Starting phenix.real_space_refine on Thu Aug 8 16:19:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ewx_50025/08_2024/9ewx_50025.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ewx_50025/08_2024/9ewx_50025.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ewx_50025/08_2024/9ewx_50025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ewx_50025/08_2024/9ewx_50025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ewx_50025/08_2024/9ewx_50025.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ewx_50025/08_2024/9ewx_50025.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 92 5.16 5 C 15111 2.51 5 N 3933 2.21 5 O 4853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 129": "OD1" <-> "OD2" Residue "A ASP 139": "OD1" <-> "OD2" Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 148": "OD1" <-> "OD2" Residue "B ASP 129": "OD1" <-> "OD2" Residue "B ASP 139": "OD1" <-> "OD2" Residue "B PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 148": "OD1" <-> "OD2" Residue "C ASP 129": "OD1" <-> "OD2" Residue "C ASP 139": "OD1" <-> "OD2" Residue "C PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 148": "OD1" <-> "OD2" Residue "D ASP 129": "OD1" <-> "OD2" Residue "D ASP 139": "OD1" <-> "OD2" Residue "D PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 148": "OD1" <-> "OD2" Residue "E ASP 129": "OD1" <-> "OD2" Residue "E ASP 139": "OD1" <-> "OD2" Residue "E PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 148": "OD1" <-> "OD2" Residue "F ASP 129": "OD1" <-> "OD2" Residue "F ASP 139": "OD1" <-> "OD2" Residue "F PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 148": "OD1" <-> "OD2" Residue "G ASP 129": "OD1" <-> "OD2" Residue "G ASP 139": "OD1" <-> "OD2" Residue "G PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 148": "OD1" <-> "OD2" Residue "H ASP 129": "OD1" <-> "OD2" Residue "H ASP 139": "OD1" <-> "OD2" Residue "H PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 148": "OD1" <-> "OD2" Residue "I ASP 129": "OD1" <-> "OD2" Residue "I ASP 139": "OD1" <-> "OD2" Residue "I PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 148": "OD1" <-> "OD2" Residue "J ASP 129": "OD1" <-> "OD2" Residue "J ASP 139": "OD1" <-> "OD2" Residue "J PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 148": "OD1" <-> "OD2" Residue "K ASP 129": "OD1" <-> "OD2" Residue "K ASP 139": "OD1" <-> "OD2" Residue "K PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 148": "OD1" <-> "OD2" Residue "L ASP 129": "OD1" <-> "OD2" Residue "L ASP 139": "OD1" <-> "OD2" Residue "L PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 148": "OD1" <-> "OD2" Residue "M ASP 129": "OD1" <-> "OD2" Residue "M ASP 139": "OD1" <-> "OD2" Residue "M PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 148": "OD1" <-> "OD2" Residue "N ASP 129": "OD1" <-> "OD2" Residue "N ASP 139": "OD1" <-> "OD2" Residue "N PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ASP 148": "OD1" <-> "OD2" Residue "O ASP 129": "OD1" <-> "OD2" Residue "O ASP 139": "OD1" <-> "OD2" Residue "O PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 148": "OD1" <-> "OD2" Residue "P ASP 129": "OD1" <-> "OD2" Residue "P ASP 139": "OD1" <-> "OD2" Residue "P PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 148": "OD1" <-> "OD2" Residue "Q ASP 129": "OD1" <-> "OD2" Residue "Q ASP 139": "OD1" <-> "OD2" Residue "Q PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 148": "OD1" <-> "OD2" Residue "R ASP 129": "OD1" <-> "OD2" Residue "R ASP 139": "OD1" <-> "OD2" Residue "R PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 148": "OD1" <-> "OD2" Residue "S ASP 129": "OD1" <-> "OD2" Residue "S ASP 139": "OD1" <-> "OD2" Residue "S PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 148": "OD1" <-> "OD2" Residue "T ASP 129": "OD1" <-> "OD2" Residue "T ASP 139": "OD1" <-> "OD2" Residue "T PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ASP 148": "OD1" <-> "OD2" Residue "U ASP 129": "OD1" <-> "OD2" Residue "U ASP 139": "OD1" <-> "OD2" Residue "U PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ASP 148": "OD1" <-> "OD2" Residue "V ASP 129": "OD1" <-> "OD2" Residue "V ASP 139": "OD1" <-> "OD2" Residue "V PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 148": "OD1" <-> "OD2" Residue "W ASP 129": "OD1" <-> "OD2" Residue "W ASP 139": "OD1" <-> "OD2" Residue "W PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 148": "OD1" <-> "OD2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 23989 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "B" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "C" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "D" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "E" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "F" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "G" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "H" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "I" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "J" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "K" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "L" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "M" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "N" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "O" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "P" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "Q" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "R" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "S" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "T" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "U" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "V" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Chain: "W" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 136} Time building chain proxies: 13.78, per 1000 atoms: 0.57 Number of scatterers: 23989 At special positions: 0 Unit cell: (71.688, 71.688, 319.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 92 16.00 O 4853 8.00 N 3933 7.00 C 15111 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=23, symmetry=0 Simple disulfide: pdb=" SG CYS A 134 " - pdb=" SG CYS A 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 134 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS C 134 " - pdb=" SG CYS C 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 134 " - pdb=" SG CYS D 147 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 147 " distance=2.03 Simple disulfide: pdb=" SG CYS F 134 " - pdb=" SG CYS F 147 " distance=2.03 Simple disulfide: pdb=" SG CYS G 134 " - pdb=" SG CYS G 147 " distance=2.03 Simple disulfide: pdb=" SG CYS H 134 " - pdb=" SG CYS H 147 " distance=2.03 Simple disulfide: pdb=" SG CYS I 134 " - pdb=" SG CYS I 147 " distance=2.03 Simple disulfide: pdb=" SG CYS J 134 " - pdb=" SG CYS J 147 " distance=2.03 Simple disulfide: pdb=" SG CYS K 134 " - pdb=" SG CYS K 147 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 147 " distance=2.03 Simple disulfide: pdb=" SG CYS M 134 " - pdb=" SG CYS M 147 " distance=2.03 Simple disulfide: pdb=" SG CYS N 134 " - pdb=" SG CYS N 147 " distance=2.03 Simple disulfide: pdb=" SG CYS O 134 " - pdb=" SG CYS O 147 " distance=2.03 Simple disulfide: pdb=" SG CYS P 134 " - pdb=" SG CYS P 147 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 134 " - pdb=" SG CYS Q 147 " distance=2.03 Simple disulfide: pdb=" SG CYS R 134 " - pdb=" SG CYS R 147 " distance=2.03 Simple disulfide: pdb=" SG CYS S 134 " - pdb=" SG CYS S 147 " distance=2.03 Simple disulfide: pdb=" SG CYS T 134 " - pdb=" SG CYS T 147 " distance=2.03 Simple disulfide: pdb=" SG CYS U 134 " - pdb=" SG CYS U 147 " distance=2.03 Simple disulfide: pdb=" SG CYS V 134 " - pdb=" SG CYS V 147 " distance=2.03 Simple disulfide: pdb=" SG CYS W 134 " - pdb=" SG CYS W 147 " 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: 9.07 Conformation dependent library (CDL) restraints added in 4.3 seconds 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6026 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 46 sheets defined 34.3% alpha, 16.