Starting phenix.real_space_refine on Fri Apr 12 16:17:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2l_11987/04_2024/7b2l_11987_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2l_11987/04_2024/7b2l_11987.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2l_11987/04_2024/7b2l_11987_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2l_11987/04_2024/7b2l_11987_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2l_11987/04_2024/7b2l_11987_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2l_11987/04_2024/7b2l_11987.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2l_11987/04_2024/7b2l_11987.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2l_11987/04_2024/7b2l_11987_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b2l_11987/04_2024/7b2l_11987_updated.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= 0.034 sd= 0.230 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: 5 Type Number sf(0) Gaussians P 60 5.49 5 S 120 5.16 5 C 16400 2.51 5 N 4480 2.21 5 O 5132 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 7": "NH1" <-> "NH2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A GLU 107": "OE1" <-> "OE2" Residue "A GLU 114": "OE1" <-> "OE2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A GLU 141": "OE1" <-> "OE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 135": "OE1" <-> "OE2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "C GLU 107": "OE1" <-> "OE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D GLU 135": "OE1" <-> "OE2" Residue "D GLU 176": "OE1" <-> "OE2" Residue "D ARG 177": "NH1" <-> "NH2" Residue "F ARG 7": "NH1" <-> "NH2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "F GLU 107": "OE1" <-> "OE2" Residue "F GLU 114": "OE1" <-> "OE2" Residue "F GLU 137": "OE1" <-> "OE2" Residue "F GLU 141": "OE1" <-> "OE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G GLU 108": "OE1" <-> "OE2" Residue "G TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 134": "OE1" <-> "OE2" Residue "G GLU 135": "OE1" <-> "OE2" Residue "G ARG 177": "NH1" <-> "NH2" Residue "H ARG 7": "NH1" <-> "NH2" Residue "H GLU 97": "OE1" <-> "OE2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "I GLU 20": "OE1" <-> "OE2" Residue "I GLU 73": "OE1" <-> "OE2" Residue "I GLU 108": "OE1" <-> "OE2" Residue "I GLU 134": "OE1" <-> "OE2" Residue "I GLU 135": "OE1" <-> "OE2" Residue "I GLU 176": "OE1" <-> "OE2" Residue "I ARG 177": "NH1" <-> "NH2" Residue "K ARG 7": "NH1" <-> "NH2" Residue "K GLU 97": "OE1" <-> "OE2" Residue "K GLU 107": "OE1" <-> "OE2" Residue "K GLU 114": "OE1" <-> "OE2" Residue "K GLU 137": "OE1" <-> "OE2" Residue "K GLU 141": "OE1" <-> "OE2" Residue "L GLU 57": "OE1" <-> "OE2" Residue "L GLU 108": "OE1" <-> "OE2" Residue "L TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 134": "OE1" <-> "OE2" Residue "L GLU 135": "OE1" <-> "OE2" Residue "L ARG 177": "NH1" <-> "NH2" Residue "M ARG 7": "NH1" <-> "NH2" Residue "M GLU 97": "OE1" <-> "OE2" Residue "M GLU 107": "OE1" <-> "OE2" Residue "N GLU 20": "OE1" <-> "OE2" Residue "N GLU 73": "OE1" <-> "OE2" Residue "N GLU 108": "OE1" <-> "OE2" Residue "N GLU 134": "OE1" <-> "OE2" Residue "N GLU 135": "OE1" <-> "OE2" Residue "N GLU 176": "OE1" <-> "OE2" Residue "N ARG 177": "NH1" <-> "NH2" Residue "P ARG 7": "NH1" <-> "NH2" Residue "P GLU 97": "OE1" <-> "OE2" Residue "P GLU 107": "OE1" <-> "OE2" Residue "P GLU 114": "OE1" <-> "OE2" Residue "P GLU 137": "OE1" <-> "OE2" Residue "P GLU 141": "OE1" <-> "OE2" Residue "Q GLU 57": "OE1" <-> "OE2" Residue "Q GLU 108": "OE1" <-> "OE2" Residue "Q TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 134": "OE1" <-> "OE2" Residue "Q GLU 135": "OE1" <-> "OE2" Residue "Q ARG 177": "NH1" <-> "NH2" Residue "R ARG 7": "NH1" <-> "NH2" Residue "R GLU 97": "OE1" <-> "OE2" Residue "R GLU 107": "OE1" <-> "OE2" Residue "S GLU 20": "OE1" <-> "OE2" Residue "S GLU 73": "OE1" <-> "OE2" Residue "S GLU 108": "OE1" <-> "OE2" Residue "S GLU 134": "OE1" <-> "OE2" Residue "S GLU 135": "OE1" <-> "OE2" Residue "S GLU 176": "OE1" <-> "OE2" Residue "S ARG 177": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 26192 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'TRANS': 146} Chain: "B" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2009 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 7, 'TRANS': 239} Chain breaks: 1 Chain: "C" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'TRANS': 146} Chain: "D" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2009 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 7, 'TRANS': 239} Chain breaks: 1 Chain: "F" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'TRANS': 146} Chain: "G" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2009 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 7, 'TRANS': 239} Chain breaks: 1 Chain: "H" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'TRANS': 146} Chain: "I" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2009 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 7, 'TRANS': 239} Chain breaks: 1 Chain: "K" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'TRANS': 146} Chain: "L" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2009 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 7, 'TRANS': 239} Chain breaks: 1 Chain: "M" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'TRANS': 146} Chain: "N" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2009 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 7, 'TRANS': 239} Chain breaks: 1 Chain: "P" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'TRANS': 146} Chain: "Q" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2009 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 7, 'TRANS': 239} Chain breaks: 1 Chain: "R" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'TRANS': 146} Chain: "S" Number of atoms: 2009 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 2009 Classifications: {'peptide': 247} Link IDs: {'PTRANS': 7, 'TRANS': 239} Chain breaks: 1 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'PIO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PIO:plan-2': 2, 'PIO:plan-1': 2} Unresolved non-hydrogen planarities: 16 Chain: "B" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PIO:plan-2': 1, 'PIO:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'PIO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PIO:plan-2': 2, 'PIO:plan-1': 2} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'PIO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PIO:plan-2': 2, 'PIO:plan-1': 2} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PIO:plan-2': 1, 'PIO:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "H" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'PIO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PIO:plan-2': 2, 'PIO:plan-1': 2} Unresolved non-hydrogen planarities: 16 Chain: "K" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'PIO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PIO:plan-2': 2, 'PIO:plan-1': 2} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PIO:plan-2': 1, 'PIO:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "M" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'PIO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PIO:plan-2': 2, 'PIO:plan-1': 2} Unresolved non-hydrogen planarities: 16 Chain: "P" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'PIO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PIO:plan-2': 2, 'PIO:plan-1': 2} Unresolved non-hydrogen planarities: 16 Chain: "Q" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'PIO': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PIO:plan-2': 1, 'PIO:plan-1': 1} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'PIO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PIO:plan-2': 2, 'PIO:plan-1': 2} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 11.75, per 1000 atoms: 0.45 Number of scatterers: 26192 At special positions: 0 Unit cell: (152.295, 154.425, 122.475, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 60 15.00 O 5132 8.00 N 4480 7.00 C 16400 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 9.49 Conformation dependent library (CDL) restraints added in 4.3 seconds 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6096 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 164 helices and 0 sheets defined 77.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.99 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 Processing helix chain 'A' and resid 18 through 26 Processing helix chain 'A' and resid 36 through 46 Processing helix chain 'A' and resid 52 through 64 Processing helix chain 'A' and resid 67 through 86 removed outlier: 5.452A pdb=" N ARG A 71 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA A 74 " --> pdb=" O ARG A 71 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 77 " --> pdb=" O ALA A 74 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE A 86 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 99 through 107 removed outlier: 3.765A pdb=" N THR A 104 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU A 107 " --> pdb=" O THR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 134 Processing helix chain 'A' and resid 136 through 146 Processing helix chain 'B' and resid 4 through 15 removed outlier: 3.523A pdb=" N GLN B 9 " --> pdb=" O SER B 6 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS B 10 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU B 12 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 37 Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 57 through 73 Processing helix chain 'B' and resid 76 through 95 removed outlier: 3.868A pdb=" N GLU B 81 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG B 86 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP B 87 " --> pdb=" O ARG B 84 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG B 90 " --> pdb=" O ASP B 87 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL B 95 " --> pdb=" O LEU B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 122 Processing helix chain 'B' and resid 135 through 143 Processing helix chain 'B' and resid 145 through 175 Processing helix chain 'B' and resid 183 through 211 removed outlier: 3.531A pdb=" N ILE B 188 " --> pdb=" O ILE B 184 " (cutoff:3.500A) Proline residue: B 189 - end of helix removed outlier: 3.610A pdb=" N ALA B 192 " --> pdb=" O ILE B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 244 removed outlier: 3.578A pdb=" N TYR B 228 " --> pdb=" O LYS B 225 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA B 233 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU