Starting phenix.real_space_refine on Wed Feb 21 21:05:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzw_0562/02_2024/6nzw_0562_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzw_0562/02_2024/6nzw_0562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzw_0562/02_2024/6nzw_0562.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzw_0562/02_2024/6nzw_0562.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzw_0562/02_2024/6nzw_0562_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nzw_0562/02_2024/6nzw_0562_neut_trim_updated.pdb" } resolution = 3.21 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 102 5.16 5 Cl 2 4.86 5 C 10606 2.51 5 N 2532 2.21 5 O 2764 1.98 5 H 15714 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 389": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 389": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 389": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 389": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 389": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 148": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 262": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 306": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 308": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 345": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 346": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 357": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 389": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31720 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "B" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "C" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "D" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "E" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "F" Number of atoms: 5245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 5245 Classifications: {'peptide': 313} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 2 Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 65 Unusual residues: {'L9Y': 1, 'POV': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 23 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 23 Chain: "D" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 23 Chain: "E" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 23 Chain: "F" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Unusual residues: {'POV': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 107 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'POV:plan-3': 1, 'POV:plan-2': 2, 'POV:plan-1': 3} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 14.13, per 1000 atoms: 0.45 Number of scatterers: 31720 At special positions: 0 Unit cell: (109.888, 103.36, 131.648, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 102 16.00 O 2764 8.00 N 2532 7.00 C 10606 6.00 H 15714 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.03 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.03 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 310 " distance=2.03 Simple disulfide: pdb=" SG CYS F 57 " - pdb=" SG CYS F 65 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 295 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 25.92 Conformation dependent library (CDL) restraints added in 3.2 seconds 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3660 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 84 helices and 6 sheets defined 66.1% alpha, 2.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.63 Creating SS restraints... Processing helix chain 'A' and resid 17 through 20 Processing helix chain 'A' and resid 23 through 48 removed outlier: 4.118A pdb=" N THR A 28 " --> pdb=" O TRP A 24 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP A 29 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR A 30 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 115 removed outlier: 4.251A pdb=" N VAL A 109 " --> pdb=" O GLN A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 123 No H-bonds generated for 'chain 'A' and resid 120 through 123' Processing helix chain 'A' and resid 125 through 145 removed outlier: 3.518A pdb=" N LEU A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 131 " --> pdb=" O TYR A 127 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER A 140 " --> pdb=" O PHE A 136 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N TRP A 143 " --> pdb=" O CYS A 139 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 164 removed outlier: 4.495A pdb=" N LYS A 152 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 173 removed outlier: 3.605A pdb=" N LEU A 173 " --> pdb=" O THR A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 253 removed outlier: 3.673A pdb=" N LYS A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR A 252 " --> pdb=" O LYS A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 288 removed outlier: 3.520A pdb=" N THR A 268 " --> pdb=" O TYR A 264 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE A 270 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR A 284 " --> pdb=" O CYS A 280 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N HIS A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASN A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 345 removed outlier: 4.177A pdb=" N THR A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE A 320 " --> pdb=" O LEU A 317 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA A 322 " --> pdb=" O LYS A 319 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE A 326 " --> pdb=" O SER A 323 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE A 330 " --> pdb=" O SER A 327 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE A 331 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 334 " --> pdb=" O PHE A 331 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR A 339 " --> pdb=" O CYS A 336 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU A 340 " --> pdb=" O MET A 337 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TRP A 342 " --> pdb=" O THR A 339 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG A 345 " --> pdb=" O TRP A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 360 Processing helix chain 'A' and resid 373 through 382 removed outlier: 3.821A pdb=" N GLN A 381 " --> pdb=" O HIS A 377 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N TYR A 382 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 388 No H-bonds generated for 'chain 'A' and resid 385 through 388' Processing helix chain 'A' and resid 396 through 407 Processing helix chain 'B' and resid 17 through 20 Processing helix chain 'B' and resid 23 through 48 removed outlier: 4.117A pdb=" N THR B 28 " --> pdb=" O TRP B 24 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR B 30 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 115 removed outlier: 4.251A pdb=" N VAL B 109 " --> pdb=" O GLN B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 123 No H-bonds generated for 'chain 'B' and resid 120 through 123' Processing helix chain 'B' and resid 125 through 145 removed outlier: 3.518A pdb=" N LEU B 130 " --> pdb=" O PRO B 126 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU B 131 " --> pdb=" O TYR B 127 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER B 140 " --> pdb=" O PHE B 136 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TRP B 143 " --> pdb=" O CYS B 139 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 164 removed outlier: 4.495A pdb=" N LYS B 152 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS B 162 " --> pdb=" O SER B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 173 removed outlier: 3.605A pdb=" N LEU B 173 " --> pdb=" O THR B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 253 removed outlier: 3.673A pdb=" N LYS B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR B 252 " --> pdb=" O LYS B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 288 removed outlier: 3.521A pdb=" N THR B 268 " --> pdb=" O TYR B 264 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE B 270 " --> pdb=" O ARG B 266 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL B 283 " --> pdb=" O ILE B 279 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR B 284 " --> pdb=" O CYS B 280 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N HIS B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASN B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 345 removed outlier: 4.177A pdb=" N THR B 316 " --> pdb=" O PRO B 313 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE B 318 " --> pdb=" O ALA B 315 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE B 320 " --> pdb=" O LEU B 317 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA B 322 " --> pdb=" O LYS B 319 