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 8 through 23 Processing helix chain 'A' and resid 30 through 47 Processing helix chain 'A' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'B' and resid 8 through 23 Processing helix chain 'B' and resid 30 through 47 Processing helix chain 'B' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR B 52 " --> pdb=" O PRO B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'C' and resid 8 through 23 Processing helix chain 'C' and resid 30 through 47 Processing helix chain 'C' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR C 52 " --> pdb=" O PRO C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'D' and resid 8 through 23 Processing helix chain 'D' and resid 30 through 47 Processing helix chain 'D' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR D 52 " --> pdb=" O PRO D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'E' and resid 8 through 23 Processing helix chain 'E' and resid 30 through 47 Processing helix chain 'E' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR E 52 " --> pdb=" O PRO E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 64 No H-bonds generated for 'chain 'E' and resid 62 through 64' Processing helix chain 'F' and resid 8 through 23 Processing helix chain 'F' and resid 30 through 47 Processing helix chain 'F' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR F 52 " --> pdb=" O PRO F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 64 No H-bonds generated for 'chain 'F' and resid 62 through 64' Processing helix chain 'G' and resid 8 through 23 Processing helix chain 'G' and resid 30 through 47 Processing helix chain 'G' and resid 48 through 59 removed outlier: 3.596A pdb=" N THR G 52 " --> pdb=" O PRO G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 64 No H-bonds generated for 'chain 'G' and resid 62 through 64' Processing helix chain 'H' and resid 8 through 23 Processing helix chain 'H' and resid 30 through 47 Processing helix chain 'H' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR H 52 " --> pdb=" O PRO H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'I' and resid 8 through 23 Processing helix chain 'I' and resid 30 through 47 Processing helix chain 'I' and resid 48 through 59 removed outlier: 3.594A pdb=" N THR I 52 " --> pdb=" O PRO I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 64 No H-bonds generated for 'chain 'I' and resid 62 through 64' Processing helix chain 'J' and resid 8 through 23 Processing helix chain 'J' and resid 30 through 47 Processing helix chain 'J' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR J 52 " --> pdb=" O PRO J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 64 No H-bonds generated for 'chain 'J' and resid 62 through 64' Processing helix chain 'K' and resid 8 through 23 Processing helix chain 'K' and resid 30 through 47 Processing helix chain 'K' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR K 52 " --> pdb=" O PRO K 48 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 64 No H-bonds generated for 'chain 'K' and resid 62 through 64' Processing helix chain 'L' and resid 8 through 23 Processing helix chain 'L' and resid 30 through 47 Processing helix chain 'L' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR L 52 " --> pdb=" O PRO L 48 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 64 No H-bonds generated for 'chain 'L' and resid 62 through 64' Processing helix chain 'M' and resid 8 through 23 Processing helix chain 'M' and resid 30 through 47 Processing helix chain 'M' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR M 52 " --> pdb=" O PRO M 48 " (cutoff:3.500A) Processing helix chain 'M' and resid 62 through 64 No H-bonds generated for 'chain 'M' and resid 62 through 64' Processing helix chain 'N' and resid 8 through 23 Processing helix chain 'N' and resid 30 through 47 Processing helix chain 'N' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR N 52 " --> pdb=" O PRO N 48 " (cutoff:3.500A) Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'O' and resid 8 through 23 Processing helix chain 'O' and resid 30 through 47 Processing helix chain 'O' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR O 52 " --> pdb=" O PRO O 48 " (cutoff:3.500A) Processing helix chain 'O' and resid 62 through 64 No H-bonds generated for 'chain 'O' and resid 62 through 64' Processing helix chain 'P' and resid 8 through 23 Processing helix chain 'P' and resid 30 through 47 Processing helix chain 'P' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR P 52 " --> pdb=" O PRO P 48 " (cutoff:3.500A) Processing helix chain 'P' and resid 62 through 64 No H-bonds generated for 'chain 'P' and resid 62 through 64' Processing helix chain 'Q' and resid 8 through 23 Processing helix chain 'Q' and resid 30 through 47 Processing helix chain 'Q' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR Q 52 " --> pdb=" O PRO Q 48 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 64 No H-bonds generated for 'chain 'Q' and resid 62 through 64' Processing helix chain 'R' and resid 8 through 23 Processing helix chain 'R' and resid 30 through 47 Processing helix chain 'R' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR R 52 " --> pdb=" O PRO R 48 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 64 No H-bonds generated for 'chain 'R' and resid 62 through 64' Processing helix chain 'S' and resid 8 through 23 Processing helix chain 'S' and resid 30 through 47 Processing helix chain 'S' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR S 52 " --> pdb=" O PRO S 48 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 64 No H-bonds generated for 'chain 'S' and resid 62 through 64' Processing helix chain 'T' and resid 8 through 23 Processing helix chain 'T' and resid 30 through 47 Processing helix chain 'T' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR T 52 " --> pdb=" O PRO T 48 " (cutoff:3.500A) Processing helix chain 'T' and resid 62 through 64 No H-bonds generated for 'chain 'T' and resid 62 through 64' Processing helix chain 'U' and resid 8 through 23 Processing helix chain 'U' and resid 30 through 47 Processing helix chain 'U' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR U 52 " --> pdb=" O PRO U 48 " (cutoff:3.500A) Processing helix chain 'U' and resid 62 through 64 No H-bonds generated for 'chain 'U' and resid 62 through 64' Processing helix chain 'V' and resid 8 through 23 Processing helix chain 'V' and resid 30 through 47 Processing helix chain 'V' and resid 48 through 59 removed outlier: 3.595A pdb=" N THR V 52 " --> pdb=" O PRO V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 62 through 64 No H-bonds generated for 'chain 'V' and resid 62 through 64' Processing helix chain 'W' and resid 8 through 23 Processing helix chain 'W' and resid 30 through 47 Processing helix chain 'W' and resid 48 through 59 removed outlier: 3.594A pdb=" N THR W 52 " --> pdb=" O PRO W 48 " (cutoff:3.500A) Processing helix chain 'W' and resid 62 through 64 No H-bonds generated for 'chain 'W' and resid 62 through 64' Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 67 Processing sheet with id=AA2, first strand: chain 'A' and resid 90 through 96 Processing sheet with id=AA3, first strand: chain 'B' and resid 66 through 67 Processing sheet with id=AA4, first strand: chain 'B' and resid 90 through 96 Processing sheet with id=AA5, first strand: chain 'C' and resid 66 through 67 Processing sheet with id=AA6, first strand: chain 'C' and resid 90 through 96 Processing sheet with id=AA7, first strand: chain 'D' and resid 66 through 67 Processing sheet with id=AA8, first strand: chain 'D' and resid 90 through 96 Processing sheet with id=AA9, first strand: chain 'E' and resid 66 through 67 Processing sheet with id=AB1, first strand: chain 'E' and resid 90 through 96 Processing sheet with id=AB2, first strand: chain 'F' and resid 66 through 67 Processing sheet with id=AB3, first strand: chain 'F' and resid 90 through 96 Processing sheet with id=AB4, first strand: chain 'G' and resid 66 through 67 Processing sheet with id=AB5, first strand: chain 'G' and resid 90 through 96 Processing sheet with id=AB6, first strand: chain 'H' and resid 66 through 67 Processing sheet with id=AB7, first strand: chain 'H' and resid 90 through 96 Processing sheet with id=AB8, first strand: chain 'I' and resid 66 through 67 Processing sheet with id=AB9, first strand: chain 'I' and resid 90 through 96 Processing sheet with id=AC1, first strand: chain 'J' and resid 66 through 67 Processing sheet with id=AC2, first strand: chain 'J' and resid 90 through 96 Processing sheet with id=AC3, first strand: chain 'K' and resid 66 through 67 Processing sheet with id=AC4, first strand: chain 'K' and resid 90 through 96 Processing sheet with id=AC5, first strand: chain 'L' and resid 66 through 67 Processing sheet with id=AC6, first strand: chain 'L' and resid 90 through 96 Processing sheet with id=AC7, first strand: chain 'M' and resid 66 through 67 Processing sheet with id=AC8, first strand: chain 'M' and resid 90 through 96 Processing sheet with id=AC9, first strand: chain 'N' and resid 66 through 67 Processing sheet with id=AD1, first strand: chain 'N' and resid 90 through 96 Processing sheet with id=AD2, first strand: chain 'O' and resid 66 through 67 Processing sheet with id=AD3, first strand: chain 'O' and resid 90 through 96 Processing sheet with id=AD4, first strand: chain 'P' and resid 66 through 67 Processing sheet with id=AD5, first strand: chain 'P' and resid 90 through 96 Processing sheet with id=AD6, first strand: chain 'Q' and resid 66 through 67 Processing sheet with id=AD7, first strand: chain 'Q' and resid 90 through 96 Processing sheet with id=AD8, first strand: chain 'R' and resid 66 through 67 Processing sheet with id=AD9, first strand: chain 'R' and resid 90 through 96 Processing sheet with id=AE1, first strand: chain 'S' and resid 66 through 67 Processing sheet with id=AE2, first strand: chain 'S' and resid 90 through 96 Processing sheet with id=AE3, first strand: chain 'T' and resid 66 through 67 Processing sheet with id=AE4, first strand: chain 'T' and resid 90 through 96 Processing sheet with id=AE5, first strand: chain 'U' and resid 66 through 67 Processing sheet with id=AE6, first strand: chain 'U' and resid 90 through 96 Processing sheet with id=AE7, first strand: chain 'V' and resid 66 through 67 Processing sheet with id=AE8, first strand: chain 'V' and resid 90 through 96 Processing sheet with id=AE9, first strand: chain 'W' and resid 66 through 67 Processing sheet with id=AF1, first strand: chain 'W' and resid 90 through 96 1150 hydrogen bonds defined for protein. 