B 237 " --> pdb=" O ARG B 234 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA B 240 " --> pdb=" O GLU B 237 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS B 242 " --> pdb=" O TYR B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 250 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 18 through 26 Processing helix chain 'C' and resid 36 through 47 removed outlier: 4.251A pdb=" N TYR C 47 " --> pdb=" O ALA C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 64 Processing helix chain 'C' and resid 67 through 86 removed outlier: 5.414A pdb=" N ARG C 71 " --> pdb=" O LYS C 68 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA C 74 " --> pdb=" O ARG C 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE C 80 " --> pdb=" O LEU C 77 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR C 82 " --> pdb=" O VAL C 79 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE C 84 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE C 86 " --> pdb=" O LEU C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 97 Processing helix chain 'C' and resid 99 through 107 removed outlier: 4.163A pdb=" N THR C 104 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU C 107 " --> pdb=" O THR C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 134 removed outlier: 3.617A pdb=" N VAL C 124 " --> pdb=" O ILE C 121 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 129 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR C 130 " --> pdb=" O LYS C 127 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 134 " --> pdb=" O ALA C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 146 Processing helix chain 'D' and resid 3 through 15 removed outlier: 3.687A pdb=" N ASP D 7 " --> pdb=" O ARG D 3 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU D 8 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA D 11 " --> pdb=" O ASP D 7 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS D 14 " --> pdb=" O LYS D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 37 Processing helix chain 'D' and resid 42 through 50 Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 57 through 73 Processing helix chain 'D' and resid 76 through 84 Processing helix chain 'D' and resid 86 through 95 removed outlier: 3.646A pdb=" N ARG D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 122 removed outlier: 3.748A pdb=" N LEU D 105 " --> pdb=" O SER D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 176 removed outlier: 3.523A pdb=" N ASP D 144 " --> pdb=" O VAL D 140 " (cutoff:3.500A) Proline residue: D 145 - end of helix Processing helix chain 'D' and resid 181 through 211 Proline residue: D 189 - end of helix Processing helix chain 'D' and resid 223 through 244 removed outlier: 3.535A pdb=" N TYR D 228 " --> pdb=" O LYS D 225 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS D 232 " --> pdb=" O GLU D 229 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU D 237 " --> pdb=" O ARG D 234 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR D 239 " --> pdb=" O PHE D 236 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS D 242 " --> pdb=" O TYR D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 251 No H-bonds generated for 'chain 'D' and resid 248 through 251' Processing helix chain 'F' and resid 2 through 14 Processing helix chain 'F' and resid 18 through 26 Processing helix chain 'F' and resid 36 through 46 Processing helix chain 'F' and resid 52 through 64 Processing helix chain 'F' and resid 67 through 86 removed outlier: 5.452A pdb=" N ARG F 71 " --> pdb=" O LYS F 68 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA F 74 " --> pdb=" O ARG F 71 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU F 77 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE F 86 " --> pdb=" O LEU F 83 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 97 Processing helix chain 'F' and resid 99 through 107 removed outlier: 3.765A pdb=" N THR F 104 " --> pdb=" O ILE F 101 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU F 107 " --> pdb=" O THR F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 134 Processing helix chain 'F' and resid 136 through 146 Processing helix chain 'G' and resid 4 through 15 removed outlier: 3.523A pdb=" N GLN G 9 " --> pdb=" O SER G 6 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS G 10 " --> pdb=" O ASP G 7 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU G 12 " --> pdb=" O GLN G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 37 Processing helix chain 'G' and resid 42 through 50 Processing helix chain 'G' and resid 57 through 73 Processing helix chain 'G' and resid 76 through 95 removed outlier: 3.868A pdb=" N GLU G 81 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG G 86 " --> pdb=" O ILE G 83 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP G 87 " --> pdb=" O ARG G 84 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG G 90 " --> pdb=" O ASP G 87 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL G 95 " --> pdb=" O LEU G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 122 Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 145 through 175 Processing helix chain 'G' and resid 183 through 211 removed outlier: 3.531A pdb=" N ILE G 188 " --> pdb=" O ILE G 184 " (cutoff:3.500A) Proline residue: G 189 - end of helix removed outlier: 3.610A pdb=" N ALA G 192 " --> pdb=" O ILE G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 223 through 244 removed outlier: 3.578A pdb=" N TYR G 228 " --> pdb=" O LYS G 225 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA G 233 " --> pdb=" O LEU G 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU G 237 " --> pdb=" O ARG G 234 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA G 240 " --> pdb=" O GLU G 237 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS G 242 " --> pdb=" O TYR G 239 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 250 Processing helix chain 'H' and resid 2 through 13 Processing helix chain 'H' and resid 18 through 26 Processing helix chain 'H' and resid 36 through 47 removed outlier: 4.251A pdb=" N TYR H 47 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 64 Processing helix chain 'H' and resid 67 through 86 removed outlier: 5.414A pdb=" N ARG H 71 " --> pdb=" O LYS H 68 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA H 74 " --> pdb=" O ARG H 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE H 80 " --> pdb=" O LEU H 77 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR H 82 " --> pdb=" O VAL H 79 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE H 84 " --> pdb=" O ASP H 81 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE H 86 " --> pdb=" O LEU H 83 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 97 Processing helix chain 'H' and resid 99 through 107 removed outlier: 4.163A pdb=" N THR H 104 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU H 107 " --> pdb=" O THR H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 134 removed outlier: 3.617A pdb=" N VAL H 124 " --> pdb=" O ILE H 121 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU H 129 " --> pdb=" O ALA H 126 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR H 130 " --> pdb=" O LYS H 127 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER H 134 " --> pdb=" O ALA H 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 146 Processing helix chain 'I' and resid 3 through 15 removed outlier: 3.687A pdb=" N ASP I 7 " --> pdb=" O ARG I 3 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU I 8 " --> pdb=" O ILE I 4 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA I 11 " --> pdb=" O ASP I 7 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS I 14 " --> pdb=" O LYS I 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 25 through 37 Processing helix chain 'I' and resid 42 through 50 Processing helix chain 'I' and resid 53 through 55 No H-bonds generated for 'chain 'I' and resid 53 through 55' Processing helix chain 'I' and resid 57 through 73 Processing helix chain 'I' and resid 76 through 84 Processing helix chain 'I' and resid 86 through 95 removed outlier: 3.646A pdb=" N ARG I 94 " --> pdb=" O ARG I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 101 through 122 removed outlier: 3.748A pdb=" N LEU I 105 " --> pdb=" O SER I 101 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 176 removed outlier: 3.523A pdb=" N ASP I 144 " --> pdb=" O VAL I 140 " (cutoff:3.500A) Proline residue: I 145 - end of helix Processing helix chain 'I' and resid 181 through 211 Proline residue: I 189 - end of helix Processing helix chain 'I' and resid 223 through 244 removed outlier: 3.535A pdb=" N TYR I 228 " --> pdb=" O LYS I 225 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS I 232 " --> pdb=" O GLU I 229 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU I 237 " --> pdb=" O ARG I 234 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR I 239 " --> pdb=" O PHE I 236 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS I 242 " --> pdb=" O TYR I 239 " (cutoff:3.500A) Processing helix chain 'I' and resid 248 through 251 No H-bonds generated for 'chain 'I' and resid 248 through 251' Processing helix chain 'K' and resid 2 through 14 Processing helix chain 'K' and resid 18 through 26 Processing helix chain 'K' and resid 36 through 46 Processing helix chain 'K' and resid 52 through 64 Processing helix chain 'K' and resid 67 through 86 removed outlier: 5.452A pdb=" N ARG K 71 " --> pdb=" O LYS K 68 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA K 74 " --> pdb=" O ARG K 71 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU K 77 " --> pdb=" O ALA K 74 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE K 86 " --> pdb=" O LEU K 83 " (cutoff:3.500A) Processing helix chain 'K' and resid 89 through 97 Processing helix chain 'K' and resid 99 through 107 removed outlier: 3.765A pdb=" N THR K 104 " --> pdb=" O ILE K 101 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU K 107 " --> pdb=" O THR K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 120 through 134 Processing helix chain 'K' and resid 136 through 146 Processing helix chain 'L' and resid 4 through 15 removed outlier: 3.523A pdb=" N GLN L 9 " --> pdb=" O SER L 6 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS L 10 " --> pdb=" O ASP L 7 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU L 12 " --> pdb=" O GLN L 9 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 37 Processing helix chain 'L' and resid 42 through 50 Processing helix chain 'L' and resid 57 through 73 Processing helix chain 'L' and resid 76 through 95 removed outlier: 3.868A