 3 18 " pdb=" CA ARG 3 18 " pdb=" CB ARG 3 18 " pdb=" CG ARG 3 18 " ideal model delta sinusoidal sigma weight residual -60.00 -117.96 57.96 3 1.50e+01 4.44e-03 9.45e+00 dihedral pdb=" N ARG P 18 " pdb=" CA ARG P 18 " pdb=" CB ARG P 18 " pdb=" CG ARG P 18 " ideal model delta sinusoidal sigma weight residual -60.00 -117.95 57.95 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 13482 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2160 0.028 - 0.055: 1019 0.055 - 0.083: 362 0.083 - 0.110: 148 0.110 - 0.138: 41 Chirality restraints: 3730 Sorted by residual: chirality pdb=" CA PRO B 34 " pdb=" N PRO B 34 " pdb=" C PRO B 34 " pdb=" CB PRO B 34 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA PRO W 34 " pdb=" N PRO W 34 " pdb=" C PRO W 34 " pdb=" CB PRO W 34 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.69e-01 chirality pdb=" CA PRO L 34 " pdb=" N PRO L 34 " pdb=" C PRO L 34 " pdb=" CB PRO L 34 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 3727 not shown) Planarity restraints: 3980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 33 " -0.027 5.00e-02 4.00e+02 4.07e-02 2.65e+00 pdb=" N PRO B 34 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO B 34 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 34 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER W 33 " 0.027 5.00e-02 4.00e+02 4.07e-02 2.64e+00 pdb=" N PRO W 34 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO W 34 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO W 34 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER L 33 " 0.027 5.00e-02 4.00e+02 4.05e-02 2.63e+00 pdb=" N PRO L 34 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO L 34 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO L 34 " 0.023 5.00e-02 4.00e+02 ... (remaining 3977 not shown) Histogram of nonbonded interaction distances: 0.64 - 1.49: 15 1.49 - 2.34: 95 2.34 - 3.19: 22118 3.19 - 4.05: 53403 4.05 - 4.90: 91998 Warning: very small nonbonded interaction distances. Nonbonded interactions: 167629 Sorted by model distance: nonbonded pdb=" CB GLU A 35 " pdb=" OE2 GLU G 28 " model vdw 0.636 3.440 nonbonded pdb=" CB GLU V 35 " pdb=" OE2 GLU 3 28 " model vdw 0.636 3.440 nonbonded pdb=" CB GLU G 35 " pdb=" OE2 GLU P 28 " model vdw 0.636 3.440 nonbonded pdb=" OE2 GLU A 28 " pdb=" CB GLU 3 35 " model vdw 0.636 3.440 nonbonded pdb=" CB GLU P 35 " pdb=" OE2 GLU V 28 " model vdw 0.636 3.440 ... (remaining 167624 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 '0' selection = chain 'D' selection = chain 'J' selection = chain 'N' selection = chain 'S' } ncs_group { reference = chain '1' selection = (chain '2' and (resid 313 through 315 or (resid 316 and (name N or name CA or na \ me C or name O or name CB )) or resid 317 through 318 or (resid 319 and (name N \ or name CA or name C or name O or name CB )) or resid 320 through 325)) selection = chain 'E' selection = (chain 'F' and (resid 313 through 315 or (resid 316 and (name N or name CA or na \ me C or name O or name CB )) or resid 317 through 318 or (resid 319 and (name N \ or name CA or name C or name O or name CB )) or resid 320 through 325)) selection = chain 'K' selection = (chain 'O' and (resid 313 through 315 or (resid 316 and (name N or name CA or na \ me C or name O or name CB )) or resid 317 through 318 or (resid 319 and (name N \ or name CA or name C or name O or name CB )) or resid 320 through 325)) selection = chain 'T' selection = (chain 'U' and (resid 313 through 315 or (resid 316 and (name N or name CA or na \ me C or name O or name CB )) or resid 317 through 318 or (resid 319 and (name N \ or name CA or name C or name O or name CB )) or resid 320 through 325)) selection = chain 'Y' selection = (chain 'Z' and (resid 313 through 315 or (resid 316 and (name N or name CA or na \ me C or name O or name CB )) or resid 317 through 318 or (resid 319 and (name N \ or name CA or name C or name O or name CB )) or resid 320 through 325)) } ncs_group { reference = (chain '3' and (resid 1 through 12 or (resid 13 through 14 and (name N or name C \ A or name C or name O or name CB )) or resid 15 through 17 or (resid 18 and (nam \ e N or name CA or name C or name O or name CB )) or resid 19 through 27 or (resi \ d 28 through 29 and (name N or name CA or name C or name O or name CB )) or resi \ d 30 through 44 or (resid 45 and (name N or name CA or name C or name O or name \ CB )) or resid 46 through 67 or (resid 68 and (name N or name CA or name C or na \ me O or name CB )) or resid 69 through 75 or (resid 76 through 78 and (name N or \ name CA or name C or name O or name CB )) or resid 79 through 110 or (resid 111 \ through 113 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 14 through 118 or (resid 119 and (name N or name CA or name C or name O or name \ CB )) or resid 120 or (resid 121 and (name N or name CA or name C or name O or n \ ame CB )) or resid 122 through 127 or (resid 128 and (name N or name CA or name \ C or name O or name CB )) or resid 129 through 145 or (resid 146 and (name N or \ name CA or name C or name O or name CB )) or resid 147 through 158 or (resid 159 \ and (name N or name CA or name C or name O or name CB )) or resid 160 through 1 \ 64 or (resid 165 through 166 and (name N or name CA or name C or name O or name \ CB )) or resid 167 through 191 or (resid 192 and (name N or name CA or name C or \ name O or name CB )) or resid 193 through 199 or (resid 200 and (name N or name \ CA or name C or name O or name CB )) or resid 201 through 217 or (resid 218 thr \ ough 219 and (name N or name CA or name C or name O or name CB )) or resid 220 t \ hrough 221)) selection = (chain 'A' and (resid 1 through 12 or (resid 13 through 14 and (name N or name C \ A or name C or name O or name CB )) or resid 15 through 17 or (resid 18 and (nam \ e N or name CA or name C or name O or name CB )) or resid 19 through 27 or (resi \ d 28 through 29 and (name N or name CA or name C or name O or name CB )) or resi \ d 30 through 44 or (resid 45 and (name N or name CA or name C or name O or name \ CB )) or resid 46 through 67 or (resid 68 and (name N or name CA or name C or na \ me O or name CB )) or resid 69 through 75 or (resid 76 through 78 and (name N or \ name CA or name C or name O or name CB )) or resid 79 through 110 or (resid 111 \ through 113 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 14 through 118 or (resid 119 and (name N or name CA or name C or name O or name \ CB )) or resid 120 or (resid 121 and (name N or name CA or name C or name O or n \ ame CB )) or resid 122 through 127 or (resid 128 and (name N or name CA or name \ C or name O or name CB )) or resid 129 through 145 or (resid 146 and (name N or \ name CA or name C or name O or name CB )) or resid 147 through 158 or (resid 159 \ and (name N or name CA or name C or name O or name CB )) or resid 160 through 1 \ 64 or (resid 165 through 166 and (name N or name CA or name C or name O or name \ CB )) or resid 167 through 191 or (resid 192 and (name N or name CA or name C or \ name O or name CB )) or resid 193 through 199 or (resid 200 and (name N or name \ CA or name C or name O or name CB )) or resid 201 through 217 or (resid 218 thr \ ough 219 and (name N or name CA or name C or name O or name CB )) or resid 220 t \ hrough 221)) selection = (chain 'B' and (resid 1 through 62 or (resid 63 through 65 and (name N or name C \ A or name C or name O or name CB )) or resid 66 through 80 or (resid 81 and (nam \ e N or name CA or name C or name O or name CB )) or resid 99 through 142 or (res \ id 143 and (name N or name CA or name C or name O or name CB )) or resid 144 thr \ ough 161 or (resid 162 through 163 and (name N or name CA or name C or name O or \ name CB )) or resid 164 through 165 or (resid 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 169 or (resid 170 and (name N o \ r name CA or name C or name O or name CB )) or resid 171 through 172 or (resid 1 \ 73 through 177 and (name N or name CA or name C or name O or name CB )) or resid \ 178 through 221)) selection = (chain 'G' and (resid 1 through 12 or (resid 13 through 14 and (name N or name C \ A or name C or name O or name CB )) or resid 15 through 17 or (resid 18 and (nam \ e N or name CA or name C or name O or name CB )) or resid 19 through 27 or (resi \ d 28 through 29 and (name N or name CA or name C or name O or name CB )) or resi \ d 30 through 44 or (resid 45 and (name N or name CA or name C or name O or name \ CB )) or resid 46 through 67 or (resid 68 and (name N or name CA or name C or na \ me O or name CB )) or resid 69 through 75 or (resid 76 through 78 and (name N or \ name CA or name C or name O or name CB )) or resid 79 through 110 or (resid 111 \ through 113 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 14 through 118 or (resid 119 and (name N or name CA or name C or name O or name \ CB )) or resid 120 or (resid 121 and (name N or name CA or name C or name O or n \ ame CB )) or resid 122 through 127 or (resid 128 and (name N or name CA or name \ C or