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE B 326 " --> pdb=" O SER B 323 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE B 330 " --> pdb=" O SER B 327 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE B 331 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 334 " --> pdb=" O PHE B 331 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR B 339 " --> pdb=" O CYS B 336 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU B 340 " --> pdb=" O MET B 337 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP B 342 " --> pdb=" O THR B 339 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG B 345 " --> pdb=" O TRP B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 360 Processing helix chain 'B' and resid 373 through 382 removed outlier: 3.821A pdb=" N GLN B 381 " --> pdb=" O HIS B 377 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR B 382 " --> pdb=" O LEU B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 388 No H-bonds generated for 'chain 'B' and resid 385 through 388' Processing helix chain 'B' and resid 396 through 407 Processing helix chain 'C' and resid 17 through 20 Processing helix chain 'C' and resid 23 through 48 removed outlier: 4.117A pdb=" N THR C 28 " --> pdb=" O TRP C 24 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP C 29 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR C 30 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 115 removed outlier: 4.251A pdb=" N VAL C 109 " --> pdb=" O GLN C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 123 No H-bonds generated for 'chain 'C' and resid 120 through 123' Processing helix chain 'C' and resid 125 through 145 removed outlier: 3.519A pdb=" N LEU C 130 " --> pdb=" O PRO C 126 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU C 131 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER C 140 " --> pdb=" O PHE C 136 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TRP C 143 " --> pdb=" O CYS C 139 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 164 removed outlier: 4.494A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS C 162 " --> pdb=" O SER C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 173 removed outlier: 3.605A pdb=" N LEU C 173 " --> pdb=" O THR C 170 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 253 removed outlier: 3.673A pdb=" N LYS C 246 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR C 252 " --> pdb=" O LYS C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 259 through 288 removed outlier: 3.521A pdb=" N THR C 268 " --> pdb=" O TYR C 264 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE C 270 " --> pdb=" O ARG C 266 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL C 283 " --> pdb=" O ILE C 279 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR C 284 " --> pdb=" O CYS C 280 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N HIS C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASN C 288 " --> pdb=" O TYR C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 345 removed outlier: 4.178A pdb=" N THR C 316 " --> pdb=" O PRO C 313 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE C 318 " --> pdb=" O ALA C 315 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE C 320 " --> pdb=" O LEU C 317 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA C 322 " --> pdb=" O LYS C 319 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE C 326 " --> pdb=" O SER C 323 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE C 330 " --> pdb=" O SER C 327 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE C 331 " --> pdb=" O LEU C 328 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 334 " --> pdb=" O PHE C 331 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR C 339 " --> pdb=" O CYS C 336 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 340 " --> pdb=" O MET C 337 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP C 342 " --> pdb=" O THR C 339 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG C 345 " --> pdb=" O TRP C 342 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 360 Processing helix chain 'C' and resid 373 through 382 removed outlier: 3.820A pdb=" N GLN C 381 " --> pdb=" O HIS C 377 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR C 382 " --> pdb=" O LEU C 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 388 No H-bonds generated for 'chain 'C' and resid 385 through 388' Processing helix chain 'C' and resid 396 through 407 Processing helix chain 'D' and resid 17 through 20 Processing helix chain 'D' and resid 23 through 48 removed outlier: 4.117A pdb=" N THR D 28 " --> pdb=" O TRP D 24 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP D 29 " --> pdb=" O ASP D 25 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR D 30 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ILE D 33 " --> pdb=" O ASP D 29 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 115 removed outlier: 4.250A pdb=" N VAL D 109 " --> pdb=" O GLN D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 123 No H-bonds generated for 'chain 'D' and resid 120 through 123' Processing helix chain 'D' and resid 125 through 145 removed outlier: 3.518A pdb=" N LEU D 130 " --> pdb=" O PRO D 126 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU D 131 " --> pdb=" O TYR D 127 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER D 140 " --> pdb=" O PHE D 136 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 164 removed outlier: 4.494A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS D 162 " --> pdb=" O SER D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 173 removed outlier: 3.606A pdb=" N LEU D 173 " --> pdb=" O THR D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 253 removed outlier: 3.673A pdb=" N LYS D 246 " --> pdb=" O ALA D 242 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR D 252 " --> pdb=" O LYS D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 288 removed outlier: 3.521A pdb=" N THR D 268 " --> pdb=" O TYR D 264 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL D 283 " --> pdb=" O ILE D 279 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR D 284 " --> pdb=" O CYS D 280 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N HIS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ASN D 288 " --> pdb=" O TYR D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 313 through 345 removed outlier: 4.176A pdb=" N THR D 316 " --> pdb=" O PRO D 313 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE D 318 " --> pdb=" O ALA D 315 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE D 320 " --> pdb=" O LEU D 317 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA D 322 " --> pdb=" O LYS D 319 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE D 326 " --> pdb=" O SER D 323 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE D 330 " --> pdb=" O SER D 327 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE D 331 " --> pdb=" O LEU D 328 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU D 334 " --> pdb=" O PHE D 331 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR D 339 " --> pdb=" O CYS D 336 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU D 340 " --> pdb=" O MET D 337 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TRP D 342 " --> pdb=" O THR D 339 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG D 345 " --> pdb=" O TRP D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 356 through 360 Processing helix chain 'D' and resid 373 through 382 removed outlier: 3.820A pdb=" N GLN D 381 " --> pdb=" O HIS D 377 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR D 382 " --> pdb=" O LEU D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 388 No H-bonds generated for 'chain 'D' and resid 385 through 388' Processing helix chain 'D' and resid 396 through 407 Processing helix chain 'E' and resid 17 through 20 Processing helix chain 'E' and resid 23 through 48 removed outlier: 4.116A pdb=" N THR E 28 " --> pdb=" O TRP E 24 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP E 29 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR E 30 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE E 33 " --> pdb=" O ASP E 29 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU E 36 " --> pdb=" O SER E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 115 removed outlier: 4.251A pdb=" N VAL E 109 " --> pdb=" O GLN E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 123 No H-bonds generated for 'chain 'E' and resid 120 through 123' Processing helix chain 'E' and resid 125 through 145 removed outlier: 3.519A pdb=" N LEU E 130 " --> pdb=" O PRO E 126 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 131 " --> pdb=" O TYR E 127 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER E 140 " --> pdb=" O PHE E 136 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N TRP E 143 " --> pdb=" O CYS E 139 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 164 removed outlier: 4.494A pdb=" N LYS E 152 " --> pdb=" O ARG E 148 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS E 162 " --> pdb=" O SER E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 173 removed outlier: 3.605A pdb=" N LEU E 173 " --> pdb=" O THR E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 253 removed outlier: 3.673A pdb=" N LYS E 246 " --> pdb=" O ALA E 242 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR E 252 " --> pdb=" O LYS E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 288 removed outlier: 3.521A pdb=" N THR E 268 " --> pdb=" O TYR E 264 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE E 270 " --> pdb=" O ARG E 266 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL E 283 " --> pdb=" O ILE E 279 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR E 284 " --> pdb=" O CYS E 280 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N HIS E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASN E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 313 through 345 removed outlier: 4.177A pdb=" N THR E 316 " --> pdb=" O PRO E 313 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE E 318 " --> pdb=" O ALA E 315 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE E 320 " --> pdb=" O LEU E 317 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALA E 322 " --> pdb=" O LYS E 319 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE E 326 " --> pdb=" O SER E 323 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE E 330 " --> pdb=" O SER E 327 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE E 331 " --> pdb=" O LEU E 328 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU E 334 " --> pdb=" O PHE E 331 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR E 339 " --> pdb=" O CYS E 336 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU E 340 " --> pdb=" O MET E 337 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP E 342 " --> pdb=" O THR E 339 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG E 345 " --> pdb=" O TRP E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 356 through 360 Processing helix chain 'E' and resid 373 through 382 removed outlier: 3.821A pdb=" N GLN E 381 " --> pdb=" O HIS E 377 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR E 382 " --> pdb=" O LEU E 378 " (cutoff:3.500A) Processing helix chain 'E' and resid 385 through 388 No H-bonds generated for 'chain 'E' and resid 385 through 388' Processing helix chain 'E' and resid 396 through 407 Processing helix chain 'F' and resid 17 through 20 Processing helix chain 'F' and resid 23 through 48 removed outlier: 4.117A pdb=" N THR F 28 " --> pdb=" O TRP F 24 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASP F 29 " --> pdb=" O ASP F 25 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N TYR F 30 " --> pdb=" O VAL F 26 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE F 33 " --> pdb=" O ASP F 29 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LEU F 36 " --> pdb=" O SER F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 115 removed outlier: 4.251A pdb=" N VAL F 109 " --> pdb=" O GLN F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 123 No H-bonds generated for 'chain 'F' and resid 120 through 123' Processing helix chain 'F' and resid 125 through 145 removed outlier: 3.518A pdb=" N LEU F 130 " --> pdb=" O PRO F 126 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU F 131 " --> pdb=" O TYR F 127 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER F 140 " --> pdb=" O PHE F 136 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N TRP F 143 " --> pdb=" O CYS F 139 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 164 removed outlier: 4.495A pdb=" N LYS F 152 " --> pdb=" O ARG F 148 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LYS F 162 " --> pdb=" O SER F 158 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 173 removed outlier: 3.604A pdb=" N LEU F 173 " --> pdb=" O THR F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 253 removed outlier: 3.673A pdb=" N LYS F 246 " --> pdb=" O ALA F 242 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR F 252 " --> pdb=" O LYS F 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 288 removed outlier: 3.521A pdb=" N THR F 268 " --> pdb=" O TYR F 264 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ILE F 270 " --> pdb=" O ARG F 266 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL F 283 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N TYR F 284 " --> pdb=" O CYS F 280 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N HIS F 287 " --> pdb=" O VAL F 283 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ASN F 288 " --> pdb=" O TYR F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 345 removed outlier: 4.177A pdb=" N THR F 316 " --> pdb=" O PRO F 313 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N PHE F 318 " --> pdb=" O ALA F 315 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE F 320 " --> pdb=" O LEU F 317 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA F 322 " --> pdb=" O LYS F 319 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE F 326 " --> pdb=" O SER F 323 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE F 330 " --> pdb=" O SER F 327 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE F 331 " --> pdb=" O LEU F 328 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU F 334 " --> pdb=" O PHE F 331 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N THR F 339 " --> pdb=" O CYS F 336 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU F 340 " --> pdb=" O MET F 337 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N TRP F 342 " --> pdb=" O THR F 339 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG F 345 " --> pdb=" O TRP F 342 " (cutoff:3.500A) Processing helix chain 'F' and resid 356 through 360 Processing helix chain 'F' and resid 373 through 382 removed outlier: 3.820A pdb=" N GLN F 381 " --> pdb=" O HIS F 377 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N TYR F 382 " --> pdb=" O LEU F 378 " (cutoff:3.500A) Processing helix chain 'F' and resid 385 through 388 No H-bonds generated for 'chain 'F' and resid 385 through 388' Processing helix chain 'F' and resid 396 through 407 Processing sheet with id= A, first strand: chain 'A' and resid 292 through 296 Processing sheet with id= B, first strand: chain 'B' and resid 292 through 296 Processing sheet with id= C, first strand: chain 'C' and resid 292 through 296 Processing sheet with id= D, first strand: chain 'D' and resid 292 through 296 Processing sheet with id= E, first strand: chain 'E' and resid 292 through 296 Processing sheet with id= F, first strand: chain 'F' and resid 292 through 296 732 hydrogen bonds defined for protein. 1800 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: 10.53 Time building geometry restraints manager: 26.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 15690 1.03 - 1.22: 42 1.22 - 1.42: 7124 1.42 - 1.61: 9150 1.61 - 1.81: 148 Bond restraints: 32154 Sorted by residual: bond pdb=" C31 POV C 901 " pdb=" O32 POV C 901 " ideal model delta sigma weight residual 1.206 1.355 -0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" C31 POV B 901 " pdb=" O32 POV B 901 " ideal model delta sigma weight residual 1.206 1.355 -0.149 2.00e-02 2.50e+03 5.53e+01 bond pdb=" C31 POV D 901 " pdb=" O32 POV D 901 " ideal model delta sigma weight residual 1.206 1.354 -0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" C31 POV F 901 " pdb=" O32 POV F 901 " ideal model delta sigma weight residual 1.206 1.354 -0.148 2.00e-02 2.50e+03 5.50e+01 bond pdb=" C31 POV E 901 " pdb=" O32 POV E 901 " ideal model delta sigma weight residual 1.206 1.354 -0.148 2.00e-02 2.50e+03 5.49e+01 ... (remaining 32149 not shown) Histogram of bond angle deviations from ideal: 91.86 - 100.93: 37 100.93 - 110.00: 25911 110.00 - 119.07: 17122 119.07 - 128.15: 14541 128.15 - 137.22: 200 Bond angle restraints: 57811 Sorted by residual: angle pdb=" C32 POV C 901 " pdb=" C31 POV C 901 " pdb=" O31 POV C 901 " ideal model delta sigma weight residual 110.66 124.80 -14.14 3.00e+00 1.11e-01 2.22e+01 angle pdb=" C32 POV B 901 " pdb=" C31 POV B 901 " pdb=" O31 POV B 901 " ideal model delta sigma weight residual 110.66 124.76 -14.10 3.00e+00 1.11e-01 2.21e+01 angle pdb=" C32 POV E 901 " pdb=" C31 POV E 901 " pdb=" O31 POV E 901 " ideal model delta sigma weight residual 110.66 124.76 -14.10 3.00e+00 1.11e-01 2.21e+01 angle pdb=" C32 POV A 901 " pdb=" C31 POV A 901 " pdb=" O31 POV A 901 " ideal model delta