pdb=" N GLU L 81 " --> pdb=" O ALA L 78 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG L 86 " --> pdb=" O ILE L 83 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP L 87 " --> pdb=" O ARG L 84 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG L 90 " --> pdb=" O ASP L 87 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL L 95 " --> pdb=" O LEU L 92 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 122 Processing helix chain 'L' and resid 135 through 143 Processing helix chain 'L' and resid 145 through 175 Processing helix chain 'L' and resid 183 through 211 removed outlier: 3.531A pdb=" N ILE L 188 " --> pdb=" O ILE L 184 " (cutoff:3.500A) Proline residue: L 189 - end of helix removed outlier: 3.610A pdb=" N ALA L 192 " --> pdb=" O ILE L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 223 through 244 removed outlier: 3.578A pdb=" N TYR L 228 " --> pdb=" O LYS L 225 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA L 233 " --> pdb=" O LEU L 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU L 237 " --> pdb=" O ARG L 234 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA L 240 " --> pdb=" O GLU L 237 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS L 242 " --> pdb=" O TYR L 239 " (cutoff:3.500A) Processing helix chain 'L' and resid 246 through 250 Processing helix chain 'M' and resid 2 through 13 Processing helix chain 'M' and resid 18 through 26 Processing helix chain 'M' and resid 36 through 47 removed outlier: 4.251A pdb=" N TYR M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 52 through 64 Processing helix chain 'M' and resid 67 through 86 removed outlier: 5.414A pdb=" N ARG M 71 " --> pdb=" O LYS M 68 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA M 74 " --> pdb=" O ARG M 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE M 80 " --> pdb=" O LEU M 77 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR M 82 " --> pdb=" O VAL M 79 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE M 84 " --> pdb=" O ASP M 81 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE M 86 " --> pdb=" O LEU M 83 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 97 Processing helix chain 'M' and resid 99 through 107 removed outlier: 4.163A pdb=" N THR M 104 " --> pdb=" O ILE M 101 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU M 107 " --> pdb=" O THR M 104 " (cutoff:3.500A) Processing helix chain 'M' and resid 115 through 134 removed outlier: 3.617A pdb=" N VAL M 124 " --> pdb=" O ILE M 121 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU M 129 " --> pdb=" O ALA M 126 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR M 130 " --> pdb=" O LYS M 127 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER M 134 " --> pdb=" O ALA M 131 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 146 Processing helix chain 'N' and resid 3 through 15 removed outlier: 3.687A pdb=" N ASP N 7 " --> pdb=" O ARG N 3 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU N 8 " --> pdb=" O ILE N 4 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA N 11 " --> pdb=" O ASP N 7 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS N 14 " --> pdb=" O LYS N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 25 through 37 Processing helix chain 'N' and resid 42 through 50 Processing helix chain 'N' and resid 53 through 55 No H-bonds generated for 'chain 'N' and resid 53 through 55' Processing helix chain 'N' and resid 57 through 73 Processing helix chain 'N' and resid 76 through 84 Processing helix chain 'N' and resid 86 through 95 removed outlier: 3.646A pdb=" N ARG N 94 " --> pdb=" O ARG N 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 122 removed outlier: 3.748A pdb=" N LEU N 105 " --> pdb=" O SER N 101 " (cutoff:3.500A) Processing helix chain 'N' and resid 135 through 176 removed outlier: 3.523A pdb=" N ASP N 144 " --> pdb=" O VAL N 140 " (cutoff:3.500A) Proline residue: N 145 - end of helix Processing helix chain 'N' and resid 181 through 211 Proline residue: N 189 - end of helix Processing helix chain 'N' and resid 223 through 244 removed outlier: 3.535A pdb=" N TYR N 228 " --> pdb=" O LYS N 225 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS N 232 " --> pdb=" O GLU N 229 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU N 237 " --> pdb=" O ARG N 234 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR N 239 " --> pdb=" O PHE N 236 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS N 242 " --> pdb=" O TYR N 239 " (cutoff:3.500A) Processing helix chain 'N' and resid 248 through 251 No H-bonds generated for 'chain 'N' and resid 248 through 251' Processing helix chain 'P' and resid 2 through 14 Processing helix chain 'P' and resid 18 through 26 Processing helix chain 'P' and resid 36 through 46 Processing helix chain 'P' and resid 52 through 64 Processing helix chain 'P' and resid 67 through 86 removed outlier: 5.452A pdb=" N ARG P 71 " --> pdb=" O LYS P 68 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ALA P 74 " --> pdb=" O ARG P 71 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU P 77 " --> pdb=" O ALA P 74 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE P 86 " --> pdb=" O LEU P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 89 through 97 Processing helix chain 'P' and resid 99 through 107 removed outlier: 3.765A pdb=" N THR P 104 " --> pdb=" O ILE P 101 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU P 107 " --> pdb=" O THR P 104 " (cutoff:3.500A) Processing helix chain 'P' and resid 120 through 134 Processing helix chain 'P' and resid 136 through 146 Processing helix chain 'Q' and resid 4 through 15 removed outlier: 3.523A pdb=" N GLN Q 9 " --> pdb=" O SER Q 6 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS Q 10 " --> pdb=" O ASP Q 7 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LEU Q 12 " --> pdb=" O GLN Q 9 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 37 Processing helix chain 'Q' and resid 42 through 50 Processing helix chain 'Q' and resid 57 through 73 Processing helix chain 'Q' and resid 76 through 95 removed outlier: 3.868A pdb=" N GLU Q 81 " --> pdb=" O ALA Q 78 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG Q 86 " --> pdb=" O ILE Q 83 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP Q 87 " --> pdb=" O ARG Q 84 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG Q 90 " --> pdb=" O ASP Q 87 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL Q 95 " --> pdb=" O LEU Q 92 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 122 Processing helix chain 'Q' and resid 135 through 143 Processing helix chain 'Q' and resid 145 through 175 Processing helix chain 'Q' and resid 183 through 211 removed outlier: 3.531A pdb=" N ILE Q 188 " --> pdb=" O ILE Q 184 " (cutoff:3.500A) Proline residue: Q 189 - end of helix removed outlier: 3.610A pdb=" N ALA Q 192 " --> pdb=" O ILE Q 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 223 through 244 removed outlier: 3.578A pdb=" N TYR Q 228 " --> pdb=" O LYS Q 225 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA Q 233 " --> pdb=" O LEU Q 230 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU Q 237 " --> pdb=" O ARG Q 234 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA Q 240 " --> pdb=" O GLU Q 237 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N CYS Q 242 " --> pdb=" O TYR Q 239 " (cutoff:3.500A) Processing helix chain 'Q' and resid 246 through 250 Processing helix chain 'R' and resid 2 through 13 Processing helix chain 'R' and resid 18 through 26 Processing helix chain 'R' and resid 36 through 47 removed outlier: 4.251A pdb=" N TYR R 47 " --> pdb=" O ALA R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 64 Processing helix chain 'R' and resid 67 through 86 removed outlier: 5.414A pdb=" N ARG R 71 " --> pdb=" O LYS R 68 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA R 74 " --> pdb=" O ARG R 71 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE R 80 " --> pdb=" O LEU R 77 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR R 82 " --> pdb=" O VAL R 79 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE R 84 " --> pdb=" O ASP R 81 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE R 86 " --> pdb=" O LEU R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 97 Processing helix chain 'R' and resid 99 through 107 removed outlier: 4.163A pdb=" N THR R 104 " --> pdb=" O ILE R 101 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU R 107 " --> pdb=" O THR R 104 " (cutoff:3.500A) Processing helix chain 'R' and resid 115 through 134 removed outlier: 3.617A pdb=" N VAL R 124 " --> pdb=" O ILE R 121 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU R 129 " --> pdb=" O ALA R 126 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR R 130 " --> pdb=" O LYS R 127 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER R 134 " --> pdb=" O ALA R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 146 Processing helix chain 'S' and resid 3 through 15 removed outlier: 3.687A pdb=" N ASP S 7 " --> pdb=" O ARG S 3 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU S 8 " --> pdb=" O ILE S 4 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ALA S 11 " --> pdb=" O ASP S 7 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS S 14 " --> pdb=" O LYS S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 37 Processing helix chain 'S' and resid 42 through 50 Processing helix chain 'S' and resid 53 through 55 No H-bonds generated for 'chain 'S' and resid 53 through 55' Processing helix chain 'S' and resid 57 through 73 Processing helix chain 'S' and resid 76 through 84 Processing helix chain 'S' and resid 86 through 95 removed outlier: 3.646A pdb=" N ARG S 94 " --> pdb=" O ARG S 90 " (cutoff:3.500A) Processing helix chain 'S' and resid 101 through 122 removed outlier: 3.748A pdb=" N LEU S 105 " --> pdb=" O SER S 101 " (cutoff:3.500A) Processing helix chain 'S' and resid 135 through 176 removed outlier: 3.523A pdb=" N ASP S 144 " --> pdb=" O VAL S 140 " (cutoff:3.500A) Proline residue: S 145 - end of helix Processing helix chain 'S' and resid 181 through 211 Proline residue: S 189 - end of helix Processing helix chain 'S' and resid 223 through 244 removed outlier: 3.535A pdb=" N TYR S 228 " --> pdb=" O LYS S 225 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS S 232 " --> pdb=" O GLU S 229 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU S 237 " --> pdb=" O ARG S 234 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR S 239 " --> pdb=" O PHE S 236 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N CYS S 242 " --> pdb=" O TYR S 239 " (cutoff:3.500A) Processing helix chain 'S' and resid 248 through 251 No H-bonds generated for 'chain 'S' and resid 248 through 251' 1596 hydrogen bonds defined for protein. 