name O or name CB )) or resid 129 through 145 or (resid 146 and (name N or \ name CA or name C or name O or name CB )) or resid 147 through 158 or (resid 159 \ and (name N or name CA or name C or name O or name CB )) or resid 160 through 1 \ 64 or (resid 165 through 166 and (name N or name CA or name C or name O or name \ CB )) or resid 167 through 191 or (resid 192 and (name N or name CA or name C or \ name O or name CB )) or resid 193 through 199 or (resid 200 and (name N or name \ CA or name C or name O or name CB )) or resid 201 through 217 or (resid 218 thr \ ough 219 and (name N or name CA or name C or name O or name CB )) or resid 220 t \ hrough 221)) selection = (chain 'H' and (resid 1 through 62 or (resid 63 through 65 and (name N or name C \ A or name C or name O or name CB )) or resid 66 through 80 or (resid 81 and (nam \ e N or name CA or name C or name O or name CB )) or resid 99 through 142 or (res \ id 143 and (name N or name CA or name C or name O or name CB )) or resid 144 thr \ ough 161 or (resid 162 through 163 and (name N or name CA or name C or name O or \ name CB )) or resid 164 through 165 or (resid 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 169 or (resid 170 and (name N o \ r name CA or name C or name O or name CB )) or resid 171 through 172 or (resid 1 \ 73 through 177 and (name N or name CA or name C or name O or name CB )) or resid \ 178 through 221)) selection = (chain 'L' and (resid 1 through 62 or (resid 63 through 65 and (name N or name C \ A or name C or name O or name CB )) or resid 66 through 80 or (resid 81 and (nam \ e N or name CA or name C or name O or name CB )) or resid 99 through 142 or (res \ id 143 and (name N or name CA or name C or name O or name CB )) or resid 144 thr \ ough 161 or (resid 162 through 163 and (name N or name CA or name C or name O or \ name CB )) or resid 164 through 165 or (resid 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 169 or (resid 170 and (name N o \ r name CA or name C or name O or name CB )) or resid 171 through 172 or (resid 1 \ 73 through 177 and (name N or name CA or name C or name O or name CB )) or resid \ 178 through 221)) selection = (chain 'P' and (resid 1 through 12 or (resid 13 through 14 and (name N or name C \ A or name C or name O or name CB )) or resid 15 through 17 or (resid 18 and (nam \ e N or name CA or name C or name O or name CB )) or resid 19 through 27 or (resi \ d 28 through 29 and (name N or name CA or name C or name O or name CB )) or resi \ d 30 through 44 or (resid 45 and (name N or name CA or name C or name O or name \ CB )) or resid 46 through 67 or (resid 68 and (name N or name CA or name C or na \ me O or name CB )) or resid 69 through 75 or (resid 76 through 78 and (name N or \ name CA or name C or name O or name CB )) or resid 79 through 110 or (resid 111 \ through 113 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 14 through 118 or (resid 119 and (name N or name CA or name C or name O or name \ CB )) or resid 120 or (resid 121 and (name N or name CA or name C or name O or n \ ame CB )) or resid 122 through 127 or (resid 128 and (name N or name CA or name \ C or name O or name CB )) or resid 129 through 145 or (resid 146 and (name N or \ name CA or name C or name O or name CB )) or resid 147 through 158 or (resid 159 \ and (name N or name CA or name C or name O or name CB )) or resid 160 through 1 \ 64 or (resid 165 through 166 and (name N or name CA or name C or name O or name \ CB )) or resid 167 through 191 or (resid 192 and (name N or name CA or name C or \ name O or name CB )) or resid 193 through 199 or (resid 200 and (name N or name \ CA or name C or name O or name CB )) or resid 201 through 217 or (resid 218 thr \ ough 219 and (name N or name CA or name C or name O or name CB )) or resid 220 t \ hrough 221)) selection = (chain 'Q' and (resid 1 through 62 or (resid 63 through 65 and (name N or name C \ A or name C or name O or name CB )) or resid 66 through 80 or (resid 81 and (nam \ e N or name CA or name C or name O or name CB )) or resid 99 through 142 or (res \ id 143 and (name N or name CA or name C or name O or name CB )) or resid 144 thr \ ough 161 or (resid 162 through 163 and (name N or name CA or name C or name O or \ name CB )) or resid 164 through 165 or (resid 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 169 or (resid 170 and (name N o \ r name CA or name C or name O or name CB )) or resid 171 through 172 or (resid 1 \ 73 through 177 and (name N or name CA or name C or name O or name CB )) or resid \ 178 through 221)) selection = (chain 'V' and (resid 1 through 12 or (resid 13 through 14 and (name N or name C \ A or name C or name O or name CB )) or resid 15 through 17 or (resid 18 and (nam \ e N or name CA or name C or name O or name CB )) or resid 19 through 27 or (resi \ d 28 through 29 and (name N or name CA or name C or name O or name CB )) or resi \ d 30 through 44 or (resid 45 and (name N or name CA or name C or name O or name \ CB )) or resid 46 through 67 or (resid 68 and (name N or name CA or name C or na \ me O or name CB )) or resid 69 through 75 or (resid 76 through 78 and (name N or \ name CA or name C or name O or name CB )) or resid 79 through 110 or (resid 111 \ through 113 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 14 through 118 or (resid 119 and (name N or name CA or name C or name O or name \ CB )) or resid 120 or (resid 121 and (name N or name CA or name C or name O or n \ ame CB )) or resid 122 through 127 or (resid 128 and (name N or name CA or name \ C or name O or name CB )) or resid 129 through 145 or (resid 146 and (name N or \ name CA or name C or name O or name CB )) or resid 147 through 158 or (resid 159 \ and (name N or name CA or name C or name O or name CB )) or resid 160 through 1 \ 64 or (resid 165 through 166 and (name N or name CA or name C or name O or name \ CB )) or resid 167 through 191 or (resid 192 and (name N or name CA or name C or \ name O or name CB )) or resid 193 through 199 or (resid 200 and (name N or name \ CA or name C or name O or name CB )) or resid 201 through 217 or (resid 218 thr \ ough 219 and (name N or name CA or name C or name O or name CB )) or resid 220 t \ hrough 221)) selection = (chain 'W' and (resid 1 through 62 or (resid 63 through 65 and (name N or name C \ A or name C or name O or name CB )) or resid 66 through 80 or (resid 81 and (nam \ e N or name CA or name C or name O or name CB )) or resid 99 through 142 or (res \ id 143 and (name N or name CA or name C or name O or name CB )) or resid 144 thr \ ough 161 or (resid 162 through 163 and (name N or name CA or name C or name O or \ name CB )) or resid 164 through 165 or (resid 166 and (name N or name CA or nam \ e C or name O or name CB )) or resid 167 through 169 or (resid 170 and (name N o \ r name CA or name C or name O or name CB )) or resid 171 through 172 or (resid 1 \ 73 through 177 and (name N or name CA or name C or name O or name CB )) or resid \ 178 through 221)) } ncs_group { reference = chain 'C' selection = chain 'I' selection = chain 'M' selection = chain 'R' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.660 Check model and map are aligned: 0.370 Set scattering table: 0.260 Process input model: 55.710 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.160 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 : 0.005 0.029 22690 Z= 0.337 Angle : 0.545 6.319 31140 Z= 0.287 Chirality : 0.039 0.138 3730 Planarity : 0.004 0.041 3980 Dihedral : 11.630 73.846 7695 Min Nonbonded Distance : 0.636 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.04 % Allowed : 7.26 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 1.75 (0.16), residues: 2985 helix: 1.34 (0.12), residues: 1990 sheet: None (None), residues: 0 loop : 1.06 (0.21), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 184 HIS 0.002 0.001 HIS I 120 PHE 0.008 0.002 PHE W 168 TYR 0.008 0.001 TYR G 145 ARG 0.002 0.001 ARG 3 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 531 time to evaluate : 2.