sigma weight residual 110.66 124.73 -14.07 3.00e+00 1.11e-01 2.20e+01 angle pdb=" C32 POV F 901 " pdb=" C31 POV F 901 " pdb=" O31 POV F 901 " ideal model delta sigma weight residual 110.66 124.72 -14.06 3.00e+00 1.11e-01 2.20e+01 ... (remaining 57806 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.60: 13201 14.60 - 29.20: 1432 29.20 - 43.80: 461 43.80 - 58.40: 161 58.40 - 73.00: 31 Dihedral angle restraints: 15286 sinusoidal: 8014 harmonic: 7272 Sorted by residual: dihedral pdb=" CA GLN C 105 " pdb=" C GLN C 105 " pdb=" N TYR C 106 " pdb=" CA TYR C 106 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA GLN B 105 " pdb=" C GLN B 105 " pdb=" N TYR B 106 " pdb=" CA TYR B 106 " ideal model delta harmonic sigma weight residual 180.00 156.60 23.40 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA GLN D 105 " pdb=" C GLN D 105 " pdb=" N TYR D 106 " pdb=" CA TYR D 106 " ideal model delta harmonic sigma weight residual 180.00 156.61 23.39 0 5.00e+00 4.00e-02 2.19e+01 ... (remaining 15283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1822 0.048 - 0.095: 477 0.095 - 0.143: 108 0.143 - 0.191: 0 0.191 - 0.238: 1 Chirality restraints: 2408 Sorted by residual: chirality pdb=" C24 L9Y A 904 " pdb=" C05 L9Y A 904 " pdb=" C25 L9Y A 904 " pdb=" C28 L9Y A 904 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE C 365 " pdb=" N ILE C 365 " pdb=" C ILE C 365 " pdb=" CB ILE C 365 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE D 365 " pdb=" N ILE D 365 " pdb=" C ILE D 365 " pdb=" CB ILE D 365 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 2405 not shown) Planarity restraints: 4479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN E 49 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.62e+00 pdb=" C GLN E 49 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN E 49 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP E 50 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN D 49 " 0.006 2.00e-02 2.50e+03 1.27e-02 1.61e+00 pdb=" C GLN D 49 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN D 49 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP D 50 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 49 " 0.006 2.00e-02 2.50e+03 1.26e-02 1.60e+00 pdb=" C GLN F 49 " -0.022 2.00e-02 2.50e+03 pdb=" O GLN F 49 " 0.008 2.00e-02 2.50e+03 pdb=" N ASP F 50 " 0.007 2.00e-02 2.50e+03 ... (remaining 4476 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.29: 5680 2.29 - 2.87: 70724 2.87 - 3.44: 79752 3.44 - 4.02: 107760 4.02 - 4.60: 164833 Nonbonded interactions: 428749 Sorted by model distance: nonbonded pdb=" O CYS A 139 " pdb="HE21 GLN A 267 " model vdw 1.711 1.850 nonbonded pdb=" O CYS E 139 " pdb="HE21 GLN E 267 " model vdw 1.712 1.850 nonbonded pdb=" O CYS B 139 " pdb="HE21 GLN B 267 " model vdw 1.712 1.850 nonbonded pdb=" O CYS D 139 " pdb="HE21 GLN D 267 " model vdw 1.712 1.850 nonbonded pdb=" O CYS C 139 " pdb="HE21 GLN C 267 " model vdw 1.712 1.850 ... (remaining 428744 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 15 through 408 or resid 901 through 903)) selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.460 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: 0.440 Extract box with map and model: 11.480 Check model and map are aligned: 0.470 Set scattering table: 0.320 Process input model: 100.080 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.150 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 119.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 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 : 0.008 0.149 16440 Z= 0.532 Angle : 0.897 14.138 22189 Z= 0.450 Chirality : 0.043 0.238 2408 Planarity : 0.003 0.027 2673 Dihedral : 13.903 72.998 6028 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.09 % Allowed : 9.97 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.71 (0.17), residues: 1842 helix: -2.99 (0.11), residues: 1134 sheet: -0.61 (0.54), residues: 96 loop : -1.19 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F 143 HIS 0.007 0.002 HIS F 377 PHE 0.015 0.002 PHE D 156 TYR 0.017 0.002 TYR D 106 ARG 0.003 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 337 time to evaluate : 2.659 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: A 50 ASP cc_start: 0.7157 (t70) cc_final: 0.6934 (t70) REVERT: A 262 ARG cc_start: 0.7705 (mmt90) cc_final: 0.7219 (mtm-85) REVERT: A 269 ILE cc_start: 0.8312 (tt) cc_final: 0.8090 (tp) REVERT: A 288 ASN cc_start: 0.8648 (OUTLIER) cc_final: 0.8440 (t0) REVERT: B 244 PHE cc_start: 0.7403 (m-80) cc_final: 0.7114 (m-80) REVERT: B 262 ARG cc_start: 0.7526 (mmt90) cc_final: 0.7252 (mtm-85) REVERT: B 269 ILE cc_start: 0.8140 (tt) cc_final: 0.7854 (tp) REVERT: B 381 GLN cc_start: 0.6533 (tp40) cc_final: 0.6310 (mm-40) REVERT: B 388 LYS cc_start: 0.6780 (tttt) cc_final: 0.6568 (tptp) REVERT: B 399 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7479 (tp30) REVERT: C 50 ASP cc_start: 0.7422 (t70) cc_final: 0.7219 (t70) REVERT: C 168 TRP cc_start: 0.7878 (t60) cc_final: 0.7573 (t60) REVERT: C 262 ARG cc_start: 0.7463 (mmt90) cc_final: 0.7116 (mtm-85) REVERT: C 269 ILE cc_start: 0.8187 (tt) cc_final: 0.7970 (tp) REVERT: C 284 TYR cc_start: 0.8470 (t80) cc_final: 0.8164 (t80) REVERT: C 377 HIS cc_start: 0.7694 (OUTLIER) cc_final: 0.6928 (m170) REVERT: C 381 GLN cc_start: 0.6858 (tp40) cc_final: 0.6597 (mm-40) REVERT: C 394 LEU cc_start: 0.8205 (tp) cc_final: 0.7817 (tp) REVERT: C 399 GLU cc_start: 0.7793 (tm-30) cc_final: 0.7471 (tp30) REVERT: D 50 ASP cc_start: 0.7029 (t70) cc_final: 0.6810 (t70) REVERT: D 168 TRP cc_start: 0.7961 (t60) cc_final: 0.7613 (t60) REVERT: D 244 PHE cc_start: 0.7257 (m-80) cc_final: 0.6640 (m-80) REVERT: D 262 ARG cc_start: 0.7620 (mmt90) cc_final: 0.7152 (mtm-85) REVERT: D 269 ILE cc_start: 0.8191 (tt) cc_final: 0.7961 (tp) REVERT: D 288 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8347 (t0) REVERT: D 381 GLN cc_start: 0.6640 (tp40) cc_final: 0.6334 (mm110) REVERT: E 244 PHE cc_start: 0.7411 (m-80) cc_final: 0.6990 (m-80) REVERT: E 262 ARG cc_start: 0.7587 (mmt90) cc_final: 0.7286 (mtm-85) REVERT: E 269 ILE cc_start: 0.8188 (tt) cc_final: 0.7902 (tp) REVERT: E 381 GLN cc_start: 0.6593 (tp40) cc_final: 0.6367 (mm-40) REVERT: E 399 GLU cc_start: 0.7856 (tm-30) cc_final: 0.7485 (tp30) REVERT: F 50 ASP cc_start: 0.7409 (t70) cc_final: 0.7204 (t70) REVERT: F 168 TRP cc_start: 0.7911 (t60) cc_final: 0.7555 (t60) REVERT: F 262 ARG cc_start: 0.7331 (mmt90) cc_final: 0.6971 (mtm-85) REVERT: F 284 TYR cc_start: 0.8409 (t80) cc_final: 0.8129 (t80) REVERT: F 377 HIS cc_start: 0.7649 (OUTLIER) cc_final: 0.6960 (m170) REVERT: F 381 GLN cc_start: 0.6907 (tp40) cc_final: 0.6638 (mm110) REVERT: F 394 LEU cc_start: 0.8354 (tp) cc_final: 0.7974 (tp) REVERT: F 399 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7439 (tp30) REVERT: F 402 LEU cc_start: 0.8135 (tp) cc_final: 0.7906 (tp) outliers start: 54 outliers final: 22 residues processed: 391 average time/residue: 0.6691 time to fit residues: 376.1843 Evaluate side-chains 280 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 254 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 377 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 0.9990 chunk 140 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 145 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 108 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS B 253 HIS B 288 ASN C 253 HIS D 253 HIS E 253 HIS E 288 ASN F 253 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16440 Z= 0.249 Angle : 0.559 5.125 22189 Z= 0.310 Chirality : 0.037 0.118 2408 Planarity : 0.004 0.023 2673 Dihedral : 8.412 52.752 2302 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.98 % Allowed : 12.54 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.18), residues: 1842 helix: -1.49 (0.13), residues: 1242 sheet: -0.75 (0.50), residues: 96 loop : -1.86 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 143 HIS 0.008 0.002 HIS F 253 PHE 0.011 0.001 PHE C 244 TYR 0.012 0.001 TYR B 281 ARG 0.003 0.000 ARG F 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 269 time to evaluate : 2.749 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: A 262 ARG cc_start: 0.7913 (mmt90) cc_final: 0.7404 (mtm-85) REVERT: A 288 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8515 (t0) REVERT: A 377 HIS cc_start: 0.7460 (OUTLIER) cc_final: 0.7202 (m170) REVERT: B 154 GLU cc_start: 0.7613 (pt0) cc_final: 0.7374 (pt0) REVERT: B 262 ARG cc_start: 0.7891 (mmt90) cc_final: 0.7510 (mtm-85) REVERT: B 284 TYR cc_start: 0.8605 (t80) cc_final: 0.8401 (t80) REVERT: B 377 HIS cc_start: 0.7389 (OUTLIER) cc_final: 0.7091 (m170) REVERT: B 388 LYS cc_start: 0.6789 (tttt) cc_final: 0.6568 (tptp) REVERT: B 399 GLU cc_start: 