3672 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: 7.21 Time building geometry restraints manager: 10.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.11 - 1.25: 4036 1.25 - 1.39: 4956 1.39 - 1.54: 14844 1.54 - 1.68: 2620 1.68 - 1.82: 192 Bond restraints: 26648 Sorted by residual: bond pdb=" C VAL K 23 " pdb=" O VAL K 23 " ideal model delta sigma weight residual 1.237 1.107 0.130 1.17e-02 7.31e+03 1.24e+02 bond pdb=" C VAL P 23 " pdb=" O VAL P 23 " ideal model delta sigma weight residual 1.237 1.107 0.130 1.17e-02 7.31e+03 1.24e+02 bond pdb=" C VAL A 23 " pdb=" O VAL A 23 " ideal model delta sigma weight residual 1.237 1.107 0.130 1.17e-02 7.31e+03 1.24e+02 bond pdb=" C VAL F 23 " pdb=" O VAL F 23 " ideal model delta sigma weight residual 1.237 1.107 0.130 1.17e-02 7.31e+03 1.24e+02 bond pdb=" O13 PIO M 301 " pdb=" P1 PIO M 301 " ideal model delta sigma weight residual 1.648 1.505 0.143 2.00e-02 2.50e+03 5.10e+01 ... (remaining 26643 not shown) Histogram of bond angle deviations from ideal: 95.83 - 103.78: 156 103.78 - 111.73: 9688 111.73 - 119.68: 13640 119.68 - 127.63: 12316 127.63 - 135.57: 204 Bond angle restraints: 36004 Sorted by residual: angle pdb=" CA SER P 28 " pdb=" C SER P 28 " pdb=" O SER P 28 " ideal model delta sigma weight residual 120.60 110.51 10.09 1.20e+00 6.94e-01 7.06e+01 angle pdb=" CA SER A 28 " pdb=" C SER A 28 " pdb=" O SER A 28 " ideal model delta sigma weight residual 120.60 110.51 10.09 1.20e+00 6.94e-01 7.06e+01 angle pdb=" CA SER F 28 " pdb=" C SER F 28 " pdb=" O SER F 28 " ideal model delta sigma weight residual 120.60 110.51 10.09 1.20e+00 6.94e-01 7.06e+01 angle pdb=" CA SER K 28 " pdb=" C SER K 28 " pdb=" O SER K 28 " ideal model delta sigma weight residual 120.60 110.51 10.09 1.20e+00 6.94e-01 7.06e+01 angle pdb=" CA ASP L 7 " pdb=" CB ASP L 7 " pdb=" CG ASP L 7 " ideal model delta sigma weight residual 112.60 120.72 -8.12 1.00e+00 1.00e+00 6.59e+01 ... (remaining 35999 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.41: 15012 23.41 - 46.83: 844 46.83 - 70.24: 224 70.24 - 93.66: 96 93.66 - 117.07: 24 Dihedral angle restraints: 16200 sinusoidal: 6840 harmonic: 9360 Sorted by residual: dihedral pdb=" CA VAL L 252 " pdb=" C VAL L 252 " pdb=" N THR L 253 " pdb=" CA THR L 253 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA VAL B 252 " pdb=" C VAL B 252 " pdb=" N THR B 253 " pdb=" CA THR B 253 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA VAL G 252 " pdb=" C VAL G 252 " pdb=" N THR G 253 " pdb=" CA THR G 253 " ideal model delta harmonic sigma weight residual 180.00 151.39 28.61 0 5.00e+00 4.00e-02 3.27e+01 ... (remaining 16197 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 2708 0.096 - 0.193: 1092 0.193 - 0.289: 204 0.289 - 0.385: 36 0.385 - 0.482: 16 Chirality restraints: 4056 Sorted by residual: chirality pdb=" CA ASN M 31 " pdb=" N ASN M 31 " pdb=" C ASN M 31 " pdb=" CB ASN M 31 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" CA ASN C 31 " pdb=" N ASN C 31 " pdb=" C ASN C 31 " pdb=" CB ASN C 31 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.80e+00 chirality pdb=" CA ASN R 31 " pdb=" N ASN R 31 " pdb=" C ASN R 31 " pdb=" CB ASN R 31 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.80e+00 ... (remaining 4053 not shown) Planarity restraints: 4464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR I 133 " -0.166 2.00e-02 2.50e+03 9.72e-02 1.89e+02 pdb=" CG TYR I 133 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR I 133 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 TYR I 133 " 0.070 2.00e-02 2.50e+03 pdb=" CE1 TYR I 133 " 0.067 2.00e-02 2.50e+03 pdb=" CE2 TYR I 133 " 0.065 2.00e-02 2.50e+03 pdb=" CZ TYR I 133 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR I 133 " -0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 133 " -0.166 2.00e-02 2.50e+03 9.72e-02 1.89e+02 pdb=" CG TYR N 133 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR N 133 " 0.072 2.00e-02 2.50e+03 pdb=" CD2 TYR N 133 " 0.070 2.00e-02 2.50e+03 pdb=" CE1 TYR N 133 " 0.067 2.00e-02 2.50e+03 pdb=" CE2 TYR N 133 " 0.065 2.00e-02 2.50e+03 pdb=" CZ TYR N 133 " 0.021 2.00e-02 2.50e+03 pdb=" OH TYR N 133 " -0.165 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 133 " 0.166 2.00e-02 2.50e+03 9.72e-02 1.89e+02 pdb=" CG TYR S 133 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR S 133 " -0.072 2.00e-02 2.50e+03 pdb=" CD2 TYR S 133 " -0.070 2.00e-02 2.50e+03 pdb=" CE1 TYR S 133 " -0.067 2.00e-02 2.50e+03 pdb=" CE2 TYR S 133 " -0.065 2.00e-02 2.50e+03 pdb=" CZ TYR S 133 " -0.021 2.00e-02 2.50e+03 pdb=" OH TYR S 133 " 0.165 2.00e-02 2.50e+03 ... (remaining 4461 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 208 2.63 - 3.20: 23908 3.20 - 3.76: 41176 3.76 - 4.33: 55118 4.33 - 4.90: 89222 Nonbonded interactions: 209632 Sorted by model distance: nonbonded pdb=" O51 PIO C 301 " pdb=" O6 PIO C 301 " model vdw 2.060 2.440 nonbonded pdb=" O51 PIO H 301 " pdb=" O6 PIO H 301 " model vdw 2.060 2.440 nonbonded pdb=" O52 PIO M 301 " pdb=" O6 PIO M 301 " model vdw 2.060 2.440 nonbonded pdb=" O52 PIO R 301 " pdb=" O6 PIO R 301 " model vdw 2.060 2.440 nonbonded pdb=" O52 PIO F 202 " pdb=" O6 PIO F 202 " model vdw 2.103 2.440 ... (remaining 209627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'F' selection = chain 'H' selection = chain 'K' selection = chain 'M' selection = chain 'P' selection = chain 'R' } ncs_group { reference = (chain 'B' and resid 1 through 256) selection = chain 'D' selection = (chain 'G' and resid 1 through 256) selection = chain 'I' selection = (chain 'L' and resid 1 through 256) selection = chain 'N' selection = (chain 'Q' and resid 1 through 256) selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 4.310 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 61.920 Find NCS groups from input model: 2.160 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 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 : 0.014 0.143 26648 Z= 0.885 Angle : 1.943 10.086 36004 Z= 1.336 Chirality : 0.106 0.482 4056 Planarity : 0.019 0.219 4464 Dihedral : 18.124 117.070 10104 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.64 % Allowed : 5.80 % Favored : 93.56 % Rotamer: Outliers : 3.78 % Allowed : 8.40 % Favored : 87.82 % Cbeta Deviations : 1.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.12), residues: 3104 helix: -0.46 (0.08), residues: 2432 sheet: None (None), residues: 0 loop : -1.68 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.158 0.029 TRP R 70 HIS 0.029 0.006 HIS M 32 PHE 0.107 0.018 PHE S 200 TYR 0.184 0.030 TYR L 112 ARG 0.023 0.002 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 808 time to evaluate : 3.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 ASN cc_start: 0.8007 (m110) cc_final: 0.7785 (t0) REVERT: B 9 GLN cc_start: 0.7739 (mt0) cc_final: 0.7338 (mt0) REVERT: B 136 TYR cc_start: 0.6985 (t80) cc_final: 0.6635 (t80) REVERT: B 152 ILE cc_start: 0.6953 (OUTLIER) cc_final: 0.6508 (tt) REVERT: B 195 TYR cc_start: 0.6687 (t80) cc_final: 0.6397 (t80) REVERT: C 14 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8698 (mmtm) REVERT: C 66 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8387 (mtmt) REVERT: C 136 ASP cc_start: 0.7125 (p0) cc_final: 0.6906 (p0) REVERT: D 59 GLN cc_start: 0.8730 (mt0) cc_final: 0.8516 (mt0) REVERT: D 63 MET cc_start: 0.8875 (ttp) cc_final: 0.8575 (tmm) REVERT: F 11 ASN cc_start: 0.8007 (m110) cc_final: 0.7786 (t0) REVERT: G 9 GLN cc_start: 0.7729 (mt0) cc_final: 0.7319 (mt0) REVERT: G 136 TYR cc_start: 0.6987 (t80) cc_final: 0.6635 (t80) REVERT: G 152 ILE cc_start: 0.6965 (OUTLIER) cc_final: 0.6515 (tt) REVERT: G 195 TYR cc_start: 0.6684 (t80) cc_final: 0.6393 (t80) REVERT: H 14 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8695 (mmtm) REVERT: H 66 LYS cc_start: 0.8719 (OUTLIER) cc_final: 0.8401 (mtmt) REVERT: H 136 ASP cc_start: 0.7129 (p0) cc_final: 0.6911 (p0) REVERT: I 59 GLN cc_start: 0.8732 (mt0) cc_final: 0.8517 (mt0) REVERT: I 63 MET cc_start: 0.8876 (ttp) cc_final: 0.8572 (tmm) REVERT: K 11 ASN cc_start: 0.8008 (m110) cc_final: 0.7789 (t0) REVERT: L 9 GLN cc_start: 0.7732 (mt0) cc_final: 0.7329 (mt0) REVERT: L 136 TYR cc_start: 0.6991 (t80) cc_final: 0.6640 (t80) REVERT: L 152 ILE cc_start: 0.6959 (OUTLIER) cc_final: 0.6508 (tt) REVERT: L 195 TYR cc_start: 0.6682 (t80) cc_final: 0.6389 (t80) REVERT: M 14 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8697 (mmtm) REVERT: M 66 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8400 (mtmt) REVERT: M 136 ASP cc_start: 0.7132 (p0) cc_final: 0.6912 (p0) REVERT: N 59 GLN cc_start: 0.8728 (mt0) cc_final: 0.8514 (mt0) REVERT: N 63 MET cc_start: 0.8873 (ttp) cc_final: 0.8575 (tmm) REVERT: P 11 ASN cc_start: 0.8009 (m110) cc_final: 0.7795 (t0) REVERT: Q 9 GLN cc_start: 0.7728 (mt0) cc_final: 0.7317 (mt0) REVERT: Q 136 TYR cc_start: 0.6990 (t80) cc_final: 0.6637 (t80) REVERT: Q 152 ILE cc_start: 0.6962 (OUTLIER) cc_final: 0.6511 (tt) REVERT: Q 195 TYR cc_start: 0.6684 (t80) cc_final: 0.6396 (t80) REVERT: R 14 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8698 (mmtm) REVERT: R 66 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8402 (mtmt) REVERT: R 136 ASP cc_start: 0.7130 (p0) cc_final: 0.6909 (p0) REVERT: S 59 GLN cc_start: 0.8729 (mt0) cc_final: 0.8517 (mt0) REVERT: S 63 MET cc_start: 0.8875 (ttp) cc_final: 0.8576 (tmm) outliers start: 108 outliers final: 8 residues processed: 876 average time/residue: 0.4193 time to fit residues: 556.9635 Evaluate side-chains 380 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 360 time to evaluate : 3.