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 51 ASP cc_start: 0.8955 (m-30) cc_final: 0.8416 (m-30) REVERT: L 144 MET cc_start: 0.8709 (ttm) cc_final: 0.8444 (ttm) REVERT: L 214 MET cc_start: 0.9256 (mtm) cc_final: 0.9012 (mtp) REVERT: M 35 GLU cc_start: 0.8665 (pt0) cc_final: 0.8362 (tt0) REVERT: M 39 MET cc_start: 0.9085 (tpp) cc_final: 0.8807 (tpt) REVERT: N 164 TYR cc_start: 0.8991 (t80) cc_final: 0.8281 (t80) REVERT: N 192 GLN cc_start: 0.8946 (tp40) cc_final: 0.8612 (tp-100) REVERT: N 214 MET cc_start: 0.9114 (mtp) cc_final: 0.8794 (mtt) REVERT: Z 316 PHE cc_start: 0.8411 (m-80) cc_final: 0.7542 (m-80) REVERT: A 51 ASP cc_start: 0.9007 (m-30) cc_final: 0.8781 (m-30) REVERT: A 59 VAL cc_start: 0.9492 (OUTLIER) cc_final: 0.9236 (p) REVERT: B 67 GLN cc_start: 0.8808 (tp40) cc_final: 0.8293 (tp40) REVERT: B 84 HIS cc_start: 0.8443 (m90) cc_final: 0.8083 (m90) REVERT: B 214 MET cc_start: 0.9256 (mtm) cc_final: 0.9033 (mtp) REVERT: C 32 PHE cc_start: 0.7980 (OUTLIER) cc_final: 0.7463 (m-80) REVERT: C 35 GLU cc_start: 0.8760 (pt0) cc_final: 0.8445 (tt0) REVERT: C 39 MET cc_start: 0.9226 (tpp) cc_final: 0.8947 (tpt) REVERT: D 164 TYR cc_start: 0.8925 (t80) cc_final: 0.8163 (t80) REVERT: D 171 THR cc_start: 0.9396 (m) cc_final: 0.9111 (p) REVERT: D 214 MET cc_start: 0.9125 (mtp) cc_final: 0.8879 (mtt) REVERT: G 185 MET cc_start: 0.9205 (mtt) cc_final: 0.8985 (mtm) REVERT: H 26 VAL cc_start: 0.9431 (t) cc_final: 0.9219 (t) REVERT: H 67 GLN cc_start: 0.8957 (tp40) cc_final: 0.8700 (tp40) REVERT: H 84 HIS cc_start: 0.8339 (m90) cc_final: 0.8027 (m90) REVERT: I 35 GLU cc_start: 0.8621 (pt0) cc_final: 0.8298 (tt0) REVERT: J 164 TYR cc_start: 0.8973 (t80) cc_final: 0.8501 (t80) REVERT: J 214 MET cc_start: 0.9113 (mtp) cc_final: 0.8841 (mtt) REVERT: P 51 ASP cc_start: 0.8920 (m-30) cc_final: 0.8649 (m-30) REVERT: Q 51 ASP cc_start: 0.8855 (m-30) cc_final: 0.8470 (m-30) REVERT: Q 67 GLN cc_start: 0.8812 (tp40) cc_final: 0.8529 (tp40) REVERT: Q 84 HIS cc_start: 0.8504 (m90) cc_final: 0.8060 (m90) REVERT: Q 214 MET cc_start: 0.9302 (mtm) cc_final: 0.9096 (mtp) REVERT: R 35 GLU cc_start: 0.8699 (pt0) cc_final: 0.8092 (tp30) REVERT: R 39 MET cc_start: 0.9269 (tpp) cc_final: 0.9060 (tpt) REVERT: S 164 TYR cc_start: 0.8974 (t80) cc_final: 0.8237 (t80) REVERT: S 214 MET cc_start: 0.9097 (mtp) cc_final: 0.8797 (mtt) REVERT: S 215 MET cc_start: 0.9065 (mtm) cc_final: 0.8815 (mtm) REVERT: V 144 MET cc_start: 0.9051 (ttm) cc_final: 0.8785 (ttm) REVERT: W 51 ASP cc_start: 0.8998 (m-30) cc_final: 0.8505 (m-30) REVERT: W 67 GLN cc_start: 0.8824 (tp40) cc_final: 0.8460 (tp40) REVERT: X 35 GLU cc_start: 0.8512 (pt0) cc_final: 0.8066 (tt0) REVERT: 0 164 TYR cc_start: 0.9010 (t80) cc_final: 0.8386 (t80) REVERT: 3 51 ASP cc_start: 0.8946 (m-30) cc_final: 0.8728 (m-30) outliers start: 65 outliers final: 36 residues processed: 581 average time/residue: 0.2873 time to fit residues: 265.7991 Evaluate side-chains 427 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 389 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 144 MET Chi-restraints excluded: chain N residue 150 ILE Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 144 MET Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain I residue 32 PHE Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain R residue 32 PHE Chi-restraints excluded: chain S residue 150 ILE Chi-restraints excluded: chain S residue 178 SER Chi-restraints excluded: chain S residue 195 ASN Chi-restraints excluded: chain V residue 33 SER Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 32 PHE Chi-restraints excluded: chain X residue 144 MET Chi-restraints excluded: chain 0 residue 150 ILE Chi-restraints excluded: chain 0 residue 178 SER Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 3 residue 33 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 10.0000 chunk 227 optimal weight: 7.9990 chunk 126 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 153 optimal weight: 2.9990 chunk 121 optimal weight: 6.9990 chunk 235 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 175 optimal weight: 1.9990 chunk 272 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 155 GLN ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 179 GLN A 112 GLN A 195 ASN B 155 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 GLN G 112 GLN G 195 ASN H 155 GLN ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 179 GLN ** O 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 195 ASN Q 155 GLN ** Q 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 179 GLN V 195 ASN W 155 GLN ** W 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 193 ASN 0 179 GLN 3 195 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22690 Z= 0.233 Angle : 0.561 7.517 31140 Z= 0.288 Chirality : 0.041 0.179 3730 Planarity : 0.005 0.049 3980 Dihedral : 6.126 58.896 3213 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 4.68 % Allowed : 13.91 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 2.18 (0.15), residues: 2985 helix: 1.73 (0.11), residues: 2125 sheet: None (None), residues: 0 loop : 0.94 (0.22), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 133 HIS 0.004 0.001 HIS M 62 PHE 0.013 0.002 PHE G 161 TYR 0.022 0.001 TYR B 164 ARG 0.007 0.001 ARG H 82 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 503 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 51 ASP cc_start: 0.8947 (m-30) cc_final: 0.8434 (m-30) REVERT: L 55 MET cc_start: 0.9250 (ttp) cc_final: 0.8954 (tmm) REVERT: L 117 TRP cc_start: 0.8448 (OUTLIER) cc_final: 0.7995 (m-90) REVERT: L 144 MET cc_start: 0.8866 (ttm) cc_final: 0.8519 (ttm) REVERT: L 214 MET cc_start: 0.9169 (mtm) cc_final: 0.8869 (mtp) REVERT: M 35 GLU cc_start: 0.8639 (pt0) cc_final: 0.8302 (tt0) REVERT: N 164 TYR cc_start: 0.9003 (t80) cc_final: 0.8319 (t80) REVERT: N 192 GLN cc_start: 0.8943 (tp40) cc_final: 0.8581 (tp-100) REVERT: A 45 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8528 (tm-30) REVERT: A 51 ASP cc_start: 0.9072 (m-30) cc_final: 0.8830 (m-30) REVERT: A 195 ASN cc_start: 0.9029 (OUTLIER) cc_final: 0.8737 (p0) REVERT: B 51 ASP cc_start: 0.8952 (m-30) cc_final: 0.8542 (m-30) REVERT: B 67 GLN cc_start: 0.8718 (tp40) cc_final: 0.8112 (tp40) REVERT: B 117 TRP cc_start: 0.8304 (OUTLIER) cc_final: 0.7937 (m-90) REVERT: C 32 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7501 (m-80) REVERT: C 35 GLU cc_start: 0.8759 (pt0) cc_final: 0.8219 (tt0) REVERT: C 76 GLU cc_start: 0.8629 (tp30) cc_final: 0.8295 (tp30) REVERT: C 114 GLN cc_start: 0.9266 (mt0) cc_final: 0.8419 (mp-120) REVERT: D 164 TYR cc_start: 0.8918 (t80) cc_final: 0.8038 (t80) REVERT: D 171 THR cc_start: 0.9274 (m) cc_final: 0.8951 (p) REVERT: D 192 GLN cc_start: 0.8934 (tp40) cc_final: 0.8676 (tp-100) REVERT: G 195 ASN cc_start: 0.9119 (OUTLIER) cc_final: 0.8867 (p0) REVERT: H 53 ASN cc_start: 0.8909 (m-40) cc_final: 0.8635 (t0) REVERT: H 55 MET cc_start: 0.9294 (ttp) cc_final: 0.9007 (tmm) REVERT: H 67 GLN cc_start: 0.8840 (tp40) cc_final: 0.8541 (tp40) REVERT: H 84 HIS cc_start: 0.8234 (m90) cc_final: 0.7957 (m90) REVERT: I 35 GLU cc_start: 0.8558 (pt0) cc_final: 0.8183 (tp30) REVERT: I 39 MET cc_start: 0.8793 (tpp) cc_final: 0.8353 (mmm) REVERT: I 76 GLU cc_start: 0.8744 (tp30) cc_final: 0.8206 (tp30) REVERT: J 164 TYR cc_start: 0.8930 (t80) cc_final: 0.8512 (t80) REVERT: J 214 MET cc_start: 0.9023 (mtp) cc_final: 0.8803 (mtt) REVERT: P 29 GLU cc_start: 0.8294 (mt-10) cc_final: 0.8070 (mt-10) REVERT: P 51 ASP cc_start: 0.8993 (m-30) cc_final: 0.8777 (m-30) REVERT: P 109 SER cc_start: 0.6979 (OUTLIER) cc_final: 0.6726 (m) REVERT: P 195 ASN cc_start: 0.9071 (OUTLIER) cc_final: 0.8800 (p0) REVERT: P 215 MET cc_start: 0.8842 (mtt) cc_final: 0.8611 (mtt) REVERT: Q 51 ASP cc_start: 0.8861 (m-30) cc_final: 0.8444 (m-30) REVERT: Q 67 GLN cc_start: 0.8842 (tp40) cc_final: 0.8531 (tp40) REVERT: Q 79 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8286 (mm-30) REVERT: R 35 GLU cc_start: 0.8845 (pt0) cc_final: 0.8044 (tp30) REVERT: R 76 GLU cc_start: 0.8699 (tp30) cc_final: 0.8342 (tp30) REVERT: R 114 GLN cc_start: 0.9432 (mt0) cc_final: 0.8683 (mp-120) REVERT: S 164 TYR cc_start: 0.8946 (t80) cc_final: 0.8180 (t80) REVERT: S 214 MET cc_start: 0.9081 (mtp) cc_final: 0.8837 (mtt) REVERT: V 45 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8510 (tm-30) REVERT: V 109 SER cc_start: 0.7548 (OUTLIER) cc_final: 0.7306 (m) REVERT: V 195 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8787 (p0) REVERT: V 215 MET cc_start: 0.8788 (mtt) cc_final: 0.8359 (mtt) REVERT: W 51 ASP cc_start: 0.8999 (m-30) cc_final: 0.8511 (m-30) REVERT: W 53 ASN cc_start: 0.8915 (m-40) cc_final: 0.8650 (t0) REVERT: W 67 GLN cc_start: 0.8839 (tp40) cc_final: 0.8412 (tp40) REVERT: X 35 GLU cc_start: 0.8651 (pt0) cc_final: 0.7987 (tt0) REVERT: 0 164 TYR cc_start: 0.8954 (t80) cc_final: 0.8375 (t80) REVERT: 3 51 ASP cc_start: 0.9113 (m-30) cc_final: 0.8842 (m-30) REVERT: 3 66 MET cc_start: 0.8903 (tpt) cc_final: 0.8391 (tpp) REVERT: 3 109 SER cc_start: 0.7421 (OUTLIER) cc_final: 0.7172 (m) REVERT: 3 128 GLU cc_start: 0.8111 (tm-30) cc_final: 0.7785 (tm-30) REVERT: 3 195 ASN cc_start: 0.9008 (OUTLIER) cc_final: 0.8746 (p0) REVERT: 3 215 MET cc_start: 0.8932 (mtt) cc_final: 0.8693 (mtt) outliers start: 100 outliers final: 62 residues processed: 563 average time/residue: 0.2977 time to fit residues: 265.5943 Evaluate side-chains 479 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 406 time to evaluate : 2.