3381 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.22 Time building geometry restraints manager: 10.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 7843 1.35 - 1.46: 4991 1.46 - 1.58: 11339 1.58 - 1.69: 0 1.69 - 1.81: 138 Bond restraints: 24311 Sorted by residual: bond pdb=" CG GLN K 109 " pdb=" CD GLN K 109 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 5.54e-01 bond pdb=" CG GLN F 109 " pdb=" CD GLN F 109 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.47e-01 bond pdb=" CG GLN J 109 " pdb=" CD GLN J 109 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.36e-01 bond pdb=" CG GLN O 109 " pdb=" CD GLN O 109 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.35e-01 bond pdb=" CG GLN P 109 " pdb=" CD GLN P 109 " ideal model delta sigma weight residual 1.516 1.534 -0.018 2.50e-02 1.60e+03 5.30e-01 ... (remaining 24306 not shown) Histogram of bond angle deviations from ideal: 100.85 - 107.48: 805 107.48 - 114.12: 14791 114.12 - 120.75: 9500 120.75 - 127.38: 7886 127.38 - 134.01: 161 Bond angle restraints: 33143 Sorted by residual: angle pdb=" CB GLN E 109 " pdb=" CG GLN E 109 " pdb=" CD GLN E 109 " ideal model delta sigma weight residual 112.60 115.48 -2.88 1.70e+00 3.46e-01 2.87e+00 angle pdb=" CB GLN R 109 " pdb=" CG GLN R 109 " pdb=" CD GLN R 109 " ideal model delta sigma weight residual 112.60 115.47 -2.87 1.70e+00 3.46e-01 2.86e+00 angle pdb=" CB GLN H 109 " pdb=" CG GLN H 109 " pdb=" CD GLN H 109 " ideal model delta sigma weight residual 112.60 115.46 -2.86 1.70e+00 3.46e-01 2.84e+00 angle pdb=" CB GLN P 109 " pdb=" CG GLN P 109 " pdb=" CD GLN P 109 " ideal model delta sigma weight residual 112.60 115.46 -2.86 1.70e+00 3.46e-01 2.83e+00 angle pdb=" CB GLN N 109 " pdb=" CG GLN N 109 " pdb=" CD GLN N 109 " ideal model delta sigma weight residual 112.60 115.45 -2.85 1.70e+00 3.46e-01 2.81e+00 ... (remaining 33138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 12765 16.52 - 33.04: 1426 33.04 - 49.56: 391 49.56 - 66.07: 46 66.07 - 82.59: 115 Dihedral angle restraints: 14743 sinusoidal: 5382 harmonic: 9361 Sorted by residual: dihedral pdb=" CA GLU B 77 " pdb=" CB GLU B 77 " pdb=" CG GLU B 77 " pdb=" CD GLU B 77 " ideal model delta sinusoidal sigma weight residual 60.00 115.07 -55.07 3 1.50e+01 4.44e-03 9.32e+00 dihedral pdb=" CA GLU R 77 " pdb=" CB GLU R 77 " pdb=" CG GLU R 77 " pdb=" CD GLU R 77 " ideal model delta sinusoidal sigma weight residual 60.00 115.07 -55.07 3 1.50e+01 4.44e-03 9.32e+00 dihedral pdb=" CA GLU L 77 " pdb=" CB GLU L 77 " pdb=" CG GLU L 77 " pdb=" CD GLU L 77 " ideal model delta sinusoidal sigma weight residual 60.00 115.07 -55.07 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 14740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2396 0.026 - 0.052: 967 0.052 - 0.078: 412 0.078 - 0.104: 238 0.104 - 0.131: 173 Chirality restraints: 4186 Sorted by residual: chirality pdb=" CA ILE B 104 " pdb=" N ILE B 104 " pdb=" C ILE B 104 " pdb=" CB ILE B 104 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA ILE F 104 " pdb=" N ILE F 104 " pdb=" C ILE F 104 " pdb=" CB ILE F 104 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ILE V 104 " pdb=" N ILE V 104 " pdb=" C ILE V 104 " pdb=" CB ILE V 104 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 4183 not shown) Planarity restraints: 4209 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE S 10 " 0.004 2.00e-02 2.50e+03 7.66e-03 5.87e-01 pdb=" C ILE S 10 " -0.013 2.00e-02 2.50e+03 pdb=" O ILE S 10 " 0.005 2.00e-02 2.50e+03 pdb=" N GLU S 11 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE P 10 " 0.004 2.00e-02 2.50e+03 7.46e-03 5.56e-01 pdb=" C ILE P 10 " -0.013 2.00e-02 2.50e+03 pdb=" O ILE P 10 " 0.005 2.00e-02 2.50e+03 pdb=" N GLU P 11 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE W 10 " 0.004 2.00e-02 2.50e+03 7.42e-03 5.50e-01 pdb=" C ILE W 10 " -0.013 2.00e-02 2.50e+03 pdb=" O ILE W 10 " 0.005 2.00e-02 2.50e+03 pdb=" N GLU W 11 " 0.004 2.00e-02 2.50e+03 ... (remaining 4206 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 7980 2.83 - 3.35: 22886 3.35 - 3.87: 40923 3.87 - 4.38: 47391 4.38 - 4.90: 83514 Nonbonded interactions: 202694 Sorted by model distance: nonbonded pdb=" OG1 THR H 143 " pdb=" OD1 ASN H 149 " model vdw 2.318 3.040 nonbonded pdb=" OG1 THR V 143 " pdb=" OD1 ASN V 149 " model vdw 2.318 3.040 nonbonded pdb=" OG1 THR I 143 " pdb=" OD1 ASN I 149 " model vdw 2.318 3.040 nonbonded pdb=" OG1 THR R 143 " pdb=" OD1 ASN R 149 " model vdw 2.318 3.040 nonbonded pdb=" OG1 THR M 143 " pdb=" OD1 ASN M 149 " model vdw 2.318 3.040 ... (remaining 202689 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' } 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: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.870 Check model and map are aligned: 0.170 Set scattering table: 0.230 Process input model: 62.930 Find NCS groups from input model: 0.830 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: 0.010 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 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 : 0.002 0.019 24311 Z= 0.140 Angle : 0.416 4.536 33143 Z= 0.226 Chirality : 0.044 0.131 4186 Planarity : 0.003 0.017 4209 Dihedral : 17.574 82.593 8648 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.88 % Allowed : 26.36 % Favored : 72.76 % 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: 2.80 (0.15), residues: 3243 helix: 2.22 (0.17), residues: 1081 sheet: 0.79 (0.20), residues: 713 loop : 2.47 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP T 132 PHE 0.004 0.001 PHE Q 142 TYR 0.006 0.001 TYR D 33 ARG 0.001 0.000 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 639 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 616 time to evaluate : 2.818 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 82 VAL cc_start: 0.8742 (m) cc_final: 0.8461 (m) REVERT: A 136 SER cc_start: 0.8544 (t) cc_final: 0.8274 (p) REVERT: B 65 LYS cc_start: 0.8414 (mmtt) cc_final: 0.7720 (mttt) REVERT: B 77 GLU cc_start: 0.8336 (mp0) cc_final: 0.7999 (mp0) REVERT: C 124 LEU cc_start: 0.9135 (mt) cc_final: 0.8883 (mp) REVERT: D 65 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8327 (mmtp) REVERT: E 103 ASP cc_start: 0.8694 (p0) cc_final: 0.8433 (p0) REVERT: I 70 THR cc_start: 0.8556 (p) cc_final: 0.8238 (m) REVERT: I 97 GLU cc_start: 0.8029 (mt-10) cc_final: 0.7731 (mm-30) REVERT: I 116 LYS cc_start: 0.8061 (mmtm) cc_final: 0.7784 (mmtt) REVERT: K 29 GLN cc_start: 0.7969 (tt0) cc_final: 0.7512 (tt0) REVERT: L 103 ASP cc_start: 0.8283 (p0) cc_final: 0.7895 (p0) REVERT: M 29 GLN cc_start: 0.7881 (tt0) cc_final: 0.7350 (mt0) REVERT: M 70 THR cc_start: 0.8636 (p) cc_final: 0.8315 (m) REVERT: N 129 ASP cc_start: 0.7671 (m-30) cc_final: 0.7330 (m-30) REVERT: O 29 GLN cc_start: 0.7816 (tt0) cc_final: 0.7514 (mt0) REVERT: O 43 LEU cc_start: 0.9028 (tp) cc_final: 0.8805 (tp) REVERT: O 61 ILE cc_start: 0.8400 (mt) cc_final: 0.8197 (mt) REVERT: P 29 GLN cc_start: 0.7492 (tt0) cc_final: 0.7146 (mt0) REVERT: P 85 ASP cc_start: 0.7915 (p0) cc_final: 0.7667 (p0) REVERT: Q 116 LYS cc_start: 0.8613 (mmtm) cc_final: 0.8377 (mmtp) REVERT: Q 125 ASN cc_start: 0.8845 (t0) cc_final: 0.8610 (t0) REVERT: Q 135 LYS cc_start: 0.7812 (tptt) cc_final: 0.7470 (tttm) outliers start: 23 outliers final: 3 residues processed: 638 average time/residue: 0.3531 time to fit residues: 348.4150 Evaluate side-chains 454 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 451 time to evaluate : 2.