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASN Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain B residue 152 ILE Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 66 LYS Chi-restraints excluded: chain F residue 29 ASN Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain G residue 152 ILE Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 66 LYS Chi-restraints excluded: chain K residue 29 ASN Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain L residue 152 ILE Chi-restraints excluded: chain M residue 14 LYS Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain P residue 29 ASN Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain Q residue 152 ILE Chi-restraints excluded: chain R residue 14 LYS Chi-restraints excluded: chain R residue 66 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 256 optimal weight: 6.9990 chunk 230 optimal weight: 0.9990 chunk 127 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 123 optimal weight: 2.9990 chunk 238 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 144 optimal weight: 5.9990 chunk 177 optimal weight: 1.9990 chunk 276 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 25 ASN B 38 HIS B 55 ASN C 4 GLN C 11 ASN C 20 GLN C 29 ASN C 98 ASN D 167 GLN ** F 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 38 HIS G 55 ASN H 4 GLN H 11 ASN H 20 GLN H 29 ASN H 98 ASN I 167 GLN ** K 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 25 ASN L 38 HIS L 55 ASN M 4 GLN M 11 ASN M 20 GLN M 29 ASN M 98 ASN N 167 GLN ** P 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 25 ASN Q 38 HIS Q 55 ASN R 4 GLN R 11 ASN R 20 GLN R 29 ASN R 98 ASN S 167 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 26648 Z= 0.233 Angle : 0.712 8.036 36004 Z= 0.380 Chirality : 0.041 0.164 4056 Planarity : 0.005 0.030 4464 Dihedral : 14.488 110.300 3732 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.26 % Allowed : 2.71 % Favored : 97.04 % Rotamer: Outliers : 2.52 % Allowed : 16.67 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.14), residues: 3104 helix: 0.42 (0.09), residues: 2420 sheet: None (None), residues: 0 loop : -1.05 (0.26), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP M 70 HIS 0.006 0.001 HIS N 232 PHE 0.025 0.002 PHE G 61 TYR 0.046 0.002 TYR B 109 ARG 0.005 0.001 ARG M 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 464 time to evaluate : 3.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.6984 (pt0) REVERT: C 14 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8822 (mmtm) REVERT: C 20 GLN cc_start: 0.8438 (mt0) cc_final: 0.8208 (mt0) REVERT: C 49 SER cc_start: 0.8448 (OUTLIER) cc_final: 0.7750 (t) REVERT: D 9 GLN cc_start: 0.7288 (mt0) cc_final: 0.6725 (mt0) REVERT: D 63 MET cc_start: 0.9000 (ttp) cc_final: 0.8627 (tmm) REVERT: F 114 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6979 (pt0) REVERT: H 14 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8817 (mmtm) REVERT: H 20 GLN cc_start: 0.8442 (mt0) cc_final: 0.8208 (mt0) REVERT: H 49 SER cc_start: 0.8452 (OUTLIER) cc_final: 0.7754 (t) REVERT: I 9 GLN cc_start: 0.7282 (mt0) cc_final: 0.6719 (mt0) REVERT: I 63 MET cc_start: 0.9005 (ttp) cc_final: 0.8628 (tmm) REVERT: K 114 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6983 (pt0) REVERT: M 14 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8822 (mmtm) REVERT: M 20 GLN cc_start: 0.8442 (mt0) cc_final: 0.8210 (mt0) REVERT: M 49 SER cc_start: 0.8452 (OUTLIER) cc_final: 0.7753 (t) REVERT: N 9 GLN cc_start: 0.7280 (mt0) cc_final: 0.6724 (mt0) REVERT: N 63 MET cc_start: 0.9003 (ttp) cc_final: 0.8625 (tmm) REVERT: P 114 GLU cc_start: 0.7246 (OUTLIER) cc_final: 0.6980 (pt0) REVERT: R 14 LYS cc_start: 0.9065 (OUTLIER) cc_final: 0.8825 (mmtm) REVERT: R 20 GLN cc_start: 0.8433 (mt0) cc_final: 0.8199 (mt0) REVERT: R 49 SER cc_start: 0.8459 (OUTLIER) cc_final: 0.7764 (t) REVERT: S 9 GLN cc_start: 0.7284 (mt0) cc_final: 0.6724 (mt0) REVERT: S 63 MET cc_start: 0.9006 (ttp) cc_final: 0.8636 (tmm) outliers start: 72 outliers final: 28 residues processed: 508 average time/residue: 0.3889 time to fit residues: 311.1914 Evaluate side-chains 348 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 308 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 114 GLU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 120 GLN Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 114 GLU Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 106 ILE Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 120 GLN Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 127 ASN Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 114 GLU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 106 ILE Chi-restraints excluded: chain M residue 14 LYS Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 120 GLN Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 127 ASN Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 106 ILE Chi-restraints excluded: chain R residue 14 LYS Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 120 GLN Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain S residue 127 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 153 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 229 optimal weight: 4.9990 chunk 187 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 276 optimal weight: 1.9990 chunk 298 optimal weight: 6.9990 chunk 246 optimal weight: 1.9990 chunk 274 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 221 optimal weight: 0.0050 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 HIS C 64 ASN C 98 ASN G 68 HIS H 64 ASN H 98 ASN L 68 HIS M 64 ASN M 98 ASN Q 68 HIS R 64 ASN R 98 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 26648 Z= 0.175 Angle : 0.601 7.873 36004 Z= 0.315 Chirality : 0.036 0.164 4056 Planarity : 0.004 0.032 4464 Dihedral : 13.422 107.749 3700 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.22 % Favored : 96.65 % Rotamer: Outliers : 2.10 % Allowed : 18.91 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.14), residues: 3104 helix: 0.65 (0.10), residues: 2372 sheet: None (None), residues: 0 loop : -0.88 (0.24), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 88 HIS 0.007 0.001 HIS N 232 PHE 0.019 0.002 PHE L 165 TYR 0.031 0.002 TYR G 109 ARG 0.006 0.000 ARG C 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 392 time to evaluate : 3.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 58 MET cc_start: 0.8754 (tpp) cc_final: 0.8464 (tpp) REVERT: D 63 MET cc_start: 0.8994 (ttp) cc_final: 0.8648 (tmm) REVERT: D 72 GLN cc_start: 0.8370 (tt0) cc_final: 0.7980 (mt0) REVERT: D 195 TYR cc_start: 0.7237 (t80) cc_final: 0.6675 (t80) REVERT: D 199 LYS cc_start: 0.8684 (mttt) cc_final: 0.7848 (mttt) REVERT: D 247 TYR cc_start: 0.6022 (t80) cc_final: 0.5770 (t80) REVERT: H 58 MET cc_start: 0.8771 (tpp) cc_final: 0.8480 (tpp) REVERT: I 63 MET cc_start: 0.8995 (ttp) cc_final: 0.8651 (tmm) REVERT: I 72 GLN cc_start: 0.8367 (tt0) cc_final: 0.7974 (mt0) REVERT: I 195 TYR cc_start: 0.7247 (t80) cc_final: 0.6682 (t80) REVERT: I 199 LYS cc_start: 0.8681 (mttt) cc_final: 0.7843 (mttt) REVERT: I 247 TYR cc_start: 0.6025 (t80) cc_final: 0.5765 (t80) REVERT: K 5 PHE cc_start: 0.7455 (t80) cc_final: 0.7254 (t80) REVERT: M 58 MET cc_start: 0.8768 (tpp) cc_final: 0.8482 (tpp) REVERT: N 63 MET cc_start: 0.8998 (ttp) cc_final: 0.8648 (tmm) REVERT: N 72 GLN cc_start: 0.8367 (tt0) cc_final: 0.7972 (mt0) REVERT: N 195 TYR cc_start: 0.7244 (t80) cc_final: 0.6681 (t80) REVERT: N 199 LYS cc_start: 0.8681 (mttt) cc_final: 0.7847 (mttt) REVERT: N 247 TYR cc_start: 0.6028 (t80) cc_final: 0.5771 (t80) REVERT: R 58 MET cc_start: 0.8773 (tpp) cc_final: 0.8481 (tpp) REVERT: S 63 MET cc_start: 0.8991 (ttp) cc_final: 0.8650 (tmm) REVERT: S 72 GLN cc_start: 0.8372 (tt0) cc_final: 0.7975 (mt0) REVERT: S 195 TYR cc_start: 0.7242 (t80) cc_final: 0.6677 (t80) REVERT: S 199 LYS cc_start: 0.8679 (mttt) cc_final: 0.7842 (mttt) REVERT: S 247 TYR cc_start: 0.6019 (t80) cc_final: 0.5762 (t80) outliers start: 60 outliers final: 36 residues processed: 436 average time/residue: 0.3722 time to fit residues: 258.5494 Evaluate side-chains 344 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 308 time to evaluate : 2.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 7 ASP Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 139 LEU Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 185 SER Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 60 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 273 optimal weight: 0.7980 chunk 207 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 131 optimal weight: 4.9990 chunk 185 optimal weight: 0.8980 chunk 277 optimal weight: 2.9990 chunk 293 optimal weight: 8.9990 chunk 145 optimal weight: 0.5980 chunk 263 optimal weight: 0.0470 chunk 79 optimal weight: 5.9990 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN D 38 HIS D 59 GLN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN I 38 HIS I 59 GLN ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 ASN N 59 GLN ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 ASN S 38 HIS S 59 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.4643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 26648 Z= 0.171 Angle : 0.585 8.367 36004 Z= 0.298 Chirality : 0.035 0.137 4056 Planarity : 0.004 0.036 4464 Dihedral : 12.635 105.156 3672 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.58 % Favored : 97.29 % Rotamer: Outliers : 2.80 % Allowed : 20.87 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.14), residues: 3104 helix: 0.71 (0.10), residues: 2372 sheet: None (None), residues: 0 loop : -1.05 (0.23), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 94 HIS 0.004 0.001 HIS N 232 PHE 0.030 0.002 PHE B 165 TYR 0.013 0.001 TYR F 82 ARG 0.003 0.000 ARG H 109 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 336 time to evaluate : 2.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 63 MET cc_start: 0.9006 (ttp) cc_final: 0.8749 (tmm) REVERT: D 72 GLN cc_start: 0.8363 (tt0) cc_final: 0.7936 (mt0) REVERT: D 199 LYS cc_start: 0.8672 (mttt) cc_final: 0.8146 (mttt) REVERT: I 63 MET cc_start: 0.9004 (ttp) cc_final: 0.8750 (tmm) REVERT: I 72 GLN cc_start: 0.8354 (tt0) cc_final: 0.7930 (mt0) REVERT: I 199 LYS cc_start: 0.8672 (mttt) cc_final: 0.8146 (mttt) REVERT: N 63 MET cc_start: 0.9010 (ttp) cc_final: 0.8752 (tmm) REVERT: N 72 GLN cc_start: 0.8360 (tt0) cc_final: 0.7937 (mt0) REVERT: N 199 LYS cc_start: 0.8670 (mttt) cc_final: 0.8141 (mttt) REVERT: S 63 MET cc_start: 0.9004 (ttp) cc_final: 0.8751 (tmm) REVERT: S 72 GLN cc_start: 0.8363 (tt0) cc_final: 0.7928 (mt0) REVERT: S 199 LYS cc_start: 0.8668 (mttt) cc_final: 0.8136 (mttt) outliers start: 80 outliers final: 48 residues processed: 392 average time/residue: 0.3525 time to fit residues: 225.6564 Evaluate side-chains 356 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 308 time to evaluate : 3.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 81 GLU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain F residue 56 MET Chi-restraints excluded: chain F residue 139 LEU Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 127 ASN Chi-restraints excluded: chain K residue 56 MET Chi-restraints excluded: chain K residue 139 LEU Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 7 ASP Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 127 ASN Chi-restraints excluded: chain P residue 56 MET Chi-restraints excluded: chain P residue 139 LEU Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 81 GLU Chi-restraints excluded: chain Q residue 185 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 127 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 244 optimal weight: 2.9990 chunk 166 optimal weight: 5.9990 chunk 4 optimal weight: 9.9990 chunk 218 optimal weight: 0.6980 chunk 121 optimal weight: 0.7980 chunk 250 optimal weight: 10.0000 chunk 203 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 150 optimal weight: 10.0000 chunk 263 optimal weight: 0.1980 chunk 74 optimal weight: 9.