0.7728 (tm-30) cc_final: 0.7300 (tp30) REVERT: C 262 ARG cc_start: 0.7854 (mmt90) cc_final: 0.7586 (mtp180) REVERT: C 284 TYR cc_start: 0.8593 (t80) cc_final: 0.8338 (t80) REVERT: C 377 HIS cc_start: 0.7366 (OUTLIER) cc_final: 0.7039 (m170) REVERT: C 394 LEU cc_start: 0.8154 (tp) cc_final: 0.7887 (tp) REVERT: C 399 GLU cc_start: 0.7717 (tm-30) cc_final: 0.7399 (tp30) REVERT: D 262 ARG cc_start: 0.7957 (mmt90) cc_final: 0.7399 (mtm-85) REVERT: D 288 ASN cc_start: 0.8759 (OUTLIER) cc_final: 0.8489 (t0) REVERT: D 325 TYR cc_start: 0.8204 (t80) cc_final: 0.7958 (t80) REVERT: D 375 MET cc_start: 0.7738 (mtm) cc_final: 0.7472 (mtm) REVERT: D 381 GLN cc_start: 0.6845 (tp40) cc_final: 0.6490 (mm110) REVERT: D 399 GLU cc_start: 0.7661 (tp30) cc_final: 0.7431 (tp30) REVERT: E 154 GLU cc_start: 0.7552 (pt0) cc_final: 0.7301 (pt0) REVERT: E 244 PHE cc_start: 0.7108 (m-80) cc_final: 0.6696 (m-80) REVERT: E 262 ARG cc_start: 0.7893 (mmt90) cc_final: 0.7498 (mtm-85) REVERT: E 377 HIS cc_start: 0.7420 (OUTLIER) cc_final: 0.7104 (m170) REVERT: E 399 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7586 (tp30) REVERT: F 168 TRP cc_start: 0.7800 (t60) cc_final: 0.7571 (t60) REVERT: F 262 ARG cc_start: 0.7734 (mmt90) cc_final: 0.7436 (mtp180) REVERT: F 284 TYR cc_start: 0.8588 (t80) cc_final: 0.8365 (t80) REVERT: F 377 HIS cc_start: 0.7383 (OUTLIER) cc_final: 0.7057 (m170) REVERT: F 394 LEU cc_start: 0.8235 (tp) cc_final: 0.7884 (tp) REVERT: F 399 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7410 (tp30) outliers start: 52 outliers final: 28 residues processed: 316 average time/residue: 0.5906 time to fit residues: 277.0042 Evaluate side-chains 273 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 238 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 253 HIS Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 301 SER Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 377 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 169 optimal weight: 6.9990 chunk 182 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 135 optimal weight: 0.5980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 16440 Z= 0.308 Angle : 0.557 4.715 22189 Z= 0.307 Chirality : 0.038 0.127 2408 Planarity : 0.003 0.017 2673 Dihedral : 8.285 59.944 2292 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 3.04 % Allowed : 16.15 % 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: -2.19 (0.18), residues: 1842 helix: -1.19 (0.13), residues: 1260 sheet: -0.73 (0.51), residues: 96 loop : -1.83 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 143 HIS 0.004 0.001 HIS E 377 PHE 0.016 0.002 PHE A 244 TYR 0.012 0.001 TYR E 338 ARG 0.002 0.000 ARG F 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 261 time to evaluate : 2.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8065 (m) REVERT: A 154 GLU cc_start: 0.7432 (pt0) cc_final: 0.7178 (pt0) REVERT: A 168 TRP cc_start: 0.7894 (t60) cc_final: 0.7599 (t60) REVERT: A 245 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7748 (mp0) REVERT: A 248 LYS cc_start: 0.8615 (tptm) cc_final: 0.8343 (mtpt) REVERT: A 262 ARG cc_start: 0.8005 (mmt90) cc_final: 0.7443 (mtm-85) REVERT: A 359 GLU cc_start: 0.7297 (tp30) cc_final: 0.6986 (tm-30) REVERT: A 377 HIS cc_start: 0.7387 (OUTLIER) cc_final: 0.6899 (m170) REVERT: A 399 GLU cc_start: 0.7649 (tp30) cc_final: 0.7389 (tp30) REVERT: B 129 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8140 (m) REVERT: B 154 GLU cc_start: 0.7481 (pt0) cc_final: 0.7128 (pt0) REVERT: B 155 HIS cc_start: 0.7262 (t-170) cc_final: 0.6759 (m-70) REVERT: B 168 TRP cc_start: 0.7986 (t60) cc_final: 0.7724 (t60) REVERT: B 248 LYS cc_start: 0.8671 (tptm) cc_final: 0.8360 (mtpt) REVERT: B 262 ARG cc_start: 0.7915 (mmt90) cc_final: 0.7553 (mtm-85) REVERT: B 377 HIS cc_start: 0.7454 (OUTLIER) cc_final: 0.7186 (m170) REVERT: B 382 TYR cc_start: 0.7864 (t80) cc_final: 0.7624 (t80) REVERT: B 399 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7412 (tp30) REVERT: C 168 TRP cc_start: 0.7906 (t60) cc_final: 0.7673 (t60) REVERT: C 262 ARG cc_start: 0.7931 (mmt90) cc_final: 0.7611 (mtp180) REVERT: C 284 TYR cc_start: 0.8655 (t80) cc_final: 0.8416 (t80) REVERT: C 288 ASN cc_start: 0.8607 (t0) cc_final: 0.8231 (m-40) REVERT: C 359 GLU cc_start: 0.7513 (tp30) cc_final: 0.6929 (tp30) REVERT: C 377 HIS cc_start: 0.7399 (OUTLIER) cc_final: 0.7027 (m170) REVERT: C 399 GLU cc_start: 0.7666 (tm-30) cc_final: 0.7388 (tp30) REVERT: D 129 VAL cc_start: 0.8398 (OUTLIER) cc_final: 0.8052 (m) REVERT: D 154 GLU cc_start: 0.7524 (pt0) cc_final: 0.7243 (pt0) REVERT: D 155 HIS cc_start: 0.7190 (t-170) cc_final: 0.6780 (m-70) REVERT: D 168 TRP cc_start: 0.7921 (t60) cc_final: 0.7631 (t60) REVERT: D 248 LYS cc_start: 0.8591 (tptm) cc_final: 0.8325 (mtpt) REVERT: D 262 ARG cc_start: 0.8013 (mmt90) cc_final: 0.7444 (mtm-85) REVERT: D 399 GLU cc_start: 0.7706 (tp30) cc_final: 0.7461 (tp30) REVERT: E 129 VAL cc_start: 0.8458 (OUTLIER) cc_final: 0.8141 (m) REVERT: E 154 GLU cc_start: 0.7475 (pt0) cc_final: 0.7132 (pt0) REVERT: E 155 HIS cc_start: 0.7254 (t-170) cc_final: 0.6732 (m-70) REVERT: E 168 TRP cc_start: 0.7985 (t60) cc_final: 0.7727 (t60) REVERT: E 248 LYS cc_start: 0.8662 (tptm) cc_final: 0.8338 (mtpt) REVERT: E 262 ARG cc_start: 0.7937 (mmt90) cc_final: 0.7565 (mtm-85) REVERT: E 377 HIS cc_start: 0.7485 (OUTLIER) cc_final: 0.7212 (m170) REVERT: E 399 GLU cc_start: 0.7730 (tm-30) cc_final: 0.7331 (tp30) REVERT: F 168 TRP cc_start: 0.7844 (t60) cc_final: 0.7573 (t60) REVERT: F 262 ARG cc_start: 0.7825 (mmt90) cc_final: 0.7575 (mtp180) REVERT: F 284 TYR cc_start: 0.8623 (t80) cc_final: 0.8420 (t80) REVERT: F 288 ASN cc_start: 0.8607 (t0) cc_final: 0.8239 (m-40) REVERT: F 319 LYS cc_start: 0.8839 (ttmt) cc_final: 0.8544 (ttmt) REVERT: F 377 HIS cc_start: 0.7463 (OUTLIER) cc_final: 0.7080 (m170) REVERT: F 394 LEU cc_start: 0.8183 (tp) cc_final: 0.7902 (tp) REVERT: F 399 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7421 (tp30) outliers start: 53 outliers final: 31 residues processed: 303 average time/residue: 0.6771 time to fit residues: 307.9769 Evaluate side-chains 291 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 251 time to evaluate : 2.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 133 THR Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 270 ILE Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 377 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 1.9990 chunk 127 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 80 optimal weight: 0.5980 chunk 113 optimal weight: 0.9990 chunk 169 optimal weight: 3.9990 chunk 179 optimal weight: 0.9980 chunk 88 optimal weight: 0.2980 chunk 160 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16440 Z= 0.171 Angle : 0.487 4.479 22189 Z= 0.265 Chirality : 0.035 0.126 2408 Planarity : 0.002 0.020 2673 Dihedral : 7.786 57.202 2292 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.23 % Allowed : 18.10 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.19), residues: 1842 helix: -0.68 (0.14), residues: 1212 sheet: -0.64 (0.50), residues: 96 loop : -1.54 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 143 HIS 0.004 0.001 HIS C 377 PHE 0.015 0.001 PHE A 244 TYR 0.009 0.001 TYR B 338 ARG 0.002 0.000 ARG F 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 277 time to evaluate : 2.491 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: A 245 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7440 (mp0) REVERT: A 262 ARG cc_start: 0.7975 (mmt90) cc_final: 0.7419 (mtm-85) REVERT: A 377 HIS cc_start: 0.7295 (OUTLIER) cc_final: 0.6908 (m170) REVERT: A 399 GLU cc_start: 0.7665 (tp30) cc_final: 0.7410 (tp30) REVERT: B 154 GLU cc_start: 0.7418 (pt0) cc_final: 0.7123 (pt0) REVERT: B 155 HIS cc_start: 0.7261 (t-170) cc_final: 0.6790 (m-70) REVERT: B 168 TRP cc_start: 0.7941 (t60) cc_final: 0.7664 (t60) REVERT: B 248 LYS cc_start: 0.8637 (tptm) cc_final: 0.8346 (mtpt) REVERT: B 262 ARG cc_start: 0.7881 (mmt90) cc_final: 0.7526 (mtm-85) REVERT: B 382 TYR cc_start: 0.7815 (t80) cc_final: 0.7583 (t80) REVERT: B 399 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7374 (tp30) REVERT: C 168 TRP cc_start: 0.7910 (t60) cc_final: 0.7668 (t60) REVERT: C 262 ARG cc_start: 0.7910 (mmt90) cc_final: 0.7564 (mtp180) REVERT: C 284 TYR cc_start: 0.8609 (t80) cc_final: 0.8393 (t80) REVERT: C 288 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8231 (m-40) REVERT: C 377 HIS cc_start: 0.7223 (OUTLIER) cc_final: 0.6880 (m170) REVERT: C 399 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7371 (tp30) REVERT: D 154 GLU cc_start: 0.7491 (pt0) cc_final: 0.7170 (pt0) REVERT: D 155 HIS cc_start: 0.7249 (t-170) cc_final: 0.6798 (m-70) REVERT: D 168 TRP cc_start: 