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 52 THR Chi-restraints excluded: chain O residue 52 THR Chi-restraints excluded: chain U residue 52 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 271 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 135 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 164 optimal weight: 6.9990 chunk 130 optimal weight: 0.9990 chunk 252 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 153 optimal weight: 0.0970 chunk 187 optimal weight: 0.5980 chunk 292 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN B 29 GLN B 47 ASN B 149 ASN ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 149 ASN D 125 ASN D 149 ASN E 31 GLN E 149 ASN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 149 ASN G 109 GLN G 149 ASN H 149 ASN I 149 ASN J 109 GLN J 149 ASN K 29 GLN K 149 ASN L 29 GLN L 87 ASN L 149 ASN M 29 GLN M 149 ASN N 149 ASN O 87 ASN O 149 ASN P 149 ASN Q 29 GLN Q 149 ASN ** R 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 ASN S 29 GLN ** S 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 149 ASN T 149 ASN U 29 GLN U 149 ASN V 149 ASN W 149 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 24311 Z= 0.140 Angle : 0.439 4.568 33143 Z= 0.234 Chirality : 0.045 0.141 4186 Planarity : 0.003 0.021 4209 Dihedral : 3.527 14.784 3430 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.54 % Allowed : 21.55 % Favored : 74.91 % 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: 3.15 (0.15), residues: 3243 helix: 2.46 (0.17), residues: 1081 sheet: 1.33 (0.20), residues: 713 loop : 2.50 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 132 PHE 0.008 0.001 PHE R 108 TYR 0.009 0.001 TYR U 33 ARG 0.002 0.000 ARG D 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 495 time to evaluate : 3.454 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 82 VAL cc_start: 0.8721 (m) cc_final: 0.8427 (m) REVERT: B 65 LYS cc_start: 0.8344 (mmtt) cc_final: 0.7690 (mttt) REVERT: D 65 LYS cc_start: 0.8677 (mmtt) cc_final: 0.8279 (mmtp) REVERT: I 65 LYS cc_start: 0.8575 (mmtt) cc_final: 0.8221 (mmtm) REVERT: I 97 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7782 (mm-30) REVERT: I 116 LYS cc_start: 0.8028 (mmtm) cc_final: 0.7817 (mmtt) REVERT: I 148 ASP cc_start: 0.7953 (m-30) cc_final: 0.7669 (m-30) REVERT: L 135 LYS cc_start: 0.8338 (tmtt) cc_final: 0.7954 (mtpt) REVERT: M 29 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7398 (mt0) REVERT: N 87 ASN cc_start: 0.9090 (t0) cc_final: 0.8860 (t0) REVERT: N 129 ASP cc_start: 0.7612 (m-30) cc_final: 0.7363 (m-30) REVERT: O 43 LEU cc_start: 0.9102 (tp) cc_final: 0.8808 (tp) REVERT: P 135 LYS cc_start: 0.8436 (mmtt) cc_final: 0.7848 (mptt) REVERT: Q 135 LYS cc_start: 0.8120 (tptt) cc_final: 0.7817 (tttm) REVERT: R 135 LYS cc_start: 0.8415 (tptt) cc_final: 0.7852 (ttpp) REVERT: R 141 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8316 (ptm) REVERT: S 91 VAL cc_start: 0.9194 (m) cc_final: 0.8937 (t) REVERT: W 8 THR cc_start: 0.6847 (OUTLIER) cc_final: 0.6489 (m) REVERT: W 91 VAL cc_start: 0.9142 (m) cc_final: 0.8821 (t) REVERT: W 135 LYS cc_start: 0.8458 (tptt) cc_final: 0.8135 (mtpp) outliers start: 92 outliers final: 56 residues processed: 551 average time/residue: 0.3540 time to fit residues: 309.3677 Evaluate side-chains 502 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 443 time to evaluate : 2.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 141 MET Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain M residue 29 GLN Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 112 THR Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 112 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 141 MET Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 11 GLU Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 125 ASN Chi-restraints excluded: chain U residue 141 MET Chi-restraints excluded: chain V residue 97 GLU Chi-restraints excluded: chain V residue 136 SER Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 112 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 162 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 243 optimal weight: 8.9990 chunk 199 optimal weight: 0.9990 chunk 80 optimal weight: 7.9990 chunk 292 optimal weight: 0.9980 chunk 316 optimal weight: 6.9990 chunk 260 optimal weight: 10.0000 chunk 290 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 235 optimal weight: 6.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 138 GLN B 149 ASN ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN F 87 ASN F 149 ASN ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 149 ASN H 109 GLN H 149 ASN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 149 ASN M 109 GLN O 29 GLN O 149 ASN P 149 ASN Q 149 ASN R 109 GLN R 125 ASN R 149 ASN S 109 GLN T 109 GLN T 149 ASN U 109 GLN U 138 GLN U 149 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 24311 Z= 0.424 Angle : 0.577 4.889 33143 Z= 0.315 Chirality : 0.052 0.210 4186 Planarity : 0.004 0.040 4209 Dihedral : 4.579 26.098 3427 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 5.04 % Allowed : 19.89 % Favored : 75.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.61 (0.15), residues: 3243 helix: 1.98 (0.17), residues: 1081 sheet: 1.31 (0.19), residues: 713 loop : 2.03 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 132 PHE 0.014 0.002 PHE E 142 TYR 0.011 0.002 TYR Q 33 ARG 0.005 0.001 ARG Q 59 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 447 time to evaluate : 3.420 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 82 VAL cc_start: 0.8701 (m) cc_final: 0.8500 (m) REVERT: B 22 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8576 (mp) REVERT: B 31 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8131 (pt0) REVERT: B 65 LYS cc_start: 0.8411 (mmtt) cc_final: 0.7751 (mttt) REVERT: B 129 ASP cc_start: 0.7585 (t0) cc_final: 0.7383 (t0) REVERT: C 22 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8124 (mp) REVERT: D 65 LYS cc_start: 0.8670 (mmtt) cc_final: 0.8277 (mmtp) REVERT: E 98 ASP cc_start: 0.8406 (m-30) cc_final: 0.8206 (m-30) REVERT: E 141 MET cc_start: 0.8614 (OUTLIER) cc_final: 0.8219 (ptt) REVERT: F 22 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8192 (mp) REVERT: I 97 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7799 (mm-30) REVERT: J 22 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8120 (mp) REVERT: K 31 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7796 (pt0) REVERT: L 22 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8400 (mp) REVERT: L 135 LYS cc_start: 0.8308 (tmtt) cc_final: 0.7920 (mtpt) REVERT: M 7 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.7024 (t80) REVERT: M 22 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8197 (mp) REVERT: M 135 LYS cc_start: 0.8890 (mmtt) cc_final: 0.8551 (tttp) REVERT: N 129 ASP cc_start: 0.7644 (OUTLIER) cc_final: 0.7405 (m-30) REVERT: O 7 PHE cc_start: 0.7913 (OUTLIER) cc_final: 0.7515 (t80) REVERT: O 129 ASP cc_start: 0.8349 (t70) cc_final: 0.8074 (t70) REVERT: P 22 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8423 (mp) REVERT: P 135 LYS cc_start: 0.8419 (mmtt) cc_final: 0.8090 (ttmt) REVERT: Q 22 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8302 (mp) REVERT: Q 87 ASN cc_start: 0.8649 (t0) cc_final: 0.8411 (t0) REVERT: Q 135 LYS cc_start: 0.8229 (tptt) cc_final: 0.7737 (tttm) REVERT: R 135 LYS cc_start: 0.8508 (tptt) cc_final: 0.7844 (ttpp) REVERT: S 22 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8437 (mp) REVERT: S 91 VAL cc_start: 0.9182 (m) cc_final: 0.8943 (t) REVERT: V 109 GLN cc_start: 0.8477 (mm-40) cc_final: 0.8187 (mm-40) REVERT: V 135 LYS cc_start: 0.8577 (mptt) cc_final: 0.8191 (mttt) REVERT: W 135 LYS cc_start: 0.8567 (tptt) cc_final: 0.8241 (ttpp) outliers start: 131 outliers final: 88 residues processed: 541 average time/residue: 0.3358 time to fit residues: 292.2957 Evaluate side-chains 526 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 423 time to evaluate : 2.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 80 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 31 GLN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 78 THR Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 8 THR Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 74 THR Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 29 GLN Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 74 THR Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain Q residue 112 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 141 MET Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 103 ASP Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 125 ASN Chi-restraints excluded: chain T residue 141 MET Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 125 ASN Chi-restraints excluded: chain U residue 141 MET Chi-restraints excluded: chain V residue 139 ASP Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 112 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 289 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 152 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 196 optimal weight: 5.9990 chunk 293 optimal weight: 3.9990 chunk 311 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 278 optimal weight: 0.4980 chunk 83 optimal weight: 6.9990 overall best weight: 2.