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 HIS A 118 GLN C 98 ASN ** F 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 HIS F 118 GLN H 98 ASN ** K 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 HIS K 118 GLN M 98 ASN N 38 HIS ** P 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 110 HIS P 118 GLN R 98 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26648 Z= 0.218 Angle : 0.592 8.785 36004 Z= 0.299 Chirality : 0.036 0.138 4056 Planarity : 0.004 0.039 4464 Dihedral : 11.996 101.775 3672 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.79 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.71 % Favored : 97.16 % Rotamer: Outliers : 3.50 % Allowed : 19.75 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.15), residues: 3104 helix: 0.77 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : -0.72 (0.24), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 94 HIS 0.005 0.001 HIS N 38 PHE 0.026 0.002 PHE L 165 TYR 0.025 0.002 TYR A 82 ARG 0.006 0.001 ARG B 227 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 364 time to evaluate : 3.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.6351 (mt0) REVERT: B 167 GLN cc_start: 0.8142 (mt0) cc_final: 0.7818 (mp10) REVERT: B 195 TYR cc_start: 0.7052 (t80) cc_final: 0.6637 (t80) REVERT: C 49 SER cc_start: 0.8323 (OUTLIER) cc_final: 0.7787 (t) REVERT: D 102 TYR cc_start: 0.8268 (OUTLIER) cc_final: 0.6952 (t80) REVERT: D 195 TYR cc_start: 0.7830 (t80) cc_final: 0.7421 (t80) REVERT: G 59 GLN cc_start: 0.8075 (OUTLIER) cc_final: 0.6359 (mt0) REVERT: G 167 GLN cc_start: 0.8129 (mt0) cc_final: 0.7810 (mp10) REVERT: G 195 TYR cc_start: 0.7049 (t80) cc_final: 0.6640 (t80) REVERT: H 49 SER cc_start: 0.8328 (OUTLIER) cc_final: 0.7792 (t) REVERT: I 102 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.6956 (t80) REVERT: I 195 TYR cc_start: 0.7831 (t80) cc_final: 0.7429 (t80) REVERT: L 59 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.6353 (mt0) REVERT: L 167 GLN cc_start: 0.8144 (mt0) cc_final: 0.7815 (mp10) REVERT: L 195 TYR cc_start: 0.7055 (t80) cc_final: 0.6643 (t80) REVERT: M 49 SER cc_start: 0.8324 (OUTLIER) cc_final: 0.7788 (t) REVERT: N 102 TYR cc_start: 0.8265 (OUTLIER) cc_final: 0.6954 (t80) REVERT: N 195 TYR cc_start: 0.7829 (t80) cc_final: 0.7426 (t80) REVERT: Q 59 GLN cc_start: 0.8076 (OUTLIER) cc_final: 0.6360 (mt0) REVERT: Q 167 GLN cc_start: 0.8144 (mt0) cc_final: 0.7820 (mp10) REVERT: Q 195 TYR cc_start: 0.7052 (t80) cc_final: 0.6640 (t80) REVERT: R 49 SER cc_start: 0.8331 (OUTLIER) cc_final: 0.7798 (t) REVERT: S 102 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.6951 (t80) REVERT: S 195 TYR cc_start: 0.7831 (t80) cc_final: 0.7431 (t80) outliers start: 100 outliers final: 48 residues processed: 444 average time/residue: 0.3842 time to fit residues: 282.4575 Evaluate side-chains 356 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 296 time to evaluate : 3.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 127 ASN Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain L residue 59 GLN Chi-restraints excluded: chain L residue 162 LEU Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 7 ASP Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 102 TYR Chi-restraints excluded: chain N residue 127 ASN Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain Q residue 59 GLN Chi-restraints excluded: chain Q residue 162 LEU Chi-restraints excluded: chain Q residue 185 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 102 TYR Chi-restraints excluded: chain S residue 127 ASN Chi-restraints excluded: chain S residue 180 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 98 optimal weight: 4.9990 chunk 264 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 172 optimal weight: 0.8980 chunk 72 optimal weight: 9.9990 chunk 294 optimal weight: 0.6980 chunk 244 optimal weight: 8.9990 chunk 136 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 154 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 9 GLN C 98 ASN G 9 GLN H 98 ASN L 9 GLN M 98 ASN Q 9 GLN R 98 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 26648 Z= 0.177 Angle : 0.587 9.624 36004 Z= 0.296 Chirality : 0.035 0.148 4056 Planarity : 0.004 0.040 4464 Dihedral : 11.606 101.012 3672 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.71 % Favored : 97.16 % Rotamer: Outliers : 3.54 % Allowed : 20.69 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.15), residues: 3104 helix: 0.86 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : -0.70 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 88 HIS 0.006 0.001 HIS S 68 PHE 0.037 0.002 PHE P 86 TYR 0.039 0.002 TYR K 82 ARG 0.005 0.000 ARG Q 227 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 352 time to evaluate : 3.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 TYR cc_start: 0.8182 (t80) cc_final: 0.7949 (t80) REVERT: B 59 GLN cc_start: 0.8013 (OUTLIER) cc_final: 0.6286 (mt0) REVERT: B 123 HIS cc_start: 0.4772 (m90) cc_final: 0.4362 (m-70) REVERT: B 195 TYR cc_start: 0.7138 (t80) cc_final: 0.6594 (t80) REVERT: C 49 SER cc_start: 0.8287 (OUTLIER) cc_final: 0.7763 (t) REVERT: D 102 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.6944 (t80) REVERT: D 109 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.7709 (t80) REVERT: F 82 TYR cc_start: 0.8183 (t80) cc_final: 0.7946 (t80) REVERT: G 59 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.6289 (mt0) REVERT: G 123 HIS cc_start: 0.4762 (m90) cc_final: 0.4354 (m-70) REVERT: G 195 TYR cc_start: 0.7137 (t80) cc_final: 0.6595 (t80) REVERT: H 49 SER cc_start: 0.8294 (OUTLIER) cc_final: 0.7768 (t) REVERT: I 102 TYR cc_start: 0.8213 (OUTLIER) cc_final: 0.6949 (t80) REVERT: I 109 TYR cc_start: 0.8883 (OUTLIER) cc_final: 0.7712 (t80) REVERT: K 82 TYR cc_start: 0.8182 (t80) cc_final: 0.7948 (t80) REVERT: L 59 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.6283 (mt0) REVERT: L 123 HIS cc_start: 0.4767 (m90) cc_final: 0.4357 (m-70) REVERT: L 195 TYR cc_start: 0.7137 (t80) cc_final: 0.6593 (t80) REVERT: M 49 SER cc_start: 0.8292 (OUTLIER) cc_final: 0.7766 (t) REVERT: N 102 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.6951 (t80) REVERT: N 109 TYR cc_start: 0.8882 (OUTLIER) cc_final: 0.7706 (t80) REVERT: P 82 TYR cc_start: 0.8187 (t80) cc_final: 0.7951 (t80) REVERT: Q 59 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.6292 (mt0) REVERT: Q 123 HIS cc_start: 0.4738 (m90) cc_final: 0.4349 (m-70) REVERT: Q 195 TYR cc_start: 0.7137 (t80) cc_final: 0.6595 (t80) REVERT: R 49 SER cc_start: 0.8295 (OUTLIER) cc_final: 0.7772 (t) REVERT: S 102 TYR cc_start: 0.8211 (OUTLIER) cc_final: 0.6942 (t80) REVERT: S 109 TYR cc_start: 0.8887 (OUTLIER) cc_final: 0.7713 (t80) outliers start: 101 outliers final: 73 residues processed: 436 average time/residue: 0.3412 time to fit residues: 245.7341 Evaluate side-chains 395 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 306 time to evaluate : 3.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 109 TYR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 127 ASN Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 185 SER Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 109 TYR Chi-restraints excluded: chain I residue 127 ASN Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 121 ILE Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 59 GLN Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 127 ASN Chi-restraints excluded: chain L residue 162 LEU Chi-restraints excluded: chain L residue 185 SER Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 7 ASP Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 60 LEU Chi-restraints excluded: chain N residue 102 TYR Chi-restraints excluded: chain N residue 109 TYR Chi-restraints excluded: chain N residue 127 ASN Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain Q residue 7 ASP Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 59 GLN Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 127 ASN Chi-restraints excluded: chain Q residue 162 LEU Chi-restraints excluded: chain Q residue 185 SER Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 LEU Chi-restraints excluded: chain S residue 102 TYR Chi-restraints excluded: chain S residue 109 TYR Chi-restraints excluded: chain S residue 127 ASN Chi-restraints excluded: chain S residue 180 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 283 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 167 optimal weight: 10.0000 chunk 214 optimal weight: 6.9990 chunk 166 optimal weight: 3.9990 chunk 247 optimal weight: 0.8980 chunk 164 optimal weight: 1.9990 chunk 293 optimal weight: 0.6980 chunk 183 optimal weight: 6.9990 chunk 178 optimal weight: 20.0000 chunk 135 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN D 122 HIS I 122 HIS N 122 HIS R 98 ASN S 122 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.5329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 26648 Z= 0.173 Angle : 0.598 10.816 36004 Z= 0.296 Chirality : 0.036 0.232 4056 Planarity : 0.004 0.040 4464 Dihedral : 11.214 99.630 3672 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.85 % Allowed : 21.64 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 3104 helix: 0.88 (0.10), residues: 2340 sheet: None (None), residues: 0 loop : -0.85 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 70 HIS 0.012 0.001 HIS D 122 PHE 0.032 0.002 PHE N 126 TYR 0.042 0.002 TYR N 195 ARG 0.005 0.000 ARG Q 227 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 333 time to evaluate : 3.