Starting phenix.real_space_refine on Mon May 13 05:42:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ewx_50025/05_2024/9ewx_50025.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ewx_50025/05_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_50025/05_2024/9ewx_50025.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ewx_50025/05_2024/9ewx_50025.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ewx_50025/05_2024/9ewx_50025.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9ewx_50025/05_2024/9ewx_50025.pdb" } 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-5322/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: 12.10, per 1000 atoms: 0.50 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: 9.26 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: 2.47 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: 7.88 Time building geometry restraints manager: 10.09 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 2.440 nonbonded pdb=" OG1 THR V 143 " pdb=" OD1 ASN V 149 " model vdw 2.318 2.440 nonbonded pdb=" OG1 THR I 143 " pdb=" OD1 ASN I 149 " model vdw 2.318 2.440 nonbonded pdb=" OG1 THR R 143 " pdb=" OD1 ASN R 149 " model vdw 2.318 2.440 nonbonded pdb=" OG1 THR M 143 " pdb=" OD1 ASN M 149 " model vdw 2.318 2.440 ... (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 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: 4.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 15.510 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 63.630 Find NCS groups from input model: 1.940 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.360 ------------------------------------------------------------------------------- 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 : 2.419 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: 0.3733 time to fit residues: 367.2665 Evaluate side-chains 454 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 451 time to evaluate : 3.144 ------------------------------------------------------------------------------- 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: 8.9990 chunk 244 optimal weight: 8.9990 chunk 135 optimal weight: 9.9990 chunk 83 optimal weight: 0.9990 chunk 164 optimal weight: 6.9990 chunk 130 optimal weight: 0.7980 chunk 252 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 153 optimal weight: 0.0770 chunk 187 optimal weight: 6.9990 chunk 292 optimal weight: 4.9990 overall best weight: 1.1542 ------------------------------------------------------------------------------- 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 C 125 ASN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 31 GLN F 29 GLN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 109 GLN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN L 87 ASN M 29 GLN M 109 GLN ** N 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 87 ASN O 138 GLN ** R 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 29 GLN ** S 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24311 Z= 0.159 Angle : 0.437 4.589 33143 Z= 0.234 Chirality : 0.045 0.145 4186 Planarity : 0.003 0.021 4209 Dihedral : 3.521 15.244 3430 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.66 % Allowed : 21.97 % Favored : 74.37 % 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: 3.11 (0.15), residues: 3243 helix: 2.49 (0.17), residues: 1081 sheet: 1.24 (0.20), residues: 713 loop : 2.46 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 132 PHE 0.007 0.001 PHE L 108 TYR 0.009 0.001 TYR U 33 ARG 0.002 0.000 ARG R 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 578 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 483 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 VAL cc_start: 0.8732 (m) cc_final: 0.8428 (m) REVERT: B 65 LYS cc_start: 0.8357 (mmtt) cc_final: 0.7669 (mttt) REVERT: C 135 LYS cc_start: 0.8226 (tptt) cc_final: 0.7984 (mttp) REVERT: D 65 LYS cc_start: 0.8676 (mmtt) cc_final: 0.8285 (mmtp) REVERT: I 65 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8224 (mmtm) REVERT: I 91 VAL cc_start: 0.9192 (m) cc_final: 0.8978 (t) REVERT: I 97 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7721 (mm-30) REVERT: I 116 LYS cc_start: 0.8042 (mmtm) cc_final: 0.7823 (mmtt) REVERT: J 103 ASP cc_start: 0.7857 (OUTLIER) cc_final: 0.7541 (p0) REVERT: K 91 VAL cc_start: 0.8992 (m) cc_final: 0.8745 (t) REVERT: L 135 LYS cc_start: 0.8375 (tmtt) cc_final: 0.7989 (mtpt) REVERT: M 29 GLN cc_start: 0.7913 (OUTLIER) cc_final: 0.7515 (mt0) REVERT: N 129 ASP cc_start: 0.7641 (m-30) cc_final: 0.7367 (m-30) REVERT: O 43 LEU cc_start: 0.9069 (tp) cc_final: 0.8797 (tp) REVERT: P 135 LYS cc_start: 0.8415 (mmtt) cc_final: 0.7824 (mptt) REVERT: Q 135 LYS cc_start: 0.8038 (tptt) cc_final: 0.7780 (tttm) REVERT: R 135 LYS cc_start: 0.8393 (tptt) cc_final: 0.7884 (ttpp) REVERT: R 141 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.8343 (ptm) REVERT: W 8 THR cc_start: 0.6848 (OUTLIER) cc_final: 0.6462 (m) REVERT: W 135 LYS cc_start: 0.8420 (tptt) cc_final: 0.8115 (mtpp) outliers start: 95 outliers final: 64 residues processed: 533 average time/residue: 0.3396 time to fit residues: 288.7925 Evaluate side-chains 506 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 438 time to evaluate : 2.