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 138 GLN D 109 GLN D 125 ASN G 109 GLN H 109 GLN J 109 GLN M 109 GLN P 29 GLN U 138 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 24311 Z= 0.233 Angle : 0.473 4.678 33143 Z= 0.256 Chirality : 0.047 0.164 4186 Planarity : 0.004 0.031 4209 Dihedral : 4.183 27.650 3427 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.89 % Allowed : 19.93 % Favored : 75.18 % 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: 2.71 (0.15), residues: 3243 helix: 2.21 (0.17), residues: 1081 sheet: 1.24 (0.19), residues: 713 loop : 2.04 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 132 PHE 0.008 0.001 PHE W 108 TYR 0.006 0.001 TYR Q 33 ARG 0.003 0.000 ARG P 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 443 time to evaluate : 2.765 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 85 ASP cc_start: 0.8211 (p0) cc_final: 0.7951 (p0) REVERT: B 31 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.8026 (pt0) REVERT: B 65 LYS cc_start: 0.8435 (mmtt) cc_final: 0.7766 (mttt) REVERT: B 129 ASP cc_start: 0.7576 (t0) cc_final: 0.7367 (t0) REVERT: C 22 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8245 (mp) REVERT: C 77 GLU cc_start: 0.8317 (mp0) cc_final: 0.7953 (mp0) REVERT: D 65 LYS cc_start: 0.8688 (mmtt) cc_final: 0.8278 (mmtp) REVERT: E 141 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8258 (ptt) REVERT: I 97 GLU cc_start: 0.8080 (mt-10) cc_final: 0.7832 (mm-30) REVERT: J 13 MET cc_start: 0.8568 (mmm) cc_final: 0.8335 (mmm) REVERT: J 22 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8081 (mp) REVERT: K 22 LEU cc_start: 0.8355 (OUTLIER) cc_final: 0.8083 (mp) REVERT: K 31 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7672 (pt0) REVERT: L 103 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7492 (p0) REVERT: L 135 LYS cc_start: 0.8307 (tmtt) cc_final: 0.7912 (mtpt) REVERT: M 7 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.7115 (t80) REVERT: M 135 LYS cc_start: 0.8908 (mmtt) cc_final: 0.8578 (tttp) REVERT: N 22 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8524 (mp) REVERT: N 129 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7357 (m-30) REVERT: O 7 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7595 (t80) REVERT: O 129 ASP cc_start: 0.8354 (t70) cc_final: 0.7855 (t0) REVERT: P 135 LYS cc_start: 0.8436 (mmtt) cc_final: 0.8234 (tttp) REVERT: Q 22 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8304 (mp) REVERT: Q 77 GLU cc_start: 0.8129 (mt-10) cc_final: 0.7862 (mt-10) REVERT: Q 87 ASN cc_start: 0.8625 (t0) cc_final: 0.8404 (t0) REVERT: Q 135 LYS cc_start: 0.8315 (tptt) cc_final: 0.7796 (tttm) REVERT: R 135 LYS cc_start: 0.8464 (tptt) cc_final: 0.7747 (ttpp) REVERT: V 135 LYS cc_start: 0.8587 (mptt) cc_final: 0.8197 (mttt) REVERT: W 10 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8283 (mm) REVERT: W 135 LYS cc_start: 0.8583 (tptt) cc_final: 0.8314 (mtpp) outliers start: 127 outliers final: 90 residues processed: 532 average time/residue: 0.3195 time to fit residues: 271.9487 Evaluate side-chains 534 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 431 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 138 GLN Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 148 ASP Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 21 ILE Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain M residue 141 MET Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 141 MET Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 141 MET Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 125 ASN Chi-restraints excluded: chain T residue 141 MET Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 125 ASN Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 91 VAL Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain W residue 10 ILE Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 148 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 259 optimal weight: 7.9990 chunk 176 optimal weight: 8.9990 chunk 4 optimal weight: 5.9990 chunk 231 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 chunk 265 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 158 optimal weight: 3.9990 chunk 279 optimal weight: 0.7980 chunk 78 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 138 GLN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN D 149 ASN G 109 GLN H 109 GLN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN Q 149 ASN R 109 GLN S 109 GLN V 31 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24311 Z= 0.218 Angle : 0.464 4.652 33143 Z= 0.250 Chirality : 0.047 0.158 4186 Planarity : 0.003 0.030 4209 Dihedral : 4.123 29.210 3427 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 5.19 % Allowed : 19.78 % Favored : 75.03 % 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: 2.69 (0.15), residues: 3243 helix: 2.26 (0.17), residues: 1081 sheet: 1.13 (0.19), residues: 713 loop : 2.03 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 132 PHE 0.007 0.001 PHE B 108 TYR 0.007 0.001 TYR L 33 ARG 0.003 0.000 ARG P 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 432 time to evaluate : 2.572 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: A 85 ASP cc_start: 0.8186 (p0) cc_final: 0.7901 (p0) REVERT: B 31 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7984 (pt0) REVERT: B 65 LYS cc_start: 0.8438 (mmtt) cc_final: 0.7784 (mttt) REVERT: B 129 ASP cc_start: 0.7583 (t0) cc_final: 0.7349 (t0) REVERT: C 22 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8208 (mp) REVERT: C 77 GLU cc_start: 0.8326 (mp0) cc_final: 0.7909 (mp0) REVERT: D 65 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8288 (mmtp) REVERT: E 141 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8254 (ptt) REVERT: H 31 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7244 (pt0) REVERT: I 97 GLU cc_start: 0.8066 (mt-10) cc_final: 0.7813 (mm-30) REVERT: J 22 LEU cc_start: 0.8374 (OUTLIER) cc_final: 0.8078 (mp) REVERT: J 129 ASP cc_start: 0.7394 (m-30) cc_final: 0.6940 (t70) REVERT: K 22 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8045 (mp) REVERT: K 31 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7665 (pt0) REVERT: L 22 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8367 (mp) REVERT: L 103 ASP cc_start: 0.7863 (OUTLIER) cc_final: 0.7402 (p0) REVERT: L 135 LYS cc_start: 0.8315 (tmtt) cc_final: 0.7937 (mtpt) REVERT: M 7 PHE cc_start: 0.7454 (OUTLIER) cc_final: 0.7072 (t80) REVERT: M 22 LEU cc_start: 0.8456 (OUTLIER) cc_final: 0.8122 (mp) REVERT: M 29 GLN cc_start: 0.8082 (tt0) cc_final: 0.7592 (mt0) REVERT: M 135 LYS cc_start: 0.8917 (mmtt) cc_final: 0.8603 (tttp) REVERT: N 22 LEU cc_start: 0.9076 (OUTLIER) cc_final: 0.8502 (mp) REVERT: N 129 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.7326 (m-30) REVERT: O 7 PHE cc_start: 0.7982 (OUTLIER) cc_final: 0.7665 (t80) REVERT: O 11 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8240 (tt0) REVERT: O 129 ASP cc_start: 0.8358 (t70) cc_final: 0.7860 (t0) REVERT: P 22 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8342 (mp) REVERT: P 135 LYS cc_start: 0.8420 (mmtt) cc_final: 0.8204 (tttp) REVERT: Q 22 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8279 (mp) REVERT: Q 77 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7904 (mt-10) REVERT: Q 87 ASN cc_start: 0.8616 (t0) cc_final: 0.8400 (t0) REVERT: Q 135 LYS cc_start: 0.8361 (tptt) cc_final: 0.7729 (tttm) REVERT: R 135 LYS cc_start: 0.8471 (tptt) cc_final: 0.7760 (ttpp) REVERT: S 22 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8410 (mp) REVERT: T 31 GLN cc_start: 0.8362 (OUTLIER) cc_final: 0.8081 (pt0) REVERT: V 135 LYS cc_start: 0.8566 (mptt) cc_final: 0.8164 (mttt) REVERT: W 31 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7559 (pt0) REVERT: W 135 LYS cc_start: 0.8572 (tptt) cc_final: 0.8306 (mtpp) outliers start: 135 outliers final: 101 residues processed: 529 average time/residue: 0.3205 time to fit residues: 271.1544 Evaluate side-chains 544 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 423 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 