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 117 TRP Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 129 ILE Chi-restraints excluded: chain M residue 144 MET Chi-restraints excluded: chain N residue 150 ILE Chi-restraints excluded: chain N residue 171 THR Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 202 LEU Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 118 MET Chi-restraints excluded: chain A residue 150 ILE Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 149 SER Chi-restraints excluded: chain G residue 150 ILE Chi-restraints excluded: chain G residue 195 ASN Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 144 MET Chi-restraints excluded: chain J residue 171 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 109 SER Chi-restraints excluded: chain P residue 150 ILE Chi-restraints excluded: chain P residue 195 ASN Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain R residue 32 PHE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain S residue 150 ILE Chi-restraints excluded: chain S residue 171 THR Chi-restraints excluded: chain S residue 178 SER Chi-restraints excluded: chain S residue 195 ASN Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain V residue 150 ILE Chi-restraints excluded: chain V residue 195 ASN Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain X residue 32 PHE Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain X residue 129 ILE Chi-restraints excluded: chain X residue 144 MET Chi-restraints excluded: chain 0 residue 150 ILE Chi-restraints excluded: chain 0 residue 171 THR Chi-restraints excluded: chain 0 residue 178 SER Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 3 residue 16 SER Chi-restraints excluded: chain 3 residue 109 SER Chi-restraints excluded: chain 3 residue 144 MET Chi-restraints excluded: chain 3 residue 150 ILE Chi-restraints excluded: chain 3 residue 195 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 226 optimal weight: 10.0000 chunk 185 optimal weight: 4.9990 chunk 75 optimal weight: 0.0970 chunk 272 optimal weight: 5.9990 chunk 294 optimal weight: 20.0000 chunk 243 optimal weight: 3.9990 chunk 270 optimal weight: 0.7980 chunk 93 optimal weight: 5.9990 chunk 218 optimal weight: 4.9990 overall best weight: 2.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 319 GLN A 112 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 319 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 112 GLN ** Q 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 112 GLN X 21 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22690 Z= 0.219 Angle : 0.556 9.525 31140 Z= 0.279 Chirality : 0.040 0.180 3730 Planarity : 0.005 0.051 3980 Dihedral : 5.682 58.030 3199 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 4.31 % Allowed : 15.50 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 2.25 (0.15), residues: 2985 helix: 1.73 (0.11), residues: 2125 sheet: None (None), residues: 0 loop : 1.13 (0.23), residues: 860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 23 HIS 0.005 0.001 HIS M 84 PHE 0.009 0.001 PHE V 40 TYR 0.019 0.001 TYR Q 164 ARG 0.009 0.001 ARG L 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 432 time to evaluate : 2.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 51 ASP cc_start: 0.8938 (m-30) cc_final: 0.8415 (m-30) REVERT: L 144 MET cc_start: 0.8734 (ttm) cc_final: 0.8292 (ttm) REVERT: L 179 GLN cc_start: 0.8296 (tp40) cc_final: 0.8022 (tp40) REVERT: L 214 MET cc_start: 0.9153 (mtm) cc_final: 0.8812 (mtp) REVERT: M 35 GLU cc_start: 0.8702 (pt0) cc_final: 0.8228 (tt0) REVERT: N 164 TYR cc_start: 0.9007 (t80) cc_final: 0.8279 (t80) REVERT: N 192 GLN cc_start: 0.8956 (tp40) cc_final: 0.8601 (tp-100) REVERT: N 215 MET cc_start: 0.9028 (ttm) cc_final: 0.8600 (ttp) REVERT: A 51 ASP cc_start: 0.9103 (m-30) cc_final: 0.8829 (m-30) REVERT: B 25 LYS cc_start: 0.9635 (OUTLIER) cc_final: 0.9418 (ttmm) REVERT: B 51 ASP cc_start: 0.8946 (m-30) cc_final: 0.8353 (m-30) REVERT: C 32 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7504 (m-80) REVERT: C 35 GLU cc_start: 0.8655 (pt0) cc_final: 0.8157 (tt0) REVERT: C 76 GLU cc_start: 0.8655 (tp30) cc_final: 0.8320 (tp30) REVERT: C 114 GLN cc_start: 0.9313 (mt0) cc_final: 0.8525 (mp-120) REVERT: D 164 TYR cc_start: 0.8888 (t80) cc_final: 0.7998 (t80) REVERT: D 192 GLN cc_start: 0.8940 (tp40) cc_final: 0.8679 (tp-100) REVERT: G 109 SER cc_start: 0.7143 (OUTLIER) cc_final: 0.6899 (m) REVERT: G 215 MET cc_start: 0.8829 (mtt) cc_final: 0.8624 (mmt) REVERT: H 67 GLN cc_start: 0.8829 (tp40) cc_final: 0.8555 (tp40) REVERT: H 176 GLN cc_start: 0.8150 (mt0) cc_final: 0.7948 (mt0) REVERT: I 39 MET cc_start: 0.8874 (tpp) cc_final: 0.8358 (mmm) REVERT: J 164 TYR cc_start: 0.8938 (t80) cc_final: 0.8547 (t80) REVERT: J 214 MET cc_start: 0.9069 (mtp) cc_final: 0.8847 (mtt) REVERT: P 51 ASP cc_start: 0.9103 (m-30) cc_final: 0.8826 (m-30) REVERT: P 55 MET cc_start: 0.9162 (mtp) cc_final: 0.8772 (mtp) REVERT: P 66 MET cc_start: 0.9045 (tpt) cc_final: 0.8781 (tpt) REVERT: Q 51 ASP cc_start: 0.8897 (m-30) cc_final: 0.8336 (m-30) REVERT: R 35 GLU cc_start: 0.8753 (pt0) cc_final: 0.7992 (tt0) REVERT: R 66 MET cc_start: 0.8764 (mmm) cc_final: 0.8460 (mmm) REVERT: R 76 GLU cc_start: 0.8784 (tp30) cc_final: 0.8465 (tp30) REVERT: R 114 GLN cc_start: 0.9413 (mt0) cc_final: 0.8693 (mp-120) REVERT: S 164 TYR cc_start: 0.8990 (t80) cc_final: 0.8305 (t80) REVERT: S 214 MET cc_start: 0.9147 (mtp) cc_final: 0.8874 (mtt) REVERT: W 51 ASP cc_start: 0.9023 (m-30) cc_final: 0.8542 (m-30) REVERT: W 67 GLN cc_start: 0.8719 (tp40) cc_final: 0.8325 (tp40) REVERT: X 35 GLU cc_start: 0.8608 (pt0) cc_final: 0.7989 (tt0) REVERT: 0 164 TYR cc_start: 0.8955 (t80) cc_final: 0.8409 (t80) REVERT: 3 51 ASP cc_start: 0.9122 (m-30) cc_final: 0.8876 (m-30) REVERT: 3 66 MET cc_start: 0.8902 (tpt) cc_final: 0.8390 (tpp) outliers start: 92 outliers final: 56 residues processed: 495 average time/residue: 0.3173 time to fit residues: 248.8457 Evaluate side-chains 457 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 398 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 150 ILE Chi-restraints excluded: chain N residue 171 THR Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 144 MET Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 171 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain R residue 32 PHE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain S residue 150 ILE Chi-restraints excluded: chain S residue 171 THR Chi-restraints excluded: chain S residue 178 SER Chi-restraints excluded: chain S residue 195 ASN Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 32 PHE Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain X residue 144 MET Chi-restraints excluded: chain 0 residue 150 ILE Chi-restraints excluded: chain 0 residue 151 LEU Chi-restraints excluded: chain 0 residue 171 THR Chi-restraints excluded: chain 0 residue 178 SER Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 0 residue 210 THR Chi-restraints excluded: chain 3 residue 16 SER Chi-restraints excluded: chain 3 residue 35 GLU Chi-restraints excluded: chain 3 residue 144 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 0.9980 chunk 205 optimal weight: 2.9990 chunk 141 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 130 optimal weight: 20.0000 chunk 183 optimal weight: 1.9990 chunk 273 optimal weight: 0.0970 chunk 289 optimal weight: 5.9990 chunk 143 optimal weight: 0.2980 chunk 259 optimal weight: 8.9990 chunk 78 optimal weight: 20.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 219 GLN P 112 GLN ** Q 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 193 ASN S 219 GLN V 112 GLN ** W 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 219 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 22690 Z= 0.158 Angle : 0.525 9.930 31140 Z= 0.259 Chirality : 0.038 0.151 3730 Planarity : 0.005 0.052 3980 Dihedral : 5.321 57.436 3193 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.23 % Allowed : 16.16 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 2.40 (0.15), residues: 2985 helix: 1.85 (0.11), residues: 2100 sheet: None (None), residues: 0 loop : 1.19 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 23 HIS 0.003 0.001 HIS C 84 PHE 0.010 0.001 PHE Q 40 TYR 0.020 0.001 TYR L 164 ARG 0.007 0.001 ARG Q 82 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 461 time to evaluate : 2.