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ASP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain B residue 8 THR Chi-restraints excluded: chain C residue 103 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain D residue 73 SER Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 112 THR Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain H residue 64 SER Chi-restraints excluded: chain H residue 78 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 19 ILE 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 103 ASP Chi-restraints excluded: chain J residue 141 MET 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 N residue 73 SER Chi-restraints excluded: chain N residue 103 ASP 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 112 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 64 SER Chi-restraints excluded: chain Q residue 74 THR 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 103 ASP 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 103 ASP 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 139 ASP Chi-restraints excluded: chain U residue 141 MET Chi-restraints excluded: chain V residue 97 GLU Chi-restraints excluded: chain V residue 139 ASP 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: 3.9990 chunk 90 optimal weight: 9.9990 chunk 243 optimal weight: 8.9990 chunk 199 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 292 optimal weight: 6.9990 chunk 316 optimal weight: 9.9990 chunk 260 optimal weight: 9.9990 chunk 290 optimal weight: 0.0980 chunk 99 optimal weight: 7.9990 chunk 235 optimal weight: 8.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- 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 31 GLN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 87 ASN F 87 ASN ** F 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN O 29 GLN P 29 GLN R 109 GLN R 125 ASN S 109 GLN T 109 GLN U 109 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 24311 Z= 0.380 Angle : 0.550 4.876 33143 Z= 0.300 Chirality : 0.050 0.205 4186 Planarity : 0.004 0.038 4209 Dihedral : 4.607 29.610 3427 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 5.93 % Allowed : 19.35 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.64 (0.15), residues: 3243 helix: 2.06 (0.17), residues: 1081 sheet: 1.29 (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 0.012 0.002 PHE E 142 TYR 0.011 0.002 TYR Q 33 ARG 0.004 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 594 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 440 time to evaluate : 2.733 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: B 22 LEU cc_start: 0.8871 (OUTLIER) cc_final: 0.8591 (mp) REVERT: B 31 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.8111 (pt0) REVERT: B 65 LYS cc_start: 0.8408 (mmtt) cc_final: 0.7750 (mttt) REVERT: C 22 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8111 (mp) REVERT: C 135 LYS cc_start: 0.8383 (tptt) cc_final: 0.8006 (mttp) REVERT: C 148 ASP cc_start: 0.7547 (OUTLIER) cc_final: 0.7162 (m-30) REVERT: D 65 LYS cc_start: 0.8667 (mmtt) cc_final: 0.8274 (mmtp) REVERT: E 141 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8183 (ptt) REVERT: F 22 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8178 (mp) REVERT: I 97 GLU cc_start: 0.8037 (mt-10) cc_final: 0.7798 (mm-30) REVERT: J 22 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8133 (mp) REVERT: K 31 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.7824 (pt0) REVERT: L 22 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8371 (mp) REVERT: L 135 LYS cc_start: 0.8297 (tmtt) cc_final: 0.7912 (mtpt) REVERT: M 7 PHE cc_start: 0.7359 (OUTLIER) cc_final: 0.7027 (t80) REVERT: M 22 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8227 (mp) REVERT: M 29 GLN cc_start: 0.8105 (tt0) cc_final: 0.7852 (mt0) REVERT: M 135 LYS cc_start: 0.8897 (mmtt) cc_final: 0.8577 (tttp) REVERT: N 129 ASP cc_start: 0.7666 (OUTLIER) cc_final: 0.7385 (m-30) REVERT: O 7 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7516 (t80) REVERT: P 22 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8415 (mp) REVERT: Q 22 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8283 (mp) REVERT: Q 87 ASN cc_start: 0.8745 (t0) cc_final: 0.8538 (t0) REVERT: Q 135 LYS cc_start: 0.8103 (tptt) cc_final: 0.7721 (tttm) REVERT: R 135 LYS cc_start: 0.8510 (tptt) cc_final: 0.7852 (ttpp) REVERT: S 22 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8405 (mp) REVERT: U 103 ASP cc_start: 0.8353 (p0) cc_final: 0.8080 (p0) REVERT: V 135 LYS cc_start: 0.8567 (mptt) cc_final: 0.8177 (mttt) REVERT: W 135 LYS cc_start: 0.8559 (tptt) cc_final: 0.8238 (ttpp) outliers start: 154 outliers final: 107 residues processed: 545 average time/residue: 0.3490 time to fit residues: 303.3128 