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLN cc_start: 0.8050 (OUTLIER) cc_final: 0.6357 (mt0) REVERT: B 123 HIS cc_start: 0.4596 (m90) cc_final: 0.4250 (m-70) REVERT: B 167 GLN cc_start: 0.8065 (mt0) cc_final: 0.7750 (mp10) REVERT: B 208 MET cc_start: 0.6103 (tpp) cc_final: 0.5829 (tpp) REVERT: C 49 SER cc_start: 0.8254 (OUTLIER) cc_final: 0.7737 (t) REVERT: D 102 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.6873 (t80) REVERT: D 109 TYR cc_start: 0.8914 (OUTLIER) cc_final: 0.7757 (t80) REVERT: G 59 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.6354 (mt0) REVERT: G 123 HIS cc_start: 0.4588 (m90) cc_final: 0.4242 (m-70) REVERT: G 167 GLN cc_start: 0.8053 (mt0) cc_final: 0.7740 (mp10) REVERT: G 208 MET cc_start: 0.6109 (tpp) cc_final: 0.5832 (tpp) REVERT: H 49 SER cc_start: 0.8253 (OUTLIER) cc_final: 0.7736 (t) REVERT: I 102 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.6875 (t80) REVERT: I 109 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.7760 (t80) REVERT: L 59 GLN cc_start: 0.8047 (OUTLIER) cc_final: 0.6349 (mt0) REVERT: L 123 HIS cc_start: 0.4597 (m90) cc_final: 0.4250 (m-70) REVERT: L 167 GLN cc_start: 0.8068 (mt0) cc_final: 0.7748 (mp10) REVERT: L 208 MET cc_start: 0.6109 (tpp) cc_final: 0.5836 (tpp) REVERT: M 49 SER cc_start: 0.8256 (OUTLIER) cc_final: 0.7735 (t) REVERT: N 102 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.6874 (t80) REVERT: N 109 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.7756 (t80) REVERT: Q 59 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.6355 (mt0) REVERT: Q 123 HIS cc_start: 0.4570 (m90) cc_final: 0.4240 (m-70) REVERT: Q 167 GLN cc_start: 0.8067 (mt0) cc_final: 0.7754 (mp10) REVERT: Q 208 MET cc_start: 0.6108 (tpp) cc_final: 0.5832 (tpp) REVERT: R 49 SER cc_start: 0.8257 (OUTLIER) cc_final: 0.7740 (t) REVERT: S 102 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.6871 (t80) REVERT: S 109 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.7759 (t80) outliers start: 110 outliers final: 66 residues processed: 435 average time/residue: 0.3465 time to fit residues: 247.4740 Evaluate side-chains 359 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 277 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 228 TYR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 109 TYR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 127 ASN Chi-restraints excluded: chain G residue 228 TYR Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 109 TYR Chi-restraints excluded: chain I residue 127 ASN Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 121 ILE Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 59 GLN Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 127 ASN Chi-restraints excluded: chain L residue 228 TYR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 7 ASP Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 102 TYR Chi-restraints excluded: chain N residue 109 TYR Chi-restraints excluded: chain N residue 127 ASN Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain Q residue 7 ASP Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 59 GLN Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 127 ASN Chi-restraints excluded: chain Q residue 228 TYR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 102 TYR Chi-restraints excluded: chain S residue 109 TYR Chi-restraints excluded: chain S residue 127 ASN Chi-restraints excluded: chain S residue 180 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 181 optimal weight: 0.9980 chunk 117 optimal weight: 0.0060 chunk 174 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 186 optimal weight: 6.9990 chunk 199 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 230 optimal weight: 4.9990 overall best weight: 2.2002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 98 ASN D 122 HIS H 98 ASN I 122 HIS M 98 ASN N 122 HIS R 98 ASN S 122 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 26648 Z= 0.230 Angle : 0.619 11.162 36004 Z= 0.308 Chirality : 0.037 0.161 4056 Planarity : 0.004 0.040 4464 Dihedral : 10.696 97.340 3672 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.17 % Allowed : 21.60 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.15), residues: 3104 helix: 0.81 (0.10), residues: 2356 sheet: None (None), residues: 0 loop : -0.76 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 70 HIS 0.011 0.001 HIS N 122 PHE 0.022 0.002 PHE B 165 TYR 0.037 0.002 TYR S 195 ARG 0.005 0.000 ARG C 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 292 time to evaluate : 2.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.6350 (mt0) REVERT: B 123 HIS cc_start: 0.4573 (m90) cc_final: 0.4223 (m-70) REVERT: B 195 TYR cc_start: 0.7194 (t80) cc_final: 0.6675 (t80) REVERT: B 208 MET cc_start: 0.6220 (tpp) cc_final: 0.5937 (tpp) REVERT: C 49 SER cc_start: 0.8271 (OUTLIER) cc_final: 0.7746 (t) REVERT: D 102 TYR cc_start: 0.8235 (OUTLIER) cc_final: 0.6922 (t80) REVERT: D 109 TYR cc_start: 0.8930 (OUTLIER) cc_final: 0.7755 (t80) REVERT: G 59 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.6349 (mt0) REVERT: G 123 HIS cc_start: 0.4567 (m90) cc_final: 0.4223 (m-70) REVERT: G 195 TYR cc_start: 0.7193 (t80) cc_final: 0.6674 (t80) REVERT: G 208 MET cc_start: 0.6231 (tpp) cc_final: 0.5941 (tpp) REVERT: H 49 SER cc_start: 0.8273 (OUTLIER) cc_final: 0.7748 (t) REVERT: I 102 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.6927 (t80) REVERT: I 109 TYR cc_start: 0.8930 (OUTLIER) cc_final: 0.7760 (t80) REVERT: L 59 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.6347 (mt0) REVERT: L 123 HIS cc_start: 0.4570 (m90) cc_final: 0.4221 (m-70) REVERT: L 195 TYR cc_start: 0.7192 (t80) cc_final: 0.6672 (t80) REVERT: L 208 MET cc_start: 0.6227 (tpp) cc_final: 0.5941 (tpp) REVERT: M 49 SER cc_start: 0.8273 (OUTLIER) cc_final: 0.7747 (t) REVERT: N 102 TYR cc_start: 0.8237 (OUTLIER) cc_final: 0.6930 (t80) REVERT: N 109 TYR cc_start: 0.8929 (OUTLIER) cc_final: 0.7755 (t80) REVERT: Q 59 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.6358 (mt0) REVERT: Q 123 HIS cc_start: 0.4535 (m90) cc_final: 0.4214 (m-70) REVERT: Q 195 TYR cc_start: 0.7193 (t80) cc_final: 0.6674 (t80) REVERT: Q 208 MET cc_start: 0.6226 (tpp) cc_final: 0.5938 (tpp) REVERT: R 49 SER cc_start: 0.8273 (OUTLIER) cc_final: 0.7748 (t) REVERT: S 102 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.6923 (t80) REVERT: S 109 TYR cc_start: 0.8930 (OUTLIER) cc_final: 0.7758 (t80) outliers start: 119 outliers final: 75 residues processed: 388 average time/residue: 0.3392 time to fit residues: 218.6716 Evaluate side-chains 363 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 272 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 228 TYR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 98 ASN Chi-restraints excluded: chain C residue 121 ILE Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 21 THR Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 109 TYR Chi-restraints excluded: chain D residue 127 ASN Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 93 LEU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 162 LEU Chi-restraints excluded: chain G residue 228 TYR Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 121 ILE Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 7 ASP Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 63 MET Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 109 TYR Chi-restraints excluded: chain I residue 127 ASN Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 78 THR Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 93 LEU Chi-restraints excluded: chain K residue 121 ILE Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 59 GLN Chi-restraints excluded: chain L residue 162 LEU Chi-restraints excluded: chain L residue 228 TYR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 121 ILE Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 7 ASP Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 63 MET Chi-restraints excluded: chain N residue 102 TYR Chi-restraints excluded: chain N residue 109 TYR Chi-restraints excluded: chain N residue 127 ASN Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 59 GLN Chi-restraints excluded: chain Q residue 162 LEU Chi-restraints excluded: chain Q residue 228 TYR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 98 ASN Chi-restraints excluded: chain R residue 121 ILE Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain S residue 7 ASP Chi-restraints excluded: chain S residue 21 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 63 MET Chi-restraints excluded: chain S residue 102 TYR Chi-restraints excluded: chain S residue 109 TYR Chi-restraints excluded: chain S residue 127 ASN Chi-restraints excluded: chain S residue 180 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 266 optimal weight: 1.9990 chunk 280 optimal weight: 0.0570 chunk 256 optimal weight: 0.0870 chunk 273 optimal weight: 0.7980 chunk 164 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 246 optimal weight: 2.9990 chunk 258 optimal weight: 0.8980 chunk 272 optimal weight: 0.6980 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 HIS ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 HIS ** M 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 122 HIS ** R 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 26648 Z= 0.152 Angle : 0.584 11.595 36004 Z= 0.291 Chirality : 0.036 0.177 4056 Planarity : 0.004 0.046 4464 Dihedral : 10.178 97.736 3672 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.94 % Allowed : 22.34 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 3104 helix: 0.85 (0.11), residues: 2356 sheet: None (None), residues: 0 loop : -0.73 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 94 HIS 0.012 0.001 HIS N 122 PHE 0.022 0.002 PHE B 165 TYR 0.020 0.001 TYR B 109 ARG 0.007 0.000 ARG D 124 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 341 time to evaluate : 3.