52 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 31 GLN Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 31 GLN Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 148 ASP Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain M residue 141 MET Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 141 MET Chi-restraints excluded: chain R residue 148 ASP Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 141 MET Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 125 ASN Chi-restraints excluded: chain T residue 141 MET Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 125 ASN Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 31 GLN Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain W residue 31 GLN Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 148 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 104 optimal weight: 10.0000 chunk 280 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 182 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 311 optimal weight: 2.9990 chunk 258 optimal weight: 5.9990 chunk 144 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 163 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 29 GLN B 47 ASN ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN G 29 GLN G 109 GLN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN V 31 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 24311 Z= 0.203 Angle : 0.458 4.639 33143 Z= 0.247 Chirality : 0.047 0.153 4186 Planarity : 0.003 0.029 4209 Dihedral : 4.059 29.423 3427 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 5.39 % Allowed : 19.24 % Favored : 75.38 % 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: 2.70 (0.15), residues: 3243 helix: 2.32 (0.17), residues: 1081 sheet: 1.06 (0.19), residues: 713 loop : 2.04 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 132 PHE 0.006 0.001 PHE W 108 TYR 0.011 0.001 TYR G 33 ARG 0.003 0.000 ARG P 59 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 439 time to evaluate : 2.617 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: A 85 ASP cc_start: 0.8175 (p0) cc_final: 0.7892 (p0) REVERT: A 125 ASN cc_start: 0.8148 (t0) cc_final: 0.7862 (t0) REVERT: B 65 LYS cc_start: 0.8441 (mmtt) cc_final: 0.7790 (mttt) REVERT: C 22 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8195 (mp) REVERT: C 77 GLU cc_start: 0.8261 (mp0) cc_final: 0.7878 (mp0) REVERT: D 65 LYS cc_start: 0.8717 (mmtt) cc_final: 0.8280 (mmtp) REVERT: E 98 ASP cc_start: 0.8291 (m-30) cc_final: 0.7642 (m-30) REVERT: E 141 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.8268 (ptt) REVERT: H 31 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7288 (pt0) REVERT: I 97 GLU cc_start: 0.8070 (mt-10) cc_final: 0.7817 (mm-30) REVERT: J 13 MET cc_start: 0.8579 (OUTLIER) cc_final: 0.8326 (mmm) REVERT: J 22 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8100 (mp) REVERT: J 129 ASP cc_start: 0.7355 (m-30) cc_final: 0.6941 (t70) REVERT: K 22 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.8051 (mp) REVERT: K 31 GLN cc_start: 0.8035 (OUTLIER) cc_final: 0.7647 (pt0) REVERT: L 22 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8362 (mp) REVERT: L 103 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7249 (p0) REVERT: L 135 LYS cc_start: 0.8313 (tmtt) cc_final: 0.7933 (mtpt) REVERT: M 7 PHE cc_start: 0.7403 (OUTLIER) cc_final: 0.7039 (t80) REVERT: M 22 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8099 (mp) REVERT: M 29 GLN cc_start: 0.8064 (tt0) cc_final: 0.7582 (mt0) REVERT: N 22 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8496 (mp) REVERT: N 129 ASP cc_start: 0.7560 (OUTLIER) cc_final: 0.7298 (m-30) REVERT: O 7 PHE cc_start: 0.8020 (OUTLIER) cc_final: 0.7700 (t80) REVERT: O 11 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8253 (tt0) REVERT: O 129 ASP cc_start: 0.8367 (t70) cc_final: 0.7881 (t0) REVERT: P 7 PHE cc_start: 0.8128 (OUTLIER) cc_final: 0.7822 (t80) REVERT: P 22 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8338 (mp) REVERT: P 135 LYS cc_start: 0.8420 (mmtt) cc_final: 0.8175 (tttp) REVERT: Q 22 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8297 (mp) REVERT: Q 31 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.7926 (pt0) REVERT: Q 77 GLU cc_start: 0.8165 (mt-10) cc_final: 0.7903 (mt-10) REVERT: Q 87 ASN cc_start: 0.8604 (t0) cc_final: 0.8389 (t0) REVERT: Q 135 LYS cc_start: 0.8375 (tptt) cc_final: 0.7784 (tttm) REVERT: R 135 LYS cc_start: 0.8457 (tptt) cc_final: 0.7761 (ttpp) REVERT: S 22 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8404 (mp) REVERT: T 31 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8054 (pt0) REVERT: V 135 LYS cc_start: 0.8595 (mptt) cc_final: 0.8192 (mttt) REVERT: W 135 LYS cc_start: 0.8576 (tptt) cc_final: 0.8307 (mtpp) outliers start: 140 outliers final: 103 residues processed: 541 average time/residue: 0.3275 time to fit residues: 284.1762 Evaluate side-chains 556 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 432 time to evaluate : 2.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 73 SER Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 70 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 64 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 31 GLN Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 13 MET Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 29 GLN Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 7 PHE Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 103 ASP Chi-restraints excluded: chain L residue 112 THR Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain M residue 141 MET Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 85 ASP Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 82 VAL Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 141 MET Chi-restraints excluded: chain R residue 148 ASP Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 141 MET Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 91 VAL Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 125 ASN Chi-restraints excluded: chain T residue 141 MET Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 125 ASN Chi-restraints excluded: chain U residue 141 MET Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 148 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 300 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 177 optimal weight: 6.9990 chunk 227 optimal weight: 1.9990 chunk 176 optimal weight: 0.8980 chunk 262 optimal weight: 1.9990 chunk 173 optimal weight: 0.0670 chunk 310 optimal weight: 0.9980 chunk 194 optimal weight: 4.9990 chunk 189 optimal weight: 8.9990 chunk 143 optimal weight: 0.7980 overall best weight: 0.9520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 109 GLN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN H 109 GLN H 149 ASN K 87 ASN V 31 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 24311 Z= 0.140 Angle : 0.431 9.433 33143 Z= 0.230 Chirality : 0.045 0.142 4186 Planarity : 0.003 0.026 4209 Dihedral : 3.761 25.549 3427 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 4.08 % Allowed : 20.35 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.15), residues: 3243 helix: 2.51 (0.17), residues: 1081 sheet: 1.09 (0.19), residues: 713 loop : 2.15 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 132 PHE 0.005 0.001 PHE W 108 TYR 0.007 0.001 TYR G 33 ARG 0.003 0.000 ARG P 59 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 445 time to evaluate : 2.804 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: A 85 ASP cc_start: 0.8209 (p0) cc_final: 0.7949 (p0) REVERT: A 125 ASN cc_start: 0.8099 (t0) cc_final: 0.7844 (t0) REVERT: B 31 GLN cc_start: 0.8209 (OUTLIER) cc_final: 0.7933 (pt0) REVERT: B 65 LYS cc_start: 0.8440 (mmtt) cc_final: 0.7774 (mttt) REVERT: C 77 GLU cc_start: 0.8286 (mp0) cc_final: 0.7779 (mp0) REVERT: D 65 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8273 (mmtp) REVERT: E 141 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8240 (ptt) REVERT: H 31 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.7220 (pt0) REVERT: I 97 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7846 (mm-30) REVERT: J 13 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8336 (mmm) REVERT: J 129 ASP cc_start: 0.7363 (m-30) cc_final: 0.6938 (t70) REVERT: K 31 GLN cc_start: 0.8008 (OUTLIER) cc_final: 0.7625 (pt0) REVERT: L 22 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8332 (mp) REVERT: L 135 LYS cc_start: 0.8307 (tmtt) cc_final: 0.7947 (mtpt) REVERT: M 7 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.6955 (t80) REVERT: M 22 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.8062 (mp) REVERT: M 29 GLN cc_start: 0.8000 (tt0) cc_final: 0.7508 (mt0) REVERT: N 22 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8500 (mp) REVERT: N 87 ASN cc_start: 0.9040 (t0) cc_final: 0.8828 (t0) REVERT: O 7 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7761 (t80) REVERT: O 22 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8277 (mp) REVERT: O 129 ASP cc_start: 0.8456 (t70) cc_final: 0.7982 (t0) REVERT: P 7 PHE cc_start: 0.8123 (OUTLIER) cc_final: 0.7861 (t80) REVERT: Q 31 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7943 (pt0) REVERT: Q 77 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7943 (mt-10) REVERT: Q 135 LYS cc_start: 0.8347 (tptt) cc_final: 0.7749 (tttm) REVERT: R 135 LYS cc_start: 0.8442 (tptt) cc_final: 0.7731 (ttpp) REVERT: S 22 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8413 (mp) REVERT: T 31 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7977 (pt0) REVERT: V 103 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7599 (p0) REVERT: V 135 LYS cc_start: 0.8585 (mptt) cc_final: 0.8174 (mttt) REVERT: W 77 GLU cc_start: 0.8033 (mt-10) cc_final: 0.7647 (mt-10) REVERT: W 135 LYS cc_start: 0.8567 (tptt) cc_final: 0.8310 (mtpp) outliers start: 106 outliers final: 74 residues processed: 523 average time/residue: 0.3235 time to fit residues: 269.6198 Evaluate side-chains 517 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 427 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 31 GLN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain E residue 141 MET Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain H residue 31 GLN Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain I residue 112 THR Chi-restraints excluded: chain J residue 13 MET Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain L residue 148 ASP Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 112 THR Chi-restraints excluded: chain T residue 125 ASN Chi-restraints excluded: chain T residue 141 MET Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain U residue 141 MET Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain W residue 64 SER Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 82 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 192 optimal weight: 0.0870 chunk 123 optimal weight: 10.0000 chunk 185 optimal weight: 0.9990 chunk 93 optimal weight: 0.0770 chunk 60 optimal weight: 0.8980 chunk 197 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 243 optimal weight: 0.5980 chunk 282 optimal weight: 0.8980 overall best weight: 0.5116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 109 GLN B 149 ASN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN D 149 ASN G 29 GLN G 109 GLN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 149 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24311 Z= 0.114 Angle : 0.415 6.561 33143 Z= 0.219 Chirality : 0.045 0.141 4186 Planarity : 0.003 0.025 4209 Dihedral : 3.507 18.694 3427 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 3.46 % Allowed : 21.35 % Favored : 75.18 % 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: 3.06 (0.15), residues: 3243 helix: 2.69 (0.17), residues: 1081 sheet: 1.18 (0.19), residues: 713 loop : 2.23 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP O 132 PHE 0.004 0.001 PHE S 108 TYR 0.006 0.001 TYR L 33 ARG 0.005 0.000 ARG S 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 465 time to evaluate : 2.786 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: A 85 ASP cc_start: 0.8194 (p0) cc_final: 0.7910 (p0) REVERT: B 65 LYS cc_start: 0.8435 (mmtt) cc_final: 0.7782 (mttt) REVERT: C 77 GLU cc_start: 0.8279 (mp0) cc_final: 0.7793 (mp0) REVERT: D 65 LYS cc_start: 0.8707 (mmtt) cc_final: 0.8318 (mmtp) REVERT: D 135 LYS cc_start: 0.8693 (tppp) cc_final: 0.8347 (tppt) REVERT: H 31 GLN cc_start: 0.7339 (OUTLIER) cc_final: 0.7085 (pt0) REVERT: I 97 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7893 (mm-30) REVERT: J 129 ASP cc_start: 0.7385 (m-30) cc_final: 0.6942 (t70) REVERT: K 31 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7559 (pt0) REVERT: L 88 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8243 (mmtt) REVERT: L 129 ASP cc_start: 0.7748 (t0) cc_final: 0.7441 (t0) REVERT: L 135 LYS cc_start: 0.8277 (tmtt) cc_final: 0.7959 (mtpt) REVERT: M 7 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.7021 (t80) REVERT: M 22 LEU cc_start: 0.8310 (OUTLIER) cc_final: 0.8030 (mp) REVERT: M 29 GLN cc_start: 0.7827 (tt0) cc_final: 0.7359 (mt0) REVERT: N 7 PHE cc_start: 0.7431 (OUTLIER) cc_final: 0.6175 (m-80) REVERT: O 7 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7765 (t80) REVERT: O 43 LEU cc_start: 0.9110 (tp) cc_final: 0.8830 (tp) REVERT: O 129 ASP cc_start: 0.8485 (t70) cc_final: 0.8005 (t0) REVERT: P 7 PHE cc_start: 0.8057 (OUTLIER) cc_final: 0.7806 (t80) REVERT: Q 7 PHE cc_start: 0.7770 (OUTLIER) cc_final: 0.7334 (t80) REVERT: Q 31 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7829 (pt0) REVERT: Q 77 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7981 (mt-10) REVERT: Q 135 LYS cc_start: 0.8314 (tptt) cc_final: 0.7699 (tttm) REVERT: R 135 LYS cc_start: 0.8419 (tptt) cc_final: 0.7693 (ttpp) REVERT: T 31 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7888 (pt0) REVERT: V 103 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7484 (p0) REVERT: V 135 LYS cc_start: 0.8536 (mptt) cc_final: 0.8163 (mttt) REVERT: W 77 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7594 (mt-10) REVERT: W 135 LYS cc_start: 0.8576 (tptt) cc_final: 0.8251 (mtpp) outliers start: 90 outliers final: 62 residues processed: 533 average time/residue: 0.3327 time to fit residues: 281.7225 Evaluate side-chains 518 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 445 time to evaluate : 2.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain H residue 31 GLN Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 7 PHE Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain O residue 7 PHE Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 92 ILE Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain Q residue 7 PHE Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 82 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 297 optimal weight: 10.0000 chunk 271 optimal weight: 5.9990 chunk 289 optimal weight: 0.9980 chunk 174 optimal weight: 10.0000 chunk 125 optimal weight: 0.0040 chunk 227 optimal weight: 0.9990 chunk 88 optimal weight: 0.0870 chunk 261 optimal weight: 0.3980 chunk 273 optimal weight: 1.9990 chunk 288 optimal weight: 1.9990 chunk 189 optimal weight: 0.8980 overall best weight: 0.4770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 109 GLN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN G 29 GLN G 109 GLN I 109 GLN S 109 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 24311 Z= 0.112 Angle : 0.417 5.755 33143 Z= 0.219 Chirality : 0.045 0.142 4186 Planarity : 0.003 0.024 4209 Dihedral : 3.430 14.889 3427 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer: Outliers : 3.35 % Allowed : 21.55 % Favored : 75.11 % 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: 3.16 (0.15), residues: 3243 helix: 2.77 (0.17), residues: 1081 sheet: 1.26 (0.19), residues: 713 loop : 2.28 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP T 132 PHE 0.004 0.000 PHE I 108 TYR 0.009 0.001 TYR I 33 ARG 0.004 0.000 ARG S 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 537 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 450 time to evaluate : 2.423 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: B 65 LYS cc_start: 0.8433 (mmtt) cc_final: 0.7773 (mttt) REVERT: C 65 LYS cc_start: 0.8695 (mttm) cc_final: 0.8428 (mttt) REVERT: D 65 LYS cc_start: 0.8725 (mmtt) cc_final: 0.8328 (mmtp) REVERT: H 31 GLN cc_start: 0.7313 (OUTLIER) cc_final: 0.7059 (pt0) REVERT: J 91 VAL cc_start: 0.8703 (m) cc_final: 0.8416 (t) REVERT: J 129 ASP cc_start: 0.7391 (m-30) cc_final: 0.6926 (t0) REVERT: K 31 GLN cc_start: 0.7896 (OUTLIER) cc_final: 0.7506 (pt0) REVERT: L 88 LYS cc_start: 0.8691 (mmmt) cc_final: 0.8176 (mmtt) REVERT: L 124 LEU cc_start: 0.8820 (mp) cc_final: 0.8620 (mp) REVERT: L 135 LYS cc_start: 0.8272 (tmtt) cc_final: 0.7940 (mtpt) REVERT: M 7 PHE cc_start: 0.7331 (OUTLIER) cc_final: 0.6163 (t80) REVERT: M 22 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.8035 (mp) REVERT: M 29 GLN cc_start: 0.7788 (tt0) cc_final: 0.7330 (mt0) REVERT: M 67 LYS cc_start: 0.8448 (mtmt) cc_final: 0.7902 (mtmt) REVERT: N 7 PHE cc_start: 0.7381 (OUTLIER) cc_final: 0.6113 (m-80) REVERT: N 129 ASP cc_start: 0.7504 (OUTLIER) cc_final: 0.7282 (m-30) REVERT: O 43 LEU cc_start: 0.9097 (tp) cc_final: 0.8832 (tp) REVERT: O 129 ASP cc_start: 0.8477 (t70) cc_final: 0.8031 (t0) REVERT: P 7 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7824 (t80) REVERT: Q 7 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.7307 (t80) REVERT: Q 31 GLN cc_start: 0.8110 (OUTLIER) cc_final: 0.7802 (pt0) REVERT: Q 77 GLU cc_start: 0.8240 (mt-10) cc_final: 0.7973 (mt-10) REVERT: Q 135 LYS cc_start: 0.8293 (tptt) cc_final: 0.7690 (tttm) REVERT: R 135 LYS cc_start: 0.8423 (tptt) cc_final: 0.7683 (ttpp) REVERT: T 31 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7882 (pt0) REVERT: T 135 LYS cc_start: 0.8686 (tppt) cc_final: 0.8328 (mptt) REVERT: V 103 ASP cc_start: 0.7757 (OUTLIER) cc_final: 0.7418 (p0) REVERT: V 109 GLN cc_start: 0.8235 (mm-40) cc_final: 0.7892 (mm-40) REVERT: V 135 LYS cc_start: 0.8532 (mptt) cc_final: 0.8143 (mttt) REVERT: W 67 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8468 (mmmt) REVERT: W 77 GLU cc_start: 0.8010 (mt-10) cc_final: 0.7619 (mt-10) REVERT: W 135 LYS cc_start: 0.8542 (tptt) cc_final: 0.8199 (mtpp) outliers start: 87 outliers final: 64 residues processed: 518 average time/residue: 0.3205 time to fit residues: 264.7402 Evaluate side-chains 516 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 441 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 31 GLN Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain H residue 31 GLN Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 82 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 7 PHE Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 92 ILE Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain Q residue 7 PHE Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 82 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 305 optimal weight: 6.9990 chunk 186 optimal weight: 0.9990 chunk 145 optimal weight: 7.9990 chunk 212 optimal weight: 3.9990 chunk 320 optimal weight: 0.0010 chunk 295 optimal weight: 0.9980 chunk 255 optimal weight: 0.7980 chunk 26 optimal weight: 10.0000 chunk 197 optimal weight: 7.9990 chunk 156 optimal weight: 0.8980 chunk 202 optimal weight: 6.9990 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN B 109 GLN C 31 GLN ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN D 149 ASN E 31 GLN G 29 GLN G 109 GLN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 24311 Z= 0.129 Angle : 0.431 7.472 33143 Z= 0.227 Chirality : 0.045 0.142 4186 Planarity : 0.003 0.024 4209 Dihedral : 3.474 14.947 3427 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 3.39 % Allowed : 21.66 % Favored : 74.95 % 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: 3.16 (0.15), residues: 3243 helix: 2.75 (0.17), residues: 1081 sheet: 1.30 (0.19), residues: 713 loop : 2.28 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 132 PHE 0.005 0.001 PHE D 108 TYR 0.008 0.001 TYR I 33 ARG 0.008 0.000 ARG P 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6486 Ramachandran restraints generated. 3243 Oldfield, 0 Emsley, 3243 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 443 time to evaluate : 2.546 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: B 12 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8310 (mp) REVERT: B 65 LYS cc_start: 0.8426 (mmtt) cc_final: 0.7766 (mttt) REVERT: D 65 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8328 (mmtp) REVERT: H 31 GLN cc_start: 0.7352 (OUTLIER) cc_final: 0.7089 (pt0) REVERT: J 91 VAL cc_start: 0.8700 (m) cc_final: 0.8419 (t) REVERT: J 129 ASP cc_start: 0.7438 (m-30) cc_final: 0.6978 (t0) REVERT: K 31 GLN cc_start: 0.7889 (OUTLIER) cc_final: 0.7485 (pt0) REVERT: L 88 LYS cc_start: 0.8702 (mmmt) cc_final: 0.8207 (mmtt) REVERT: L 135 LYS cc_start: 0.8268 (tmtt) cc_final: 0.7926 (mtpt) REVERT: M 7 PHE cc_start: 0.7206 (OUTLIER) cc_final: 0.6746 (t80) REVERT: M 22 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8057 (mp) REVERT: M 29 GLN cc_start: 0.7828 (tt0) cc_final: 0.7344 (mt0) REVERT: N 7 PHE cc_start: 0.7374 (OUTLIER) cc_final: 0.6122 (m-80) REVERT: N 129 ASP cc_start: 0.7517 (OUTLIER) cc_final: 0.7277 (m-30) REVERT: O 43 LEU cc_start: 0.9116 (tp) cc_final: 0.8830 (tp) REVERT: O 129 ASP cc_start: 0.8478 (t70) cc_final: 0.7958 (t0) REVERT: P 7 PHE cc_start: 0.8069 (OUTLIER) cc_final: 0.7813 (t80) REVERT: Q 7 PHE cc_start: 0.7769 (OUTLIER) cc_final: 0.7391 (t80) REVERT: Q 31 GLN cc_start: 0.8121 (OUTLIER) cc_final: 0.7782 (pt0) REVERT: Q 77 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7990 (mt-10) REVERT: Q 135 LYS cc_start: 0.8307 (tptt) cc_final: 0.7690 (tttm) REVERT: R 135 LYS cc_start: 0.8439 (tptt) cc_final: 0.7699 (ttpp) REVERT: S 129 ASP cc_start: 0.7004 (t70) cc_final: 0.6790 (t70) REVERT: T 31 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7878 (pt0) REVERT: T 135 LYS cc_start: 0.8679 (tppt) cc_final: 0.8306 (mptt) REVERT: V 103 ASP cc_start: 0.7758 (OUTLIER) cc_final: 0.7421 (p0) REVERT: V 109 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7881 (mm-40) REVERT: V 135 LYS cc_start: 0.8515 (mptt) cc_final: 0.8150 (mttt) REVERT: W 67 LYS cc_start: 0.8734 (mtmt) cc_final: 0.8464 (mmmt) REVERT: W 77 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7622 (mt-10) REVERT: W 135 LYS cc_start: 0.8549 (tptt) cc_final: 0.8198 (mtpp) outliers start: 88 outliers final: 69 residues processed: 510 average time/residue: 0.3530 time to fit residues: 288.3201 Evaluate side-chains 515 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 434 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 PHE Chi-restraints excluded: chain A residue 31 GLN Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 94 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 136 SER Chi-restraints excluded: chain B residue 7 PHE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 82 VAL Chi-restraints excluded: chain B residue 109 GLN Chi-restraints excluded: chain C residue 31 GLN Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 7 PHE Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 8 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 109 GLN Chi-restraints excluded: chain H residue 31 GLN Chi-restraints excluded: chain H residue 76 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 85 ASP Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 92 ILE Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 141 MET Chi-restraints excluded: chain M residue 7 PHE Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 92 ILE Chi-restraints excluded: chain M residue 112 THR Chi-restraints excluded: chain N residue 7 PHE Chi-restraints excluded: chain N residue 73 SER Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 129 ASP Chi-restraints excluded: chain O residue 8 THR Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 92 ILE Chi-restraints excluded: chain O residue 112 THR Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain P residue 8 THR Chi-restraints excluded: chain P residue 77 GLU Chi-restraints excluded: chain P residue 116 LYS Chi-restraints excluded: chain Q residue 7 PHE Chi-restraints excluded: chain Q residue 8 THR Chi-restraints excluded: chain Q residue 31 GLN Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 73 SER Chi-restraints excluded: chain R residue 76 THR Chi-restraints excluded: chain R residue 78 THR Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain W residue 73 SER Chi-restraints excluded: chain W residue 82 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 272 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 235 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 70 optimal weight: 0.0870 chunk 255 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 262 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 224 optimal weight: 5.9990 overall best weight: 0.9562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 31 GLN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 GLN G 109 GLN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.099951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.090878 restraints weight = 32464.148| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.24 r_work: 0.2876 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.281 24311 Z= 0.275 Angle : 0.824 59.051 33143 Z= 0.510 Chirality : 0.049 1.091 4186 Planarity : 0.003 0.060 4209 Dihedral : 3.506 17.994 3427 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 3.54 % Allowed : 21.43 % Favored : 75.03 % Cbeta Deviations : 0.07 % 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: 3.16 (0.15), residues: 3243 helix: 2.75 (0.17), residues: 1081 sheet: 1.29 (0.19), residues: 713 loop : 2.28 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP F 132 PHE 0.005 0.001 PHE C 108 TYR 0.007 0.001 TYR D 30 ARG 0.007 0.000 ARG P 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5698.42 seconds wall clock time: 103 minutes 7.03 seconds (6187.03 seconds total)