Evaluate side-chains 541 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 418 time to evaluate : 2.892 ------------------------------------------------------------------------------- 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 103 ASP Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 136 SER 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 103 ASP Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 112 THR Chi-restraints excluded: chain C residue 148 ASP 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 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 103 ASP Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain H residue 64 SER 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 22 LEU Chi-restraints excluded: chain J residue 73 SER 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 31 GLN Chi-restraints excluded: chain K residue 37 SER 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 21 ILE Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 112 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 N residue 139 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 112 THR 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 41 SER Chi-restraints excluded: chain Q residue 64 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 Q residue 129 ASP Chi-restraints excluded: chain Q residue 141 MET 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 103 ASP Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 112 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 74 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 91 VAL Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 64 SER 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 139 ASP 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 Chi-restraints excluded: chain W residue 139 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 289 optimal weight: 9.9990 chunk 220 optimal weight: 0.9980 chunk 152 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 139 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 293 optimal weight: 2.9990 chunk 311 optimal weight: 4.9990 chunk 153 optimal weight: 6.9990 chunk 278 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 D 109 GLN D 125 ASN E 87 ASN G 109 GLN I 109 GLN J 109 GLN L 29 GLN M 29 GLN M 87 ASN M 109 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 24311 Z= 0.257 Angle : 0.476 4.712 33143 Z= 0.258 Chirality : 0.047 0.163 4186 Planarity : 0.004 0.029 4209 Dihedral : 4.288 28.431 3427 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 5.81 % Allowed : 18.78 % Favored : 75.41 % 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: 2.66 (0.15), residues: 3243 helix: 2.21 (0.17), residues: 1081 sheet: 1.19 (0.19), residues: 713 loop : 1.99 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 132 PHE 0.008 0.001 PHE E 142 TYR 0.007 0.001 TYR B 33 ARG 0.003 0.000 ARG E 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 587 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 436 time to evaluate : 2.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8517 (mp) REVERT: B 31 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8054 (pt0) REVERT: B 65 LYS cc_start: 0.8428 (mmtt) cc_final: 0.7760 (mttt) REVERT: C 22 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8234 (mp) REVERT: C 135 LYS cc_start: 0.8392 (tptt) cc_final: 0.8036 (mptt) REVERT: D 65 LYS cc_start: 0.8686 (mmtt) cc_final: 0.8274 (mmtp) REVERT: E 141 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8215 (ptt) REVERT: H 31 GLN cc_start: 0.7452 (OUTLIER) cc_final: 0.7083 (pt0) REVERT: I 97 GLU cc_start: 0.8027 (mt-10) cc_final: 0.7787 (mm-30) REVERT: J 13 MET cc_start: 0.8576 (mmm) cc_final: 0.8350 (mmm) REVERT: J 22 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8088 (mp) REVERT: J 129 ASP cc_start: 0.7377 (m-30) cc_final: 0.7028 (t70) REVERT: K 22 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8106 (mp) REVERT: K 31 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7714 (pt0) REVERT: L 103 ASP cc_start: 0.7918 (p0) cc_final: 0.7461 (p0) REVERT: L 129 ASP cc_start: 0.7722 (t0) cc_final: 0.7286 (t0) REVERT: L 135 LYS cc_start: 0.8307 (tmtt) cc_final: 0.7917 (mtpt) REVERT: M 7 PHE cc_start: 0.7364 (OUTLIER) cc_final: 0.6974 (t80) REVERT: M 29 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7557 (mt0) REVERT: M 135 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8635 (tttp) REVERT: N 22 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8521 (mp) REVERT: N 129 ASP cc_start: 0.7573 (OUTLIER) cc_final: 0.7314 (m-30) REVERT: O 7 PHE cc_start: 0.7976 (OUTLIER) cc_final: 0.7652 (t80) REVERT: Q 77 GLU cc_start: 0.8141 (mt-10) cc_final: 0.7881 (mt-10) REVERT: Q 135 LYS cc_start: 0.8179 (tptt) cc_final: 0.7731 (tttm) REVERT: R 135 LYS cc_start: 0.8508 (tptt) cc_final: 0.7833 (ttpp) REVERT: T 31 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8203 (pt0) REVERT: V 135 LYS cc_start: 0.8560 (mptt) cc_final: 0.8177 (mttt) REVERT: W 10 