0.7860 (t60) cc_final: 0.7581 (t60) REVERT: D 248 LYS cc_start: 0.8633 (tptm) cc_final: 0.8349 (mtpt) REVERT: D 262 ARG cc_start: 0.7993 (mmt90) cc_final: 0.7422 (mtm-85) REVERT: E 154 GLU cc_start: 0.7345 (pt0) cc_final: 0.7052 (pt0) REVERT: E 155 HIS cc_start: 0.7336 (t-170) cc_final: 0.6815 (m-70) REVERT: E 168 TRP cc_start: 0.7961 (t60) cc_final: 0.7693 (t60) REVERT: E 248 LYS cc_start: 0.8627 (tptm) cc_final: 0.8357 (mtpt) REVERT: E 262 ARG cc_start: 0.7873 (mmt90) cc_final: 0.7487 (mtm-85) REVERT: E 377 HIS cc_start: 0.7387 (OUTLIER) cc_final: 0.7144 (m170) REVERT: E 394 LEU cc_start: 0.8395 (tp) cc_final: 0.8064 (tp) REVERT: E 399 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7397 (tp30) REVERT: F 168 TRP cc_start: 0.7834 (t60) cc_final: 0.7546 (t60) REVERT: F 262 ARG cc_start: 0.7816 (mmt90) cc_final: 0.7451 (mtp180) REVERT: F 288 ASN cc_start: 0.8566 (OUTLIER) cc_final: 0.8215 (m-40) REVERT: F 319 LYS cc_start: 0.8799 (ttmt) cc_final: 0.8512 (ttmt) REVERT: F 359 GLU cc_start: 0.7362 (tp30) cc_final: 0.6779 (tp30) REVERT: F 377 HIS cc_start: 0.7224 (OUTLIER) cc_final: 0.6893 (m170) REVERT: F 394 LEU cc_start: 0.8204 (tp) cc_final: 0.7815 (tp) REVERT: F 399 GLU cc_start: 0.7671 (tm-30) cc_final: 0.7372 (tp30) outliers start: 39 outliers final: 28 residues processed: 312 average time/residue: 0.6371 time to fit residues: 302.5765 Evaluate side-chains 285 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 251 time to evaluate : 2.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 270 ILE Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 133 THR Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 329 VAL Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 270 ILE Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 288 ASN Chi-restraints excluded: chain F residue 329 VAL Chi-restraints excluded: chain F residue 377 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 2 optimal weight: 0.1980 chunk 133 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 153 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 161 optimal weight: 0.0980 chunk 45 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16440 Z= 0.177 Angle : 0.481 4.442 22189 Z= 0.263 Chirality : 0.036 0.121 2408 Planarity : 0.002 0.019 2673 Dihedral : 7.471 56.385 2286 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.46 % Allowed : 18.96 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.19), residues: 1842 helix: -0.43 (0.15), residues: 1212 sheet: -0.62 (0.49), residues: 96 loop : -1.45 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 143 HIS 0.005 0.001 HIS B 377 PHE 0.016 0.001 PHE A 244 TYR 0.013 0.001 TYR A 332 ARG 0.001 0.000 ARG F 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 269 time to evaluate : 2.574 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: A 154 GLU cc_start: 0.7546 (pt0) cc_final: 0.7155 (pt0) REVERT: A 168 TRP cc_start: 0.7879 (t60) cc_final: 0.7562 (t60) REVERT: A 262 ARG cc_start: 0.7976 (mmt90) cc_final: 0.7421 (mtm-85) REVERT: A 289 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8445 (pt) REVERT: A 399 GLU cc_start: 0.7789 (tp30) cc_final: 0.7558 (tp30) REVERT: B 154 GLU cc_start: 0.7381 (pt0) cc_final: 0.7105 (pt0) REVERT: B 155 HIS cc_start: 0.7301 (t-170) cc_final: 0.6815 (m-70) REVERT: B 168 TRP cc_start: 0.7961 (t60) cc_final: 0.7671 (t60) REVERT: B 248 LYS cc_start: 0.8634 (tptm) cc_final: 0.8330 (mtpt) REVERT: B 262 ARG cc_start: 0.7872 (mmt90) cc_final: 0.7481 (mtm-85) REVERT: B 382 TYR cc_start: 0.7807 (t80) cc_final: 0.7482 (t80) REVERT: B 399 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7375 (tp30) REVERT: C 168 TRP cc_start: 0.7957 (t60) cc_final: 0.7667 (t60) REVERT: C 262 ARG cc_start: 0.7892 (mmt90) cc_final: 0.7575 (mtp180) REVERT: C 284 TYR cc_start: 0.8621 (t80) cc_final: 0.8411 (t80) REVERT: C 376 LEU cc_start: 0.6293 (OUTLIER) cc_final: 0.6004 (tm) REVERT: C 377 HIS cc_start: 0.7209 (OUTLIER) cc_final: 0.6818 (m170) REVERT: C 399 GLU cc_start: 0.7690 (tm-30) cc_final: 0.7431 (tp30) REVERT: D 154 GLU cc_start: 0.7492 (pt0) cc_final: 0.7152 (pt0) REVERT: D 155 HIS cc_start: 0.7239 (t-170) cc_final: 0.6798 (m-70) REVERT: D 248 LYS cc_start: 0.8622 (tptm) cc_final: 0.8339 (mtpt) REVERT: D 262 ARG cc_start: 0.7986 (mmt90) cc_final: 0.7447 (mtm-85) REVERT: D 289 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8409 (pt) REVERT: D 359 GLU cc_start: 0.7180 (tp30) cc_final: 0.6592 (pm20) REVERT: E 154 GLU cc_start: 0.7310 (pt0) cc_final: 0.7035 (pt0) REVERT: E 155 HIS cc_start: 0.7308 (t-170) cc_final: 0.6815 (m-70) REVERT: E 168 TRP cc_start: 0.7955 (t60) cc_final: 0.7665 (t60) REVERT: E 248 LYS cc_start: 0.8604 (tptm) cc_final: 0.8352 (mtpt) REVERT: E 262 ARG cc_start: 0.7875 (mmt90) cc_final: 0.7505 (mtm-85) REVERT: E 399 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7418 (tp30) REVERT: F 168 TRP cc_start: 0.7842 (t60) cc_final: 0.7531 (t60) REVERT: F 262 ARG cc_start: 0.7812 (mmt90) cc_final: 0.7469 (mtp180) REVERT: F 319 LYS cc_start: 0.8795 (ttmt) cc_final: 0.8515 (ttmt) REVERT: F 359 GLU cc_start: 0.7362 (tp30) cc_final: 0.6781 (tp30) REVERT: F 376 LEU cc_start: 0.6281 (OUTLIER) cc_final: 0.6004 (tm) REVERT: F 377 HIS cc_start: 0.7246 (OUTLIER) cc_final: 0.6831 (m170) REVERT: F 399 GLU cc_start: 0.7618 (tm-30) cc_final: 0.7365 (tp30) outliers start: 43 outliers final: 27 residues processed: 309 average time/residue: 0.6132 time to fit residues: 281.9268 Evaluate side-chains 289 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 256 time to evaluate : 2.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 288 ASN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 288 ASN Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 377 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 2.9990 chunk 161 optimal weight: 0.5980 chunk 35 optimal weight: 0.0980 chunk 105 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 179 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16440 Z= 0.177 Angle : 0.475 4.347 22189 Z= 0.259 Chirality : 0.036 0.124 2408 Planarity : 0.002 0.019 2673 Dihedral : 7.186 56.108 2278 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.86 % Allowed : 18.38 % Favored : 78.75 % 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: -0.95 (0.20), residues: 1842 helix: -0.19 (0.15), residues: 1212 sheet: -0.60 (0.49), residues: 96 loop : -1.37 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 143 HIS 0.004 0.001 HIS C 377 PHE 0.017 0.001 PHE A 244 TYR 0.011 0.001 TYR A 332 ARG 0.001 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 269 time to evaluate : 2.730 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: A 154 GLU cc_start: 0.7530 (pt0) cc_final: 0.7088 (pt0) REVERT: A 168 TRP cc_start: 0.7900 (t60) cc_final: 0.7582 (t60) REVERT: A 248 LYS cc_start: 0.8612 (tptm) cc_final: 0.8340 (mtpt) REVERT: A 262 ARG cc_start: 0.7973 (mmt90) cc_final: 0.7420 (mtm-85) REVERT: A 289 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8446 (pt) REVERT: B 154 GLU cc_start: 0.7295 (pt0) cc_final: 0.7020 (pt0) REVERT: B 155 HIS cc_start: 0.7351 (t-170) cc_final: 0.6855 (m-70) REVERT: B 168 TRP cc_start: 0.7956 (t60) cc_final: 0.7640 (t60) REVERT: B 248 LYS cc_start: 0.8606 (tptm) cc_final: 0.8359 (mtpt) REVERT: B 262 ARG cc_start: 0.7869 (mmt90) cc_final: 0.7509 (mtm-85) REVERT: B 382 TYR cc_start: 0.7803 (t80) cc_final: 0.7450 (t80) REVERT: B 399 GLU cc_start: 0.7754 (tm-30) cc_final: 0.7458 (tp30) REVERT: C 168 TRP cc_start: 0.7974 (t60) cc_final: 0.7657 (t60) REVERT: C 262 ARG cc_start: 0.7895 (mmt90) cc_final: 0.7592 (mtp180) REVERT: C 359 GLU cc_start: 0.7443 (tp30) cc_final: 0.6928 (tp30) REVERT: C 376 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.6068 (tm) REVERT: C 377 HIS cc_start: 0.7196 (OUTLIER) cc_final: 0.6836 (m170) REVERT: C 399 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7435 (tp30) REVERT: D 154 GLU cc_start: 0.7479 (pt0) cc_final: 0.7054 (pt0) REVERT: D 155 HIS cc_start: 0.7281 (t-170) cc_final: 0.6695 (m-70) REVERT: D 168 TRP cc_start: 0.7920 (t60) cc_final: 0.7568 (t60) REVERT: D 248 LYS cc_start: 0.8599 (tptm) cc_final: 0.8342 (mtpt) REVERT: D 262 ARG cc_start: 0.7997 (mmt90) cc_final: 0.7460 (mtm-85) REVERT: D 289 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8422 (pt) REVERT: D 359 GLU cc_start: 0.7178 (tp30) cc_final: 0.6897 (tm-30) REVERT: D 377 HIS cc_start: 0.7200 (OUTLIER) cc_final: 0.6726 (m170) REVERT: E 154 GLU cc_start: 0.7297 (pt0) cc_final: 0.7025 (pt0) REVERT: E 155 HIS cc_start: 0.7347 (t-170) cc_final: 0.6836 (m-70) REVERT: E 248 LYS cc_start: 0.8602 (tptm) cc_final: 0.8351 (mtpt) REVERT: E 262 ARG cc_start: 0.7846 (mmt90) cc_final: 0.7496 (mtm-85) REVERT: F 154 GLU cc_start: 0.7560 (tp30) cc_final: 0.7356 (tp30) REVERT: F 262 ARG cc_start: 0.7829 (mmt90) cc_final: 0.7472 (mtp180) REVERT: F 319 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8402 (ttmt) REVERT: F 376 LEU cc_start: 0.6285 (OUTLIER) cc_final: 0.6033 (tm) REVERT: F 377 HIS cc_start: 0.7192 (OUTLIER) cc_final: 0.6797 (m170) REVERT: F 399 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7346 (tp30) outliers start: 50 outliers final: 30 residues processed: 316 average time/residue: 0.5895 time to fit residues: 279.9665 Evaluate side-chains 291 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 254 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 133 THR Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 376 LEU Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 376 LEU Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 377 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 0.9980 chunk 20 optimal weight: 0.0870 chunk 102 optimal weight: 0.9990 chunk 131 optimal weight: 0.9990 chunk 101 optimal weight: 0.2980 chunk 151 optimal weight: 2.9990 chunk 100 optimal weight: 0.3980 chunk 179 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 288 ASN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 288 ASN ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 16440 Z= 0.138 Angle : 0.458 4.446 22189 Z= 0.248 Chirality : 0.035 0.125 2408 Planarity : 0.002 0.021 2673 Dihedral : 6.841 56.239 2274 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.41 % Allowed : 19.64 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.20), residues: 1842 helix: 0.10 (0.15), residues: 1212 sheet: -0.41 (0.47), residues: 96 loop : -1.30 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 143 HIS 0.004 0.001 HIS B 377 PHE 0.009 0.001 PHE D 244 TYR 0.009 0.001 TYR F 332 ARG 0.001 0.000 ARG B 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 280 time to evaluate : 2.359 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: A 154 GLU cc_start: 0.7549 (pt0) cc_final: 0.7248 (pt0) REVERT: A 248 LYS cc_start: 0.8604 (tptm) cc_final: 0.8341 (mtpt) REVERT: A 262 ARG cc_start: 0.7931 (mmt90) cc_final: 0.7414 (mtm-85) REVERT: A 288 ASN cc_start: 0.8696 (t160) cc_final: 0.8345 (m-40) REVERT: A 359 GLU cc_start: 0.7170 (tp30) cc_final: 0.6935 (tm-30) REVERT: B 154 GLU cc_start: 0.7274 (pt0) cc_final: 0.7002 (pt0) REVERT: B 155 HIS cc_start: 0.7309 (t-170) cc_final: 0.6845 (m-70) REVERT: B 248 LYS cc_start: 0.8602 (tptm) cc_final: 0.8358 (mtpt) REVERT: B 262 ARG cc_start: 0.7786 (mmt90) cc_final: 0.7444 (mtm-85) REVERT: B 399 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7440 (tp30) REVERT: C 262 ARG cc_start: 0.7917 (mmt90) cc_final: 0.7564 (mtp180) REVERT: C 359 GLU cc_start: 0.7433 (tp30) cc_final: 0.6811 (pm20) REVERT: C 376 LEU cc_start: 0.6194 (OUTLIER) cc_final: 0.5981 (tm) REVERT: C 377 HIS cc_start: 0.7183 (OUTLIER) cc_final: 0.6804 (m170) REVERT: C 399 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7399 (tp30) REVERT: D 154 GLU cc_start: 0.7453 (pt0) cc_final: 0.7016 (pt0) REVERT: D 155 HIS cc_start: 0.7295 (t-170) cc_final: 0.6740 (m-70) REVERT: D 248 LYS cc_start: 0.8596 (tptm) cc_final: 0.8344 (mtpt) REVERT: D 262 ARG cc_start: 0.7902 (mmt90) cc_final: 0.7403 (mtm-85) REVERT: D 288 ASN cc_start: 0.8690 (t160) cc_final: 0.8326 (m-40) REVERT: D 289 ILE cc_start: 0.8646 (OUTLIER) cc_final: 0.8382 (pt) REVERT: D 359 GLU cc_start: 0.7137 (tp30) cc_final: 0.6593 (pm20) REVERT: D 377 HIS cc_start: 0.7033 (OUTLIER) cc_final: 0.6565 (m170) REVERT: E 154 GLU cc_start: 0.7218 (pt0) cc_final: 0.6950 (pt0) REVERT: E 155 HIS cc_start: 0.7305 (t-170) cc_final: 0.6771 (m-70) REVERT: E 248 LYS cc_start: 0.8596 (tptm) cc_final: 0.8352 (mtpt) REVERT: E 262 ARG cc_start: 0.7802 (mmt90) cc_final: 0.7378 (mtm-85) REVERT: F 154 GLU cc_start: 0.7655 (tp30) cc_final: 0.7448 (tp30) REVERT: F 262 ARG cc_start: 0.7798 (mmt90) cc_final: 0.7457 (mtp180) REVERT: F 319 LYS cc_start: 0.8695 (ttmt) cc_final: 0.8367 (ttmt) REVERT: F 376 LEU cc_start: 0.6180 (OUTLIER) cc_final: 0.5954 (tm) REVERT: F 377 HIS cc_start: 0.7192 (OUTLIER) cc_final: 0.6822 (m170) REVERT: F 399 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7317 (tp30) outliers start: 42 outliers final: 29 residues processed: 318 average time/residue: 0.5940 time to fit residues: 285.0512 Evaluate side-chains 288 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 253 time to evaluate : 2.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 377 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 107 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 34 optimal weight: 0.2980 chunk 113 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16440 Z= 0.208 Angle : 0.486 5.265 22189 Z= 0.264 Chirality : 0.036 0.136 2408 Planarity : 0.002 0.017 2673 Dihedral : 6.989 57.558 2274 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.86 % Allowed : 19.07 % Favored : 78.06 % 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: -0.56 (0.20), residues: 1842 helix: 0.15 (0.15), residues: 1212 sheet: -0.28 (0.48), residues: 96 loop : -1.37 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 143 HIS 0.004 0.001 HIS D 377 PHE 0.012 0.001 PHE A 374 TYR 0.011 0.001 TYR C 284 ARG 0.002 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 266 time to evaluate : 2.440 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: A 154 GLU cc_start: 0.7584 (pt0) cc_final: 0.7260 (pt0) REVERT: A 155 HIS cc_start: 0.7299 (t-170) cc_final: 0.6728 (m-70) REVERT: A 248 LYS cc_start: 0.8601 (tptm) cc_final: 0.8338 (mtpt) REVERT: A 262 ARG cc_start: 0.7959 (mmt90) cc_final: 0.7437 (mtm-85) REVERT: A 289 ILE cc_start: 0.8739 (OUTLIER) cc_final: 0.8452 (pt) REVERT: A 359 GLU cc_start: 0.7292 (tp30) cc_final: 0.6950 (tm-30) REVERT: A 376 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5814 (tm) REVERT: A 377 HIS cc_start: 0.7175 (OUTLIER) cc_final: 0.6653 (m170) REVERT: B 154 GLU cc_start: 0.7314 (pt0) cc_final: 0.7057 (pt0) REVERT: B 155 HIS cc_start: 0.7336 (t-170) cc_final: 0.6865 (m-70) REVERT: B 168 TRP cc_start: 0.7978 (t60) cc_final: 0.7646 (t60) REVERT: B 248 LYS cc_start: 0.8573 (tptm) cc_final: 0.8327 (mtpt) REVERT: B 262 ARG cc_start: 0.7845 (mmt90) cc_final: 0.7507 (mtm-85) REVERT: C 262 ARG cc_start: 0.7949 (mmt90) cc_final: 0.7647 (mtp180) REVERT: C 359 GLU cc_start: 0.7411 (tp30) cc_final: 0.6752 (pm20) REVERT: C 376 LEU cc_start: 0.6317 (OUTLIER) cc_final: 0.6057 (tm) REVERT: C 377 HIS cc_start: 0.7216 (OUTLIER) cc_final: 0.6766 (m170) REVERT: C 399 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7392 (tp30) REVERT: D 154 GLU cc_start: 0.7447 (pt0) cc_final: 0.7016 (pt0) REVERT: D 155 HIS cc_start: 0.7328 (t-170) cc_final: 0.6764 (m-70) REVERT: D 248 LYS cc_start: 0.8594 (tptm) cc_final: 0.8314 (mtpt) REVERT: D 262 ARG cc_start: 0.8010 (mmt90) cc_final: 0.7480 (mtm-85) REVERT: D 289 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8463 (pt) REVERT: D 377 HIS cc_start: 0.7217 (OUTLIER) cc_final: 0.6727 (m170) REVERT: E 154 GLU cc_start: 0.7244 (pt0) cc_final: 0.6985 (pt0) REVERT: E 155 HIS cc_start: 0.7331 (t-170) cc_final: 0.6794 (m-70) REVERT: E 262 ARG cc_start: 0.7878 (mmt90) cc_final: 0.7512 (mtm-85) REVERT: F 262 ARG cc_start: 0.7859 (mmt90) cc_final: 0.7589 (mtp180) REVERT: F 319 LYS cc_start: 0.8709 (ttmt) cc_final: 0.8405 (tttp) REVERT: F 376 LEU cc_start: 0.6313 (OUTLIER) cc_final: 0.6047 (tm) REVERT: F 377 HIS cc_start: 0.7223 (OUTLIER) cc_final: 0.6775 (m170) REVERT: F 399 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7362 (tp30) outliers start: 50 outliers final: 38 residues processed: 313 average time/residue: 0.5877 time to fit residues: 274.6509 Evaluate side-chains 303 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 256 time to evaluate : 2.