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 51 ASP cc_start: 0.8867 (m-30) cc_final: 0.8344 (m-30) REVERT: L 144 MET cc_start: 0.8736 (ttm) cc_final: 0.8150 (ttm) REVERT: L 214 MET cc_start: 0.9074 (mtm) cc_final: 0.8632 (mtp) REVERT: M 35 GLU cc_start: 0.8608 (pt0) cc_final: 0.8197 (tt0) REVERT: N 164 TYR cc_start: 0.8974 (t80) cc_final: 0.8303 (t80) REVERT: N 192 GLN cc_start: 0.8933 (tp40) cc_final: 0.8567 (tp-100) REVERT: N 215 MET cc_start: 0.9106 (ttm) cc_final: 0.8618 (ttp) REVERT: A 51 ASP cc_start: 0.9097 (m-30) cc_final: 0.8840 (m-30) REVERT: A 57 ASN cc_start: 0.9060 (m-40) cc_final: 0.8470 (t0) REVERT: B 51 ASP cc_start: 0.8866 (m-30) cc_final: 0.8295 (m-30) REVERT: C 32 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7811 (m-80) REVERT: C 35 GLU cc_start: 0.8610 (pt0) cc_final: 0.7897 (tt0) REVERT: C 76 GLU cc_start: 0.8691 (tp30) cc_final: 0.8388 (tp30) REVERT: C 114 GLN cc_start: 0.9413 (mt0) cc_final: 0.8749 (mp10) REVERT: D 164 TYR cc_start: 0.8889 (t80) cc_final: 0.8050 (t80) REVERT: D 192 GLN cc_start: 0.8916 (tp40) cc_final: 0.8573 (tp-100) REVERT: G 55 MET cc_start: 0.9188 (mtp) cc_final: 0.8910 (mtp) REVERT: G 109 SER cc_start: 0.7101 (OUTLIER) cc_final: 0.6853 (m) REVERT: H 51 ASP cc_start: 0.8945 (m-30) cc_final: 0.8310 (m-30) REVERT: H 143 ARG cc_start: 0.9257 (tpt90) cc_final: 0.8484 (tpm170) REVERT: I 39 MET cc_start: 0.8796 (tpp) cc_final: 0.8294 (mmm) REVERT: I 76 GLU cc_start: 0.8670 (tp30) cc_final: 0.8133 (tp30) REVERT: J 164 TYR cc_start: 0.8912 (t80) cc_final: 0.8529 (t80) REVERT: P 55 MET cc_start: 0.9087 (mtp) cc_final: 0.8784 (mtp) REVERT: P 109 SER cc_start: 0.7114 (OUTLIER) cc_final: 0.6707 (m) REVERT: Q 51 ASP cc_start: 0.8904 (m-30) cc_final: 0.8430 (m-30) REVERT: R 35 GLU cc_start: 0.8724 (pt0) cc_final: 0.8012 (tt0) REVERT: R 41 SER cc_start: 0.9253 (t) cc_final: 0.9035 (p) REVERT: R 76 GLU cc_start: 0.8770 (tp30) cc_final: 0.8441 (tp30) REVERT: R 114 GLN cc_start: 0.9450 (mt0) cc_final: 0.8763 (mp10) REVERT: S 164 TYR cc_start: 0.8916 (t80) cc_final: 0.8324 (t80) REVERT: S 214 MET cc_start: 0.9057 (mtp) cc_final: 0.8851 (mtt) REVERT: V 57 ASN cc_start: 0.9095 (m-40) cc_final: 0.8461 (t0) REVERT: V 109 SER cc_start: 0.7499 (OUTLIER) cc_final: 0.7148 (m) REVERT: W 51 ASP cc_start: 0.8972 (m-30) cc_final: 0.8489 (m-30) REVERT: W 53 ASN cc_start: 0.9171 (OUTLIER) cc_final: 0.8969 (t0) REVERT: W 67 GLN cc_start: 0.8640 (tp40) cc_final: 0.8306 (tp40) REVERT: X 35 GLU cc_start: 0.8540 (pt0) cc_final: 0.7939 (tt0) REVERT: 0 164 TYR cc_start: 0.8946 (t80) cc_final: 0.8347 (t80) REVERT: 3 57 ASN cc_start: 0.8862 (m-40) cc_final: 0.8627 (t0) outliers start: 69 outliers final: 39 residues processed: 510 average time/residue: 0.2976 time to fit residues: 240.7240 Evaluate side-chains 449 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 405 time to evaluate : 2.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain N residue 171 THR Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 219 GLN Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 109 SER Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 56 LEU Chi-restraints excluded: chain R residue 32 PHE Chi-restraints excluded: chain S residue 178 SER Chi-restraints excluded: chain S residue 195 ASN Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 53 ASN Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 32 PHE Chi-restraints excluded: chain X residue 144 MET Chi-restraints excluded: chain 0 residue 178 SER Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 0 residue 210 THR Chi-restraints excluded: chain 0 residue 219 GLN Chi-restraints excluded: chain 1 residue 315 LEU Chi-restraints excluded: chain 3 residue 16 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 4.9990 chunk 164 optimal weight: 2.9990 chunk 4 optimal weight: 7.9990 chunk 215 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 247 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 chunk 260 optimal weight: 7.9990 chunk 73 optimal weight: 9.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 67 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN P 112 GLN R 50 GLN W 179 GLN ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 22690 Z= 0.254 Angle : 0.564 10.729 31140 Z= 0.278 Chirality : 0.040 0.155 3730 Planarity : 0.005 0.053 3980 Dihedral : 5.243 53.549 3183 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 3.56 % Allowed : 17.19 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 2.44 (0.15), residues: 2985 helix: 1.89 (0.11), residues: 2100 sheet: None (None), residues: 0 loop : 1.18 (0.22), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP V 23 HIS 0.002 0.000 HIS R 84 PHE 0.016 0.001 PHE Z 321 TYR 0.021 0.001 TYR Q 164 ARG 0.002 0.000 ARG B 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 491 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 415 time to evaluate : 2.576 Fit side-chains REVERT: L 51 ASP cc_start: 0.8881 (m-30) cc_final: 0.8377 (m-30) REVERT: L 144 MET cc_start: 0.8722 (ttm) cc_final: 0.8186 (ttm) REVERT: L 214 MET cc_start: 0.9107 (mtm) cc_final: 0.8870 (mtp) REVERT: M 35 GLU cc_start: 0.8653 (pt0) cc_final: 0.8232 (tt0) REVERT: N 164 TYR cc_start: 0.9010 (t80) cc_final: 0.8289 (t80) REVERT: N 192 GLN cc_start: 0.8981 (tp40) cc_final: 0.8587 (tp-100) REVERT: N 215 MET cc_start: 0.9138 (ttm) cc_final: 0.8713 (ttp) REVERT: A 51 ASP cc_start: 0.9118 (m-30) cc_final: 0.8813 (m-30) REVERT: A 57 ASN cc_start: 0.9109 (m-40) cc_final: 0.8446 (t0) REVERT: B 51 ASP cc_start: 0.8898 (m-30) cc_final: 0.8361 (m-30) REVERT: C 32 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7801 (m-80) REVERT: C 35 GLU cc_start: 0.8643 (pt0) cc_final: 0.7921 (tt0) REVERT: C 76 GLU cc_start: 0.8717 (tp30) cc_final: 0.8348 (tp30) REVERT: C 114 GLN cc_start: 0.9441 (mt0) cc_final: 0.8787 (mp10) REVERT: D 173 ARG cc_start: 0.8734 (ttp80) cc_final: 0.8492 (ttp-170) REVERT: G 55 MET cc_start: 0.9260 (mtp) cc_final: 0.8949 (mtp) REVERT: G 109 SER cc_start: 0.7070 (OUTLIER) cc_final: 0.6869 (m) REVERT: H 51 ASP cc_start: 0.8963 (m-30) cc_final: 0.8319 (m-30) REVERT: H 143 ARG cc_start: 0.9283 (tpt90) cc_final: 0.8520 (tpm170) REVERT: I 39 MET cc_start: 0.8904 (tpp) cc_final: 0.8336 (mmm) REVERT: I 76 GLU cc_start: 0.8726 (tp30) cc_final: 0.8168 (tp30) REVERT: J 164 TYR cc_start: 0.8941 (t80) cc_final: 0.8429 (t80) REVERT: P 55 MET cc_start: 0.9085 (mtp) cc_final: 0.8708 (mtp) REVERT: P 109 SER cc_start: 0.7288 (OUTLIER) cc_final: 0.6873 (m) REVERT: Q 51 ASP cc_start: 0.8916 (m-30) cc_final: 0.8390 (m-30) REVERT: R 35 GLU cc_start: 0.8792 (pt0) cc_final: 0.8065 (tp30) REVERT: R 76 GLU cc_start: 0.8830 (tp30) cc_final: 0.8392 (tp30) REVERT: R 114 GLN cc_start: 0.9483 (mt0) cc_final: 0.8903 (mp10) REVERT: S 164 TYR cc_start: 0.8963 (t80) cc_final: 0.8337 (t80) REVERT: S 202 LEU cc_start: 0.8942 (tp) cc_final: 0.8664 (tp) REVERT: S 214 MET cc_start: 0.9047 (mtp) cc_final: 0.8802 (mtt) REVERT: V 57 ASN cc_start: 0.9107 (m-40) cc_final: 0.8476 (t0) REVERT: V 109 SER cc_start: 0.7408 (OUTLIER) cc_final: 0.7005 (m) REVERT: W 51 ASP cc_start: 0.8998 (m-30) cc_final: 0.8506 (m-30) REVERT: W 55 MET cc_start: 0.9301 (ttt) cc_final: 0.9071 (tmm) REVERT: W 67 GLN cc_start: 0.8678 (tp40) cc_final: 0.8473 (tp40) REVERT: W 176 GLN cc_start: 0.8551 (mt0) cc_final: 0.8259 (mt0) REVERT: X 35 GLU cc_start: 0.8609 (pt0) cc_final: 0.7986 (tt0) REVERT: 0 164 TYR cc_start: 0.9000 (t80) cc_final: 0.8391 (t80) outliers start: 76 outliers final: 47 residues processed: 466 average time/residue: 0.3176 time to fit residues: 235.6753 Evaluate side-chains 443 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 392 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 171 THR Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain Y residue 315 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 171 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 109 SER Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 69 LEU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain S residue 150 ILE Chi-restraints excluded: chain S residue 171 THR Chi-restraints excluded: chain S residue 178 SER Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 109 SER Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 32 PHE Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain 0 residue 150 ILE Chi-restraints excluded: chain 0 residue 171 THR Chi-restraints excluded: chain 0 residue 178 SER Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 0 residue 210 THR Chi-restraints excluded: chain 3 residue 35 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 57 optimal weight: 9.9990 chunk 170 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 290 optimal weight: 8.9990 chunk 240 optimal weight: 20.0000 chunk 134 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 96 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 319 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 219 GLN ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 63 GLN ** Q 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 179 GLN ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22690 Z= 0.285 Angle : 0.590 10.174 31140 Z= 0.293 Chirality : 0.040 0.155 3730 Planarity : 0.005 0.053 3980 Dihedral : 4.965 55.219 3174 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.70 % Allowed : 18.50 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 2.33 (0.16), residues: 2985 helix: 1.80 (0.11), residues: 2160 sheet: None (None), residues: 0 loop : 1.11 (0.24), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 184 HIS 0.003 0.001 HIS C 84 PHE 0.012 0.001 PHE V 40 TYR 0.026 0.001 TYR Q 164 ARG 0.008 0.001 ARG M 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 400 time to evaluate : 2.508 Fit side-chains revert: symmetry clash REVERT: L 51 ASP cc_start: 0.8915 (m-30) cc_final: 0.8401 (m-30) REVERT: L 144 MET cc_start: 0.8704 (ttm) cc_final: 0.8178 (ttm) REVERT: L 214 MET cc_start: 0.9169 (mtm) cc_final: 0.8856 (mtp) REVERT: M 35 GLU cc_start: 0.8633 (pt0) cc_final: 0.8226 (tt0) REVERT: N 164 TYR cc_start: 0.9009 (t80) cc_final: 0.8267 (t80) REVERT: N 192 GLN cc_start: 0.8905 (tp40) cc_final: 0.8468 (tp-100) REVERT: N 215 MET cc_start: 0.9153 (ttm) cc_final: 0.8715 (ttp) REVERT: A 51 ASP cc_start: 0.9122 (m-30) cc_final: 0.8811 (m-30) REVERT: A 57 ASN cc_start: 0.9116 (m-40) cc_final: 0.8453 (t0) REVERT: B 51 ASP cc_start: 0.8924 (m-30) cc_final: 0.8380 (m-30) REVERT: C 32 PHE cc_start: 0.8117 (OUTLIER) cc_final: 0.7687 (m-80) REVERT: C 35 GLU cc_start: 0.8643 (pt0) cc_final: 0.7933 (tt0) REVERT: C 76 GLU cc_start: 0.8794 (tp30) cc_final: 0.8413 (tp30) REVERT: C 114 GLN cc_start: 0.9475 (mt0) cc_final: 0.8890 (mp10) REVERT: G 55 MET cc_start: 0.9229 (mtp) cc_final: 0.8815 (mtp) REVERT: G 109 SER cc_start: 0.7080 (OUTLIER) cc_final: 0.6853 (m) REVERT: H 51 ASP cc_start: 0.8967 (m-30) cc_final: 0.8340 (m-30) REVERT: H 143 ARG cc_start: 0.9298 (tpt90) cc_final: 0.8462 (tpm170) REVERT: H 176 GLN cc_start: 0.8599 (mt0) cc_final: 0.8326 (mt0) REVERT: I 39 MET cc_start: 0.8939 (tpp) cc_final: 0.8329 (mmm) REVERT: I 76 GLU cc_start: 0.8734 (tp30) cc_final: 0.8187 (tp30) REVERT: J 164 TYR cc_start: 0.8929 (t80) cc_final: 0.8382 (t80) REVERT: P 55 MET cc_start: 0.9078 (mtp) cc_final: 0.8593 (mtp) REVERT: P 109 SER cc_start: 0.7200 (OUTLIER) cc_final: 0.6841 (m) REVERT: Q 51 ASP cc_start: 0.8928 (m-30) cc_final: 0.8395 (m-30) REVERT: Q 164 TYR cc_start: 0.8781 (t80) cc_final: 0.8418 (t80) REVERT: R 35 GLU cc_start: 0.8796 (pt0) cc_final: 0.8037 (tp30) REVERT: R 76 GLU cc_start: 0.8858 (tp30) cc_final: 0.8398 (tp30) REVERT: R 114 GLN cc_start: 0.9485 (mt0) cc_final: 0.8931 (mp10) REVERT: S 164 TYR cc_start: 0.9009 (t80) cc_final: 0.8343 (t80) REVERT: S 214 MET cc_start: 0.9039 (mtp) cc_final: 0.8813 (mtt) REVERT: V 57 ASN cc_start: 0.9129 (m-40) cc_final: 0.8473 (t0) REVERT: W 51 ASP cc_start: 0.8965 (m-30) cc_final: 0.8458 (m-30) REVERT: W 55 MET cc_start: 0.9308 (ttt) cc_final: 0.9065 (tmm) REVERT: W 67 GLN cc_start: 0.8748 (tp40) cc_final: 0.8546 (tp40) REVERT: W 176 GLN cc_start: 0.8580 (mt0) cc_final: 0.8275 (mt0) REVERT: X 35 GLU cc_start: 0.8614 (pt0) cc_final: 0.8021 (tt0) REVERT: 0 164 TYR cc_start: 0.9039 (t80) cc_final: 0.8406 (t80) outliers start: 79 outliers final: 57 residues processed: 451 average time/residue: 0.2936 time to fit residues: 213.2379 Evaluate side-chains 450 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 390 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain N residue 150 ILE Chi-restraints excluded: chain N residue 171 THR Chi-restraints excluded: chain N residue 178 SER Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 215 MET Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 150 ILE Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 178 SER Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 219 GLN Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 171 THR Chi-restraints excluded: chain J residue 178 SER Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 202 LEU Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 109 SER Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain S residue 150 ILE Chi-restraints excluded: chain S residue 171 THR Chi-restraints excluded: chain T residue 315 LEU Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain V residue 111 LEU Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 215 MET Chi-restraints excluded: chain X residue 32 PHE Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain 0 residue 150 ILE Chi-restraints excluded: chain 0 residue 171 THR Chi-restraints excluded: chain 0 residue 178 SER Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 0 residue 210 THR Chi-restraints excluded: chain 0 residue 215 MET Chi-restraints excluded: chain 3 residue 27 VAL Chi-restraints excluded: chain 3 residue 35 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 165 optimal weight: 0.9990 chunk 211 optimal weight: 5.9990 chunk 164 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 chunk 162 optimal weight: 3.9990 chunk 289 optimal weight: 7.9990 chunk 180 optimal weight: 20.0000 chunk 176 optimal weight: 6.9990 chunk 133 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 219 GLN ** B 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN ** Q 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 179 GLN ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 22690 Z= 0.241 Angle : 0.583 10.106 31140 Z= 0.287 Chirality : 0.039 0.172 3730 Planarity : 0.005 0.055 3980 Dihedral : 4.749 55.683 3171 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 3.09 % Allowed : 19.06 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 2.28 (0.16), residues: 2985 helix: 1.76 (0.11), residues: 2130 sheet: None (None), residues: 0 loop : 1.11 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 184 HIS 0.002 0.000 HIS Q 62 PHE 0.012 0.001 PHE V 40 TYR 0.021 0.001 TYR Q 164 ARG 0.008 0.001 ARG M 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 413 time to evaluate : 2.575 Fit side-chains revert: symmetry clash REVERT: L 51 ASP cc_start: 0.8911 (m-30) cc_final: 0.8398 (m-30) REVERT: L 143 ARG cc_start: 0.9234 (tpt90) cc_final: 0.8475 (tpm170) REVERT: L 144 MET cc_start: 0.8716 (ttm) cc_final: 0.8078 (ttm) REVERT: L 214 MET cc_start: 0.9192 (mtm) cc_final: 0.8860 (mtp) REVERT: M 35 GLU cc_start: 0.8610 (pt0) cc_final: 0.8219 (tt0) REVERT: N 164 TYR cc_start: 0.8990 (t80) cc_final: 0.8258 (t80) REVERT: N 192 GLN cc_start: 0.8897 (tp40) cc_final: 0.8441 (tp-100) REVERT: N 215 MET cc_start: 0.9199 (ttm) cc_final: 0.8827 (ttp) REVERT: A 51 ASP cc_start: 0.9100 (m-30) cc_final: 0.8792 (m-30) REVERT: A 57 ASN cc_start: 0.9116 (m-40) cc_final: 0.8497 (t0) REVERT: B 176 GLN cc_start: 0.8560 (mt0) cc_final: 0.8209 (mt0) REVERT: C 32 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7810 (m-80) REVERT: C 35 GLU cc_start: 0.8608 (pt0) cc_final: 0.7906 (tt0) REVERT: C 76 GLU cc_start: 0.8779 (tp30) cc_final: 0.8386 (tp30) REVERT: C 114 GLN cc_start: 0.9469 (mt0) cc_final: 0.8911 (mp10) REVERT: D 173 ARG cc_start: 0.8755 (ttp80) cc_final: 0.8525 (ttp-170) REVERT: G 55 MET cc_start: 0.9184 (mtp) cc_final: 0.8798 (mtp) REVERT: G 109 SER cc_start: 0.7054 (OUTLIER) cc_final: 0.6824 (m) REVERT: H 51 ASP cc_start: 0.8956 (m-30) cc_final: 0.8327 (m-30) REVERT: H 143 ARG cc_start: 0.9262 (tpt90) cc_final: 0.7846 (tpm170) REVERT: I 39 MET cc_start: 0.8949 (tpp) cc_final: 0.8370 (mmm) REVERT: I 66 MET cc_start: 0.8669 (mmm) cc_final: 0.8374 (mmm) REVERT: I 76 GLU cc_start: 0.8747 (tp30) cc_final: 0.8290 (tp30) REVERT: J 164 TYR cc_start: 0.8900 (t80) cc_final: 0.8393 (t80) REVERT: P 55 MET cc_start: 0.9098 (mtp) cc_final: 0.8760 (mtp) REVERT: P 109 SER cc_start: 0.7187 (OUTLIER) cc_final: 0.6837 (m) REVERT: Q 51 ASP cc_start: 0.8944 (m-30) cc_final: 0.8432 (m-30) REVERT: Q 118 MET cc_start: 0.8213 (mmm) cc_final: 0.7998 (mmm) REVERT: Q 143 ARG cc_start: 0.9336 (tpt90) cc_final: 0.8830 (tpm170) REVERT: R 35 GLU cc_start: 0.8768 (pt0) cc_final: 0.7991 (tt0) REVERT: R 76 GLU cc_start: 0.8852 (tp30) cc_final: 0.8384 (tp30) REVERT: R 114 GLN cc_start: 0.9502 (mt0) cc_final: 0.8937 (mp10) REVERT: S 164 TYR cc_start: 0.8995 (t80) cc_final: 0.8332 (t80) REVERT: S 214 MET cc_start: 0.8953 (mtp) cc_final: 0.8750 (mtt) REVERT: S 215 MET cc_start: 0.8978 (ttm) cc_final: 0.8708 (ttp) REVERT: V 57 ASN cc_start: 0.9113 (m-40) cc_final: 0.8485 (t0) REVERT: W 51 ASP cc_start: 0.8944 (m-30) cc_final: 0.8438 (m-30) REVERT: W 67 GLN cc_start: 0.8724 (tp40) cc_final: 0.8512 (tp40) REVERT: W 176 GLN cc_start: 0.8590 (mt0) cc_final: 0.8291 (mt0) REVERT: X 35 GLU cc_start: 0.8552 (pt0) cc_final: 0.7887 (tt0) REVERT: 0 164 TYR cc_start: 0.9027 (t80) cc_final: 0.8391 (t80) outliers start: 66 outliers final: 49 residues processed: 455 average time/residue: 0.2885 time to fit residues: 209.0793 Evaluate side-chains 447 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 395 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain M residue 32 PHE Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 171 THR Chi-restraints excluded: chain N residue 188 THR Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 171 THR Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 202 LEU Chi-restraints excluded: chain J residue 214 MET Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain P residue 109 SER Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 75 GLU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain S residue 150 ILE Chi-restraints excluded: chain S residue 171 THR Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain W residue 215 MET Chi-restraints excluded: chain X residue 32 PHE Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain 0 residue 171 THR Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 0 residue 210 THR Chi-restraints excluded: chain 0 residue 215 MET Chi-restraints excluded: chain 3 residue 27 VAL Chi-restraints excluded: chain 3 residue 35 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 20.0000 chunk 115 optimal weight: 0.8980 chunk 172 optimal weight: 1.9990 chunk 87 optimal weight: 30.0000 chunk 56 optimal weight: 10.0000 chunk 183 optimal weight: 3.9990 chunk 196 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 