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLN cc_start: 0.8042 (OUTLIER) cc_final: 0.6355 (mt0) REVERT: B 123 HIS cc_start: 0.4322 (m90) cc_final: 0.4090 (m-70) REVERT: B 208 MET cc_start: 0.6100 (tpp) cc_final: 0.5830 (tpp) REVERT: C 1 MET cc_start: 0.6943 (pmm) cc_final: 0.5551 (tpp) REVERT: C 49 SER cc_start: 0.8177 (OUTLIER) cc_final: 0.7688 (t) REVERT: D 102 TYR cc_start: 0.8155 (OUTLIER) cc_final: 0.6833 (t80) REVERT: D 109 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.7701 (t80) REVERT: D 156 MET cc_start: 0.8278 (ttm) cc_final: 0.7947 (ttm) REVERT: D 195 TYR cc_start: 0.8079 (t80) cc_final: 0.7834 (t80) REVERT: G 59 GLN cc_start: 0.8036 (OUTLIER) cc_final: 0.6351 (mt0) REVERT: G 123 HIS cc_start: 0.4315 (m90) cc_final: 0.4088 (m-70) REVERT: G 208 MET cc_start: 0.6108 (tpp) cc_final: 0.5832 (tpp) REVERT: H 1 MET cc_start: 0.6950 (pmm) cc_final: 0.5564 (tpp) REVERT: H 49 SER cc_start: 0.8177 (OUTLIER) cc_final: 0.7686 (t) REVERT: I 102 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.6826 (t80) REVERT: I 109 TYR cc_start: 0.8915 (OUTLIER) cc_final: 0.7705 (t80) REVERT: I 156 MET cc_start: 0.8271 (ttm) cc_final: 0.7941 (ttm) REVERT: I 195 TYR cc_start: 0.8072 (t80) cc_final: 0.7819 (t80) REVERT: L 59 GLN cc_start: 0.8037 (OUTLIER) cc_final: 0.6348 (mt0) REVERT: L 123 HIS cc_start: 0.4324 (m90) cc_final: 0.4087 (m-70) REVERT: L 208 MET cc_start: 0.6107 (tpp) cc_final: 0.5836 (tpp) REVERT: M 1 MET cc_start: 0.6959 (pmm) cc_final: 0.5564 (tpp) REVERT: M 49 SER cc_start: 0.8179 (OUTLIER) cc_final: 0.7688 (t) REVERT: N 102 TYR cc_start: 0.8153 (OUTLIER) cc_final: 0.6832 (t80) REVERT: N 109 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.7703 (t80) REVERT: N 156 MET cc_start: 0.8272 (ttm) cc_final: 0.7945 (ttm) REVERT: N 195 TYR cc_start: 0.8070 (t80) cc_final: 0.7819 (t80) REVERT: Q 59 GLN cc_start: 0.8039 (OUTLIER) cc_final: 0.6352 (mt0) REVERT: Q 123 HIS cc_start: 0.4300 (m90) cc_final: 0.4090 (m-70) REVERT: Q 208 MET cc_start: 0.6109 (tpp) cc_final: 0.5835 (tpp) REVERT: R 1 MET cc_start: 0.6957 (pmm) cc_final: 0.5569 (tpp) REVERT: R 49 SER cc_start: 0.8178 (OUTLIER) cc_final: 0.7689 (t) REVERT: S 102 TYR cc_start: 0.8146 (OUTLIER) cc_final: 0.6827 (t80) REVERT: S 109 TYR cc_start: 0.8913 (OUTLIER) cc_final: 0.7701 (t80) REVERT: S 156 MET cc_start: 0.8273 (ttm) cc_final: 0.7944 (ttm) REVERT: S 195 TYR cc_start: 0.8081 (t80) cc_final: 0.7836 (t80) outliers start: 84 outliers final: 52 residues processed: 409 average time/residue: 0.3484 time to fit residues: 233.9751 Evaluate side-chains 381 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 313 time to evaluate : 3.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 109 TYR Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 63 MET Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 109 TYR Chi-restraints excluded: chain I residue 122 HIS Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 121 ILE Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 59 GLN Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 63 MET Chi-restraints excluded: chain N residue 102 TYR Chi-restraints excluded: chain N residue 109 TYR Chi-restraints excluded: chain N residue 122 HIS Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain Q residue 7 ASP Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 59 GLN Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 63 MET Chi-restraints excluded: chain S residue 102 TYR Chi-restraints excluded: chain S residue 109 TYR Chi-restraints excluded: chain S residue 122 HIS Chi-restraints excluded: chain S residue 180 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 179 optimal weight: 6.9990 chunk 288 optimal weight: 8.9990 chunk 176 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 200 optimal weight: 0.9990 chunk 302 optimal weight: 2.9990 chunk 278 optimal weight: 1.9990 chunk 241 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 186 optimal weight: 8.9990 chunk 147 optimal weight: 0.7980 overall best weight: 1.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN D 122 HIS D 123 HIS ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN I 122 HIS I 123 HIS ** M 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 ASN N 122 HIS N 123 HIS ** R 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 ASN S 122 HIS S 123 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 26648 Z= 0.177 Angle : 0.597 11.218 36004 Z= 0.298 Chirality : 0.036 0.180 4056 Planarity : 0.004 0.045 4464 Dihedral : 9.642 96.221 3672 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.08 % Allowed : 21.95 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 3104 helix: 0.87 (0.10), residues: 2348 sheet: None (None), residues: 0 loop : -0.79 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 94 HIS 0.015 0.001 HIS I 122 PHE 0.034 0.002 PHE N 119 TYR 0.019 0.001 TYR P 82 ARG 0.006 0.000 ARG D 124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6208 Ramachandran restraints generated. 3104 Oldfield, 0 Emsley, 3104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 312 time to evaluate : 3.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.6374 (mt0) REVERT: B 208 MET cc_start: 0.6188 (tpp) cc_final: 0.5900 (tpp) REVERT: C 1 MET cc_start: 0.6857 (pmm) cc_final: 0.5533 (tpp) REVERT: C 49 SER cc_start: 0.8181 (OUTLIER) cc_final: 0.7692 (t) REVERT: D 102 TYR cc_start: 0.8168 (OUTLIER) cc_final: 0.6902 (t80) REVERT: D 109 TYR cc_start: 0.8970 (OUTLIER) cc_final: 0.7937 (t80) REVERT: D 156 MET cc_start: 0.8235 (ttm) cc_final: 0.7908 (ttm) REVERT: D 195 TYR cc_start: 0.8012 (t80) cc_final: 0.7806 (t80) REVERT: G 59 GLN cc_start: 0.8051 (OUTLIER) cc_final: 0.6372 (mt0) REVERT: G 208 MET cc_start: 0.6197 (tpp) cc_final: 0.5903 (tpp) REVERT: H 1 MET cc_start: 0.6856 (pmm) cc_final: 0.5533 (tpp) REVERT: H 49 SER cc_start: 0.8178 (OUTLIER) cc_final: 0.7691 (t) REVERT: I 102 TYR cc_start: 0.8165 (OUTLIER) cc_final: 0.6898 (t80) REVERT: I 109 TYR cc_start: 0.8970 (OUTLIER) cc_final: 0.7939 (t80) REVERT: I 156 MET cc_start: 0.8236 (ttm) cc_final: 0.7908 (ttm) REVERT: I 195 TYR cc_start: 0.8007 (t80) cc_final: 0.7795 (t80) REVERT: L 59 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.6377 (mt0) REVERT: L 208 MET cc_start: 0.6201 (tpp) cc_final: 0.5909 (tpp) REVERT: M 1 MET cc_start: 0.6865 (pmm) cc_final: 0.5541 (tpp) REVERT: M 49 SER cc_start: 0.8179 (OUTLIER) cc_final: 0.7691 (t) REVERT: N 102 TYR cc_start: 0.8171 (OUTLIER) cc_final: 0.6908 (t80) REVERT: N 109 TYR cc_start: 0.8969 (OUTLIER) cc_final: 0.7938 (t80) REVERT: N 156 MET cc_start: 0.8230 (ttm) cc_final: 0.7906 (ttm) REVERT: N 195 TYR cc_start: 0.8009 (t80) cc_final: 0.7798 (t80) REVERT: Q 59 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.6377 (mt0) REVERT: Q 208 MET cc_start: 0.6198 (tpp) cc_final: 0.5905 (tpp) REVERT: R 1 MET cc_start: 0.6868 (pmm) cc_final: 0.5549 (tpp) REVERT: R 49 SER cc_start: 0.8182 (OUTLIER) cc_final: 0.7695 (t) REVERT: S 102 TYR cc_start: 0.8166 (OUTLIER) cc_final: 0.6899 (t80) REVERT: S 109 TYR cc_start: 0.8967 (OUTLIER) cc_final: 0.7936 (t80) REVERT: S 156 MET cc_start: 0.8227 (ttm) cc_final: 0.7899 (ttm) REVERT: S 195 TYR cc_start: 0.8016 (t80) cc_final: 0.7806 (t80) outliers start: 88 outliers final: 58 residues processed: 388 average time/residue: 0.3352 time to fit residues: 217.2340 Evaluate side-chains 362 residues out of total 2856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 288 time to evaluate : 3.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain B residue 7 ASP Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 59 GLN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 228 TYR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain C residue 133 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 63 MET Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 109 TYR Chi-restraints excluded: chain D residue 122 HIS Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 39 LEU Chi-restraints excluded: chain F residue 83 LEU Chi-restraints excluded: chain F residue 121 ILE Chi-restraints excluded: chain G residue 7 ASP Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 59 GLN Chi-restraints excluded: chain G residue 60 LEU Chi-restraints excluded: chain G residue 228 TYR Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 49 SER Chi-restraints excluded: chain H residue 98 ASN Chi-restraints excluded: chain H residue 133 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 63 MET Chi-restraints excluded: chain I residue 102 TYR Chi-restraints excluded: chain I residue 109 TYR Chi-restraints excluded: chain I residue 122 HIS Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 39 LEU Chi-restraints excluded: chain K residue 83 LEU Chi-restraints excluded: chain K residue 121 ILE Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 8 LEU Chi-restraints excluded: chain L residue 59 GLN Chi-restraints excluded: chain L residue 60 LEU Chi-restraints excluded: chain L residue 228 TYR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 49 SER Chi-restraints excluded: chain M residue 98 ASN Chi-restraints excluded: chain M residue 133 LEU Chi-restraints excluded: chain N residue 58 VAL Chi-restraints excluded: chain N residue 63 MET Chi-restraints excluded: chain N residue 102 TYR Chi-restraints excluded: chain N residue 109 TYR Chi-restraints excluded: chain N residue 122 HIS Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain P residue 12 LEU Chi-restraints excluded: chain P residue 39 LEU Chi-restraints excluded: chain P residue 83 LEU Chi-restraints excluded: chain P residue 121 ILE Chi-restraints excluded: chain Q residue 7 ASP Chi-restraints excluded: chain Q residue 8 LEU Chi-restraints excluded: chain Q residue 59 GLN Chi-restraints excluded: chain Q residue 60 LEU Chi-restraints excluded: chain Q residue 228 TYR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 49 SER Chi-restraints excluded: chain R residue 133 LEU Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 63 MET Chi-restraints excluded: chain S residue 102 TYR Chi-restraints excluded: chain S residue 109 TYR Chi-restraints excluded: chain S residue 122 HIS Chi-restraints excluded: chain S residue 180 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 304 random chunks: chunk 191 optimal weight: 9.9990 chunk 256 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 222 optimal weight: 0.7980 chunk 35 optimal weight: 10.0000 chunk 67 optimal weight: 6.9990 chunk 241 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 248 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 98 ASN D 122 HIS ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 98 ASN I 122 HIS ** M 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 ASN N 122 HIS ** R 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 98 ASN S 122 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.122827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.099262 restraints weight = 66878.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.098081 restraints weight = 69440.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.098804 restraints weight = 75692.153| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 26648 Z= 0.182 Angle : 0.603 11.067 36004 Z= 0.304 Chirality : 0.036 0.186 4056 Planarity : 0.004 0.045 4464 Dihedral : 9.226 95.363 3672 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.22 % Allowed : 22.55 % Favored : 74.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.15), residues: 3104 helix: 0.87 (0.10), residues: 2348 sheet: None (None), residues: 0 loop : -0.81 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP M 94 HIS 0.020 0.002 HIS I 122 PHE 0.020 0.002 PHE N 165 TYR 0.019 0.001 TYR B 109 ARG 0.006 0.000 ARG D 124 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5239.56 seconds wall clock time: 98 minutes 25.81 seconds (5905.81 seconds total)