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain B residue 377 HIS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 293 VAL Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 57 CYS Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 377 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 158 optimal weight: 0.6980 chunk 166 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16440 Z= 0.202 Angle : 0.485 4.515 22189 Z= 0.263 Chirality : 0.036 0.126 2408 Planarity : 0.002 0.018 2673 Dihedral : 7.050 56.830 2274 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.98 % Allowed : 19.19 % Favored : 77.84 % 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: -0.44 (0.20), residues: 1842 helix: 0.24 (0.16), residues: 1212 sheet: -0.19 (0.49), residues: 96 loop : -1.36 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 143 HIS 0.004 0.001 HIS D 377 PHE 0.011 0.001 PHE C 374 TYR 0.011 0.001 TYR C 284 ARG 0.001 0.000 ARG A 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 266 time to evaluate : 2.573 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: A 154 GLU cc_start: 0.7595 (pt0) cc_final: 0.7249 (pt0) REVERT: A 155 HIS cc_start: 0.7316 (t-170) cc_final: 0.6730 (m-70) REVERT: A 248 LYS cc_start: 0.8604 (tptm) cc_final: 0.8321 (mtpt) REVERT: A 262 ARG cc_start: 0.7966 (mmt90) cc_final: 0.7439 (mtm-85) REVERT: A 289 ILE cc_start: 0.8728 (OUTLIER) cc_final: 0.8434 (pt) REVERT: A 377 HIS cc_start: 0.7231 (OUTLIER) cc_final: 0.6743 (m170) REVERT: B 154 GLU cc_start: 0.7332 (pt0) cc_final: 0.7068 (pt0) REVERT: B 155 HIS cc_start: 0.7335 (t-170) cc_final: 0.6862 (m-70) REVERT: B 262 ARG cc_start: 0.7838 (mmt90) cc_final: 0.7509 (mtm-85) REVERT: C 262 ARG cc_start: 0.7941 (mmt90) cc_final: 0.7633 (mtp180) REVERT: C 376 LEU cc_start: 0.6285 (OUTLIER) cc_final: 0.6029 (tm) REVERT: C 377 HIS cc_start: 0.7200 (OUTLIER) cc_final: 0.6606 (m170) REVERT: C 399 GLU cc_start: 0.7675 (tm-30) cc_final: 0.7407 (tp30) REVERT: D 154 GLU cc_start: 0.7423 (pt0) cc_final: 0.6973 (pt0) REVERT: D 155 HIS cc_start: 0.7340 (t-170) cc_final: 0.6771 (m-70) REVERT: D 248 LYS cc_start: 0.8592 (tptm) cc_final: 0.8314 (mtpt) REVERT: D 262 ARG cc_start: 0.8020 (mmt90) cc_final: 0.7478 (mtm-85) REVERT: D 288 ASN cc_start: 0.8756 (t160) cc_final: 0.8380 (m-40) REVERT: D 289 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8439 (pt) REVERT: D 359 GLU cc_start: 0.7183 (tp30) cc_final: 0.6915 (tm-30) REVERT: D 377 HIS cc_start: 0.7147 (OUTLIER) cc_final: 0.6603 (m170) REVERT: E 154 GLU cc_start: 0.7244 (pt0) cc_final: 0.6985 (pt0) REVERT: E 155 HIS cc_start: 0.7367 (t-170) cc_final: 0.6812 (m-70) REVERT: E 262 ARG cc_start: 0.7871 (mmt90) cc_final: 0.7513 (mtm-85) REVERT: F 155 HIS cc_start: 0.7354 (t-170) cc_final: 0.6816 (m-70) REVERT: F 262 ARG cc_start: 0.7936 (mmt90) cc_final: 0.7642 (mtp180) REVERT: F 319 LYS cc_start: 0.8705 (ttmt) cc_final: 0.8431 (tttp) REVERT: F 376 LEU cc_start: 0.6316 (OUTLIER) cc_final: 0.6054 (tm) REVERT: F 377 HIS cc_start: 0.7221 (OUTLIER) cc_final: 0.6609 (m170) REVERT: F 399 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7359 (tp30) outliers start: 52 outliers final: 39 residues processed: 314 average time/residue: 0.5813 time to fit residues: 274.6555 Evaluate side-chains 310 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 263 time to evaluate : 2.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 377 HIS Chi-restraints excluded: chain F residue 57 CYS Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 377 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 1.9990 chunk 176 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 chunk 147 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.4146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16440 Z= 0.251 Angle : 0.511 4.750 22189 Z= 0.279 Chirality : 0.037 0.138 2408 Planarity : 0.002 0.015 2673 Dihedral : 7.367 55.346 2274 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 3.15 % Allowed : 18.90 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.20), residues: 1842 helix: 0.16 (0.15), residues: 1218 sheet: -0.28 (0.49), residues: 96 loop : -1.48 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 143 HIS 0.004 0.001 HIS D 377 PHE 0.014 0.001 PHE B 374 TYR 0.011 0.001 TYR C 284 ARG 0.002 0.000 ARG A 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3684 Ramachandran restraints generated. 1842 Oldfield, 0 Emsley, 1842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 258 time to evaluate : 2.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 GLU cc_start: 0.7583 (pt0) cc_final: 0.7245 (pt0) REVERT: A 155 HIS cc_start: 0.7400 (t-170) cc_final: 0.6796 (m-70) REVERT: A 248 LYS cc_start: 0.8604 (tptm) cc_final: 0.8322 (mtpt) REVERT: A 262 ARG cc_start: 0.8074 (mmt90) cc_final: 0.7522 (mtm-85) REVERT: A 289 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8438 (pt) REVERT: A 376 LEU cc_start: 0.6041 (OUTLIER) cc_final: 0.5706 (tm) REVERT: A 377 HIS cc_start: 0.7397 (OUTLIER) cc_final: 0.6906 (m170) REVERT: B 154 GLU cc_start: 0.7355 (pt0) cc_final: 0.7102 (pt0) REVERT: B 155 HIS cc_start: 0.7366 (t-170) cc_final: 0.6879 (m-70) REVERT: B 262 ARG cc_start: 0.7860 (mmt90) cc_final: 0.7507 (mtm-85) REVERT: B 381 GLN cc_start: 0.6538 (tp40) cc_final: 0.6291 (mm-40) REVERT: C 155 HIS cc_start: 0.7387 (t-170) cc_final: 0.6852 (m-70) REVERT: C 262 ARG cc_start: 0.8001 (mmt90) cc_final: 0.7678 (mtp180) REVERT: C 359 GLU cc_start: 0.7291 (tp30) cc_final: 0.6606 (pm20) REVERT: C 376 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.6127 (tm) REVERT: C 377 HIS cc_start: 0.7322 (OUTLIER) cc_final: 0.6743 (m170) REVERT: C 399 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7405 (tp30) REVERT: D 155 HIS cc_start: 0.7376 (t-170) cc_final: 0.6871 (m-70) REVERT: D 248 LYS cc_start: 0.8592 (tptm) cc_final: 0.8318 (mtpt) REVERT: D 262 ARG cc_start: 0.8077 (mmt90) cc_final: 0.7526 (mtm-85) REVERT: D 289 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8479 (pt) REVERT: D 359 GLU cc_start: 0.7197 (tp30) cc_final: 0.6921 (tm-30) REVERT: E 154 GLU cc_start: 0.7269 (pt0) cc_final: 0.7017 (pt0) REVERT: E 155 HIS cc_start: 0.7379 (t-170) cc_final: 0.6893 (m-70) REVERT: E 262 ARG cc_start: 0.7891 (mmt90) cc_final: 0.7508 (mtm-85) REVERT: F 155 HIS cc_start: 0.7399 (t-170) cc_final: 0.6834 (m-70) REVERT: F 262 ARG cc_start: 0.7969 (mmt90) cc_final: 0.7663 (mtp180) REVERT: F 319 LYS cc_start: 0.8714 (ttmt) cc_final: 0.8423 (tttp) REVERT: F 376 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.6135 (tm) REVERT: F 377 HIS cc_start: 0.7314 (OUTLIER) cc_final: 0.6691 (m170) REVERT: F 399 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7343 (tp30) outliers start: 55 outliers final: 41 residues processed: 309 average time/residue: 0.5800 time to fit residues: 268.2889 Evaluate side-chains 302 residues out of total 1746 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 253 time to evaluate : 2.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 102 ASP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 163 CYS Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 377 HIS Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 57 CYS Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 163 CYS Chi-restraints excluded: chain B residue 293 VAL Chi-restraints excluded: chain B residue 301 SER Chi-restraints excluded: chain C residue 57 CYS Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 163 CYS Chi-restraints excluded: chain C residue 289 ILE Chi-restraints excluded: chain C residue 293 VAL Chi-restraints excluded: chain C residue 301 SER Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 377 HIS Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 163 CYS Chi-restraints excluded: chain D residue 289 ILE Chi-restraints excluded: chain D residue 301 SER Chi-restraints excluded: chain D residue 377 HIS Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain E residue 57 CYS Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 160 LEU Chi-restraints excluded: chain E residue 163 CYS Chi-restraints excluded: chain E residue 293 VAL Chi-restraints excluded: chain E residue 301 SER Chi-restraints excluded: chain F residue 57 CYS Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 104 HIS Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 163 CYS Chi-restraints excluded: chain F residue 289 ILE Chi-restraints excluded: chain F residue 376 LEU Chi-restraints excluded: chain F residue 377 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 0.4980 chunk 157 optimal weight: 0.9990 chunk 45 optimal weight: 6.9990 chunk 136 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 151 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.168868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.134147 restraints weight = 67460.367| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.60 r_work: 0.3585 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.4192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16440 Z= 0.206 Angle : 0.493 4.473 22189 Z= 0.268 Chirality : 0.036 0.130 2408 Planarity : 0.002 0.018 2673 Dihedral : 7.435 59.928 2274 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.21 % Allowed : 19.13 % Favored : 77.66 % 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: -0.46 (0.20), residues: 1842 helix: 0.26 (0.16), residues: 1218 sheet: -0.24 (0.49), residues: 96 loop : -1.45 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 143 HIS 0.004 0.001 HIS D 377 PHE 0.010 0.001 PHE E 374 TYR 0.012 0.001 TYR C 284 ARG 0.001 0.000 ARG A 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7618.07 seconds wall clock time: 135 minutes 37.95 seconds (8137.95 seconds total)