227 optimal weight: 6.9990 chunk 263 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 319 GLN C 67 GLN ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN ** W 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 22690 Z= 0.222 Angle : 0.595 8.594 31140 Z= 0.292 Chirality : 0.039 0.170 3730 Planarity : 0.005 0.056 3980 Dihedral : 4.692 57.228 3167 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.72 % Allowed : 19.72 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 2.23 (0.16), residues: 2985 helix: 1.71 (0.11), residues: 2130 sheet: None (None), residues: 0 loop : 1.12 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 184 HIS 0.004 0.001 HIS H 84 PHE 0.011 0.001 PHE V 40 TYR 0.027 0.001 TYR Q 164 ARG 0.010 0.001 ARG X 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 410 time to evaluate : 2.668 Fit side-chains revert: symmetry clash REVERT: L 51 ASP cc_start: 0.8913 (m-30) cc_final: 0.8398 (m-30) REVERT: L 55 MET cc_start: 0.9138 (tmm) cc_final: 0.8870 (tmm) REVERT: L 143 ARG cc_start: 0.9257 (tpt90) cc_final: 0.8462 (tpm170) REVERT: L 144 MET cc_start: 0.8618 (ttm) cc_final: 0.8065 (ttm) REVERT: L 214 MET cc_start: 0.9096 (mtm) cc_final: 0.8858 (mtp) REVERT: M 35 GLU cc_start: 0.8595 (pt0) cc_final: 0.8229 (tt0) REVERT: N 164 TYR cc_start: 0.8973 (t80) cc_final: 0.8255 (t80) REVERT: N 192 GLN cc_start: 0.8873 (tp40) cc_final: 0.8579 (tp-100) REVERT: N 215 MET cc_start: 0.9182 (ttm) cc_final: 0.8736 (ttp) REVERT: A 51 ASP cc_start: 0.9110 (m-30) cc_final: 0.8803 (m-30) REVERT: A 57 ASN cc_start: 0.9068 (m-40) cc_final: 0.8501 (t0) REVERT: B 55 MET cc_start: 0.9166 (tmm) cc_final: 0.8900 (tmm) REVERT: B 176 GLN cc_start: 0.8530 (mt0) cc_final: 0.8240 (mt0) REVERT: C 32 PHE cc_start: 0.8036 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: C 35 GLU cc_start: 0.8593 (pt0) cc_final: 0.7919 (tt0) REVERT: C 76 GLU cc_start: 0.8703 (tp30) cc_final: 0.8376 (tp30) REVERT: C 114 GLN cc_start: 0.9471 (mt0) cc_final: 0.8917 (mp10) REVERT: D 173 ARG cc_start: 0.8747 (ttp80) cc_final: 0.8522 (ttp-170) REVERT: G 55 MET cc_start: 0.9196 (mtp) cc_final: 0.8805 (mtp) REVERT: G 109 SER cc_start: 0.7041 (OUTLIER) cc_final: 0.6812 (m) REVERT: G 185 MET cc_start: 0.8730 (mtp) cc_final: 0.8250 (mtp) REVERT: H 51 ASP cc_start: 0.8950 (m-30) cc_final: 0.8322 (m-30) REVERT: H 55 MET cc_start: 0.9094 (tmm) cc_final: 0.8819 (tmm) REVERT: I 39 MET cc_start: 0.8956 (tpp) cc_final: 0.8359 (mmm) REVERT: I 76 GLU cc_start: 0.8655 (tp30) cc_final: 0.8230 (tp30) REVERT: J 164 TYR cc_start: 0.8886 (t80) cc_final: 0.8499 (t80) REVERT: P 55 MET cc_start: 0.9091 (mtp) cc_final: 0.8601 (mtp) REVERT: Q 51 ASP cc_start: 0.8916 (m-30) cc_final: 0.8459 (m-30) REVERT: Q 66 MET cc_start: 0.8158 (mmm) cc_final: 0.7841 (mmm) REVERT: Q 143 ARG cc_start: 0.9311 (tpt90) cc_final: 0.8802 (tpm170) REVERT: Q 164 TYR cc_start: 0.8769 (t80) cc_final: 0.8396 (t80) REVERT: R 35 GLU cc_start: 0.8755 (pt0) cc_final: 0.7968 (tt0) REVERT: R 76 GLU cc_start: 0.8838 (tp30) cc_final: 0.8412 (tp30) REVERT: R 114 GLN cc_start: 0.9501 (mt0) cc_final: 0.8967 (mp10) REVERT: S 164 TYR cc_start: 0.8993 (t80) cc_final: 0.8314 (t80) REVERT: V 57 ASN cc_start: 0.9099 (m-40) cc_final: 0.8498 (t0) REVERT: W 51 ASP cc_start: 0.8947 (m-30) cc_final: 0.8434 (m-30) REVERT: W 55 MET cc_start: 0.9165 (tmm) cc_final: 0.8931 (tmm) REVERT: W 176 GLN cc_start: 0.8552 (mt0) cc_final: 0.8272 (mt0) REVERT: X 35 GLU cc_start: 0.8535 (pt0) cc_final: 0.7875 (tt0) REVERT: 0 164 TYR cc_start: 0.9006 (t80) cc_final: 0.8365 (t80) REVERT: 3 57 ASN cc_start: 0.8822 (m-40) cc_final: 0.8429 (t0) REVERT: 3 185 MET cc_start: 0.9016 (mtm) cc_final: 0.8713 (ttm) REVERT: 3 214 MET cc_start: 0.8997 (mtp) cc_final: 0.8761 (mtm) outliers start: 58 outliers final: 48 residues processed: 448 average time/residue: 0.2953 time to fit residues: 212.3145 Evaluate side-chains 444 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 394 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 171 THR Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 171 THR Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 202 LEU Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 75 GLU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain S residue 171 THR Chi-restraints excluded: chain S residue 185 MET Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 32 PHE Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain 0 residue 171 THR Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 0 residue 210 THR Chi-restraints excluded: chain 3 residue 27 VAL Chi-restraints excluded: chain 3 residue 35 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 6.9990 chunk 252 optimal weight: 10.0000 chunk 269 optimal weight: 8.9990 chunk 276 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 117 optimal weight: 10.0000 chunk 211 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 243 optimal weight: 0.0980 chunk 254 optimal weight: 5.9990 chunk 268 optimal weight: 20.0000 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN I 114 GLN ** W 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 22690 Z= 0.252 Angle : 0.618 10.192 31140 Z= 0.300 Chirality : 0.040 0.201 3730 Planarity : 0.005 0.056 3980 Dihedral : 4.724 58.446 3167 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.86 % Allowed : 20.28 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 2.20 (0.16), residues: 2985 helix: 1.69 (0.11), residues: 2160 sheet: None (None), residues: 0 loop : 1.08 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 184 HIS 0.002 0.000 HIS I 84 PHE 0.012 0.001 PHE V 40 TYR 0.024 0.001 TYR Q 164 ARG 0.011 0.001 ARG X 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 402 time to evaluate : 2.433 Fit side-chains revert: symmetry clash REVERT: L 51 ASP cc_start: 0.8914 (m-30) cc_final: 0.8391 (m-30) REVERT: L 143 ARG cc_start: 0.9277 (tpt90) cc_final: 0.8474 (tpm170) REVERT: L 144 MET cc_start: 0.8628 (ttm) cc_final: 0.8098 (ttm) REVERT: L 214 MET cc_start: 0.9112 (mtm) cc_final: 0.8874 (mtp) REVERT: M 35 GLU cc_start: 0.8659 (pt0) cc_final: 0.8202 (tt0) REVERT: N 164 TYR cc_start: 0.8982 (t80) cc_final: 0.8247 (t80) REVERT: N 192 GLN cc_start: 0.8862 (tp40) cc_final: 0.8566 (tp-100) REVERT: N 215 MET cc_start: 0.9243 (ttm) cc_final: 0.8788 (ttp) REVERT: A 51 ASP cc_start: 0.9098 (m-30) cc_final: 0.8793 (m-30) REVERT: A 57 ASN cc_start: 0.9077 (m-40) cc_final: 0.8499 (t0) REVERT: B 176 GLN cc_start: 0.8551 (mt0) cc_final: 0.8266 (mt0) REVERT: C 32 PHE cc_start: 0.7951 (OUTLIER) cc_final: 0.7624 (m-80) REVERT: C 35 GLU cc_start: 0.8595 (pt0) cc_final: 0.7936 (tt0) REVERT: C 76 GLU cc_start: 0.8674 (tp30) cc_final: 0.8356 (tp30) REVERT: C 114 GLN cc_start: 0.9498 (mt0) cc_final: 0.8989 (mp10) REVERT: D 173 ARG cc_start: 0.8760 (ttp80) cc_final: 0.8532 (ttp-170) REVERT: G 55 MET cc_start: 0.9224 (mtp) cc_final: 0.8819 (mtp) REVERT: G 109 SER cc_start: 0.7045 (OUTLIER) cc_final: 0.6812 (m) REVERT: G 185 MET cc_start: 0.8729 (mtp) cc_final: 0.8326 (mtp) REVERT: H 51 ASP cc_start: 0.8941 (m-30) cc_final: 0.8323 (m-30) REVERT: H 55 MET cc_start: 0.9106 (tmm) cc_final: 0.8810 (tmm) REVERT: I 39 MET cc_start: 0.8998 (tpp) cc_final: 0.8408 (mmm) REVERT: I 76 GLU cc_start: 0.8660 (tp30) cc_final: 0.8223 (tp30) REVERT: J 164 TYR cc_start: 0.8869 (t80) cc_final: 0.8375 (t80) REVERT: P 55 MET cc_start: 0.9088 (mtp) cc_final: 0.8746 (mtp) REVERT: Q 51 ASP cc_start: 0.8915 (m-30) cc_final: 0.8446 (m-30) REVERT: Q 143 ARG cc_start: 0.9312 (tpt90) cc_final: 0.8807 (tpm170) REVERT: Q 164 TYR cc_start: 0.8769 (t80) cc_final: 0.8409 (t80) REVERT: R 35 GLU cc_start: 0.8756 (pt0) cc_final: 0.7975 (tp30) REVERT: R 68 MET cc_start: 0.9213 (OUTLIER) cc_final: 0.8660 (mpp) REVERT: R 76 GLU cc_start: 0.8849 (tp30) cc_final: 0.8424 (tp30) REVERT: R 114 GLN cc_start: 0.9500 (mt0) cc_final: 0.8961 (mp10) REVERT: S 164 TYR cc_start: 0.9008 (t80) cc_final: 0.8316 (t80) REVERT: S 215 MET cc_start: 0.8816 (ttm) cc_final: 0.8331 (ttp) REVERT: V 57 ASN cc_start: 0.9107 (m-40) cc_final: 0.8498 (t0) REVERT: W 51 ASP cc_start: 0.8937 (m-30) cc_final: 0.8425 (m-30) REVERT: W 55 MET cc_start: 0.9193 (tmm) cc_final: 0.8944 (tmm) REVERT: W 176 GLN cc_start: 0.8567 (mt0) cc_final: 0.8304 (mt0) REVERT: X 35 GLU cc_start: 0.8542 (pt0) cc_final: 0.7897 (tt0) REVERT: 0 164 TYR cc_start: 0.9033 (t80) cc_final: 0.8418 (t80) REVERT: 3 66 MET cc_start: 0.8963 (tpt) cc_final: 0.8486 (tpt) REVERT: 3 214 MET cc_start: 0.9025 (mtp) cc_final: 0.8778 (mtm) outliers start: 61 outliers final: 50 residues processed: 440 average time/residue: 0.3037 time to fit residues: 212.9813 Evaluate side-chains 450 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 397 time to evaluate : 2.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 171 THR Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain F residue 319 GLN Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 67 GLN Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 171 THR Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 202 LEU Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 75 GLU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 68 MET Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain S residue 171 THR Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 32 PHE Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain 0 residue 171 THR Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 0 residue 210 THR Chi-restraints excluded: chain 3 residue 27 VAL Chi-restraints excluded: chain 3 residue 35 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 10.0000 chunk 284 optimal weight: 0.3980 chunk 173 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 198 optimal weight: 3.9990 chunk 298 optimal weight: 8.9990 chunk 275 optimal weight: 3.9990 chunk 237 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 183 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 overall best weight: 3.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 GLN ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN I 114 GLN ** W 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 114 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 22690 Z= 0.252 Angle : 0.621 10.622 31140 Z= 0.303 Chirality : 0.040 0.186 3730 Planarity : 0.005 0.057 3980 Dihedral : 4.739 59.072 3167 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.81 % Allowed : 20.56 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 2.16 (0.16), residues: 2985 helix: 1.66 (0.11), residues: 2160 sheet: None (None), residues: 0 loop : 1.09 (0.23), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 184 HIS 0.002 0.000 HIS B 62 PHE 0.012 0.001 PHE V 40 TYR 0.023 0.001 TYR Q 164 ARG 0.012 0.001 ARG B 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5970 Ramachandran restraints generated. 2985 Oldfield, 0 Emsley, 2985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 403 time to evaluate : 2.442 Fit side-chains revert: symmetry clash REVERT: L 51 ASP cc_start: 0.8917 (m-30) cc_final: 0.8400 (m-30) REVERT: L 55 MET cc_start: 0.9041 (tmm) cc_final: 0.8785 (tmm) REVERT: L 143 ARG cc_start: 0.9277 (tpt90) cc_final: 0.8470 (tpm170) REVERT: L 144 MET cc_start: 0.8634 (ttm) cc_final: 0.8113 (ttm) REVERT: L 179 GLN cc_start: 0.7702 (tp40) cc_final: 0.7470 (tp40) REVERT: L 214 MET cc_start: 0.9111 (mtm) cc_final: 0.8873 (mtp) REVERT: M 35 GLU cc_start: 0.8665 (pt0) cc_final: 0.8178 (tt0) REVERT: N 164 TYR cc_start: 0.8980 (t80) cc_final: 0.8233 (t80) REVERT: N 192 GLN cc_start: 0.8873 (tp40) cc_final: 0.8577 (tp-100) REVERT: N 215 MET cc_start: 0.9236 (ttm) cc_final: 0.8791 (ttp) REVERT: N 218 CYS cc_start: 0.8040 (t) cc_final: 0.7636 (t) REVERT: A 51 ASP cc_start: 0.9095 (m-30) cc_final: 0.8825 (m-30) REVERT: A 57 ASN cc_start: 0.9081 (m-40) cc_final: 0.8495 (t0) REVERT: B 55 MET cc_start: 0.9144 (tmm) cc_final: 0.8910 (tmm) REVERT: B 67 GLN cc_start: 0.8557 (tp40) cc_final: 0.8257 (tp40) REVERT: B 176 GLN cc_start: 0.8548 (mt0) cc_final: 0.8267 (mt0) REVERT: C 32 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7555 (m-80) REVERT: C 35 GLU cc_start: 0.8577 (pt0) cc_final: 0.7936 (tt0) REVERT: C 76 GLU cc_start: 0.8703 (tp30) cc_final: 0.8389 (tp30) REVERT: C 114 GLN cc_start: 0.9492 (mt0) cc_final: 0.8970 (mp10) REVERT: D 173 ARG cc_start: 0.8769 (ttp80) cc_final: 0.8542 (ttp-170) REVERT: G 55 MET cc_start: 0.9228 (mtp) cc_final: 0.8903 (mtp) REVERT: G 57 ASN cc_start: 0.9029 (m-40) cc_final: 0.8511 (t0) REVERT: G 109 SER cc_start: 0.7035 (OUTLIER) cc_final: 0.6788 (m) REVERT: G 185 MET cc_start: 0.8779 (mtp) cc_final: 0.8389 (mtp) REVERT: H 51 ASP cc_start: 0.8954 (m-30) cc_final: 0.8343 (m-30) REVERT: H 55 MET cc_start: 0.9094 (tmm) cc_final: 0.8784 (tmm) REVERT: I 39 MET cc_start: 0.9001 (tpp) cc_final: 0.8406 (mmm) REVERT: I 76 GLU cc_start: 0.8670 (tp30) cc_final: 0.8246 (tp30) REVERT: J 164 TYR cc_start: 0.8877 (t80) cc_final: 0.8352 (t80) REVERT: P 55 MET cc_start: 0.9090 (mtp) cc_final: 0.8767 (mtp) REVERT: Q 51 ASP cc_start: 0.8922 (m-30) cc_final: 0.8448 (m-30) REVERT: Q 143 ARG cc_start: 0.9314 (tpt90) cc_final: 0.8802 (tpm170) REVERT: R 35 GLU cc_start: 0.8754 (pt0) cc_final: 0.7979 (tp30) REVERT: R 68 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8642 (mpp) REVERT: R 76 GLU cc_start: 0.8842 (tp30) cc_final: 0.8426 (tp30) REVERT: R 114 GLN cc_start: 0.9500 (mt0) cc_final: 0.8956 (mp10) REVERT: S 164 TYR cc_start: 0.9018 (t80) cc_final: 0.8358 (t80) REVERT: S 215 MET cc_start: 0.8844 (ttm) cc_final: 0.8365 (ttp) REVERT: V 57 ASN cc_start: 0.9115 (m-40) cc_final: 0.8493 (t0) REVERT: W 51 ASP cc_start: 0.8935 (m-30) cc_final: 0.8420 (m-30) REVERT: W 176 GLN cc_start: 0.8579 (mt0) cc_final: 0.8339 (mt0) REVERT: X 35 GLU cc_start: 0.8547 (pt0) cc_final: 0.7906 (tt0) REVERT: 0 164 TYR cc_start: 0.9036 (t80) cc_final: 0.8388 (t80) REVERT: 3 66 MET cc_start: 0.8970 (tpt) cc_final: 0.8495 (tpt) REVERT: 3 214 MET cc_start: 0.9024 (mtp) cc_final: 0.8795 (mtm) outliers start: 60 outliers final: 52 residues processed: 440 average time/residue: 0.2877 time to fit residues: 202.2936 Evaluate side-chains 454 residues out of total 2655 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 399 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 110 THR Chi-restraints excluded: chain M residue 141 ILE Chi-restraints excluded: chain N residue 171 THR Chi-restraints excluded: chain N residue 188 THR Chi-restraints excluded: chain N residue 195 ASN Chi-restraints excluded: chain N residue 210 THR Chi-restraints excluded: chain A residue 16 SER Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain C residue 32 PHE Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 195 ASN Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain E residue 315 LEU Chi-restraints excluded: chain F residue 319 GLN Chi-restraints excluded: chain G residue 16 SER Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 37 ILE Chi-restraints excluded: chain I residue 33 SER Chi-restraints excluded: chain I residue 110 THR Chi-restraints excluded: chain J residue 171 THR Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 202 LEU Chi-restraints excluded: chain P residue 16 SER Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 35 GLU Chi-restraints excluded: chain Q residue 16 SER Chi-restraints excluded: chain Q residue 37 ILE Chi-restraints excluded: chain Q residue 75 GLU Chi-restraints excluded: chain R residue 33 SER Chi-restraints excluded: chain R residue 68 MET Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 141 ILE Chi-restraints excluded: chain S residue 171 THR Chi-restraints excluded: chain V residue 59 VAL Chi-restraints excluded: chain W residue 16 SER Chi-restraints excluded: chain W residue 58 THR Chi-restraints excluded: chain X residue 32 PHE Chi-restraints excluded: chain X residue 33 SER Chi-restraints excluded: chain X residue 110 THR Chi-restraints excluded: chain 0 residue 171 THR Chi-restraints excluded: chain 0 residue 195 ASN Chi-restraints excluded: chain 0 residue 210 THR Chi-restraints excluded: chain 3 residue 27 VAL Chi-restraints excluded: chain 3 residue 35 GLU Chi-restraints excluded: chain 3 residue 144 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 20.0000 chunk 253 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 219 optimal weight: 0.0010 chunk 35 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 238 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 chunk 43 optimal weight: 7.9990 overall best weight: 3.3192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 GLN ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 GLN I 114 GLN J 219 GLN W 179 GLN ** X 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 114 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.076023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.056835 restraints weight = 82890.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.058445 restraints weight = 51593.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.059496 restraints weight = 38732.855| |-----------------------------------------------------------------------------| r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2925 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2925 r_free = 0.2925 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2925 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 22690 Z= 0.252 Angle : 0.619 11.079 31140 Z= 0.302 Chirality : 0.040 0.191 3730 Planarity : 0.005 0.057 3980 Dihedral : 4.750 59.752 3167 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.00 % Allowed : 20.66 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.52 % 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: 2.14 (0.16), residues: 2985 helix: 1.68 (0.11), residues: 2130 sheet: None (None), residues: 0 loop : 1.00 (0.23), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 184 HIS 0.002 0.000 HIS B 62 PHE 0.013 0.001 PHE V 40 TYR 0.029 0.001 TYR Q 164 ARG 0.012 0.001 ARG B 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4558.31 seconds wall clock time: 82 minutes 40.67 seconds (4960.67 seconds total)