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8350 (mm) REVERT: W 135 LYS cc_start: 0.8568 (tptt) cc_final: 0.8056 (ttpp) outliers start: 151 outliers final: 112 residues processed: 540 average time/residue: 0.3366 time to fit residues: 292.0116 Evaluate side-chains 546 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 419 time to evaluate : 2.759 ------------------------------------------------------------------------------- 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 103 ASP 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 22 LEU 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 103 ASP 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 29 GLN Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain H residue 31 GLN Chi-restraints excluded: chain H residue 64 SER 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 22 LEU Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 78 THR Chi-restraints excluded: chain J residue 141 MET Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 37 SER 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 K residue 149 ASN Chi-restraints excluded: chain L residue 8 THR Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 85 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 29 GLN 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 74 THR 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 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 Q residue 8 THR Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 64 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 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 103 ASP Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 74 THR 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 22 LEU Chi-restraints excluded: chain T residue 31 GLN Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 64 SER Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 91 VAL 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 78 THR Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 125 ASN Chi-restraints excluded: chain U residue 139 ASP Chi-restraints excluded: chain U residue 149 ASN 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 V residue 139 ASP 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 80 VAL Chi-restraints excluded: chain W residue 82 VAL Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 139 ASP Chi-restraints excluded: chain W residue 148 ASP Chi-restraints excluded: chain W residue 149 ASN 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: 0.8980 chunk 265 optimal weight: 0.9980 chunk 215 optimal weight: 0.0970 chunk 0 optimal weight: 7.9990 chunk 158 optimal weight: 0.9980 chunk 279 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 overall best weight: 1.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 ASN ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 87 ASN G 109 GLN I 109 GLN M 109 GLN ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 109 GLN S 109 GLN T 149 ASN V 31 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 24311 Z= 0.206 Angle : 0.459 11.402 33143 Z= 0.246 Chirality : 0.046 0.151 4186 Planarity : 0.003 0.029 4209 Dihedral : 4.139 26.893 3427 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 5.89 % Allowed : 18.81 % Favored : 75.30 % 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: 2.32 (0.17), residues: 1081 sheet: 1.08 (0.19), residues: 713 loop : 2.01 (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 S 7 TYR 0.011 0.001 TYR G 33 ARG 0.002 0.000 ARG E 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 579 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 426 time to evaluate : 2.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 65 LYS cc_start: 0.8426 (mmtt) cc_final: 0.7767 (mttt) REVERT: B 77 GLU cc_start: 0.8347 (mp0) cc_final: 0.8106 (mp0) REVERT: C 22 LEU cc_start: 0.8538 (OUTLIER) cc_final: 0.8192 (mp) REVERT: C 135 LYS cc_start: 0.8296 (tptt) cc_final: 0.8029 (mptt) REVERT: D 65 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8285 (mmtp) REVERT: E 141 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.8180 (ptt) REVERT: G 85 ASP cc_start: 0.8411 (p0) cc_final: 0.8136 (p0) REVERT: H 31 GLN cc_start: 0.7502 (OUTLIER) cc_final: 0.7219 (pt0) REVERT: I 97 GLU cc_start: 0.8026 (mt-10) cc_final: 0.7788 (mm-30) REVERT: J 13 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8292 (mmm) REVERT: J 22 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8076 (mp) REVERT: J 91 VAL cc_start: 0.8763 (m) cc_final: 0.8444 (t) REVERT: J 129 ASP cc_start: 0.7446 (m-30) cc_final: 0.7020 (t70) REVERT: K 22 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.8051 (mp) REVERT: K 31 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7691 (pt0) REVERT: L 22 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8311 (mp) REVERT: L 103 ASP cc_start: 0.7859 (p0) cc_final: 0.7407 (p0) REVERT: L 135 LYS cc_start: 0.8331 (tmtt) cc_final: 0.7931 (mtpt) REVERT: M 7 PHE cc_start: 0.7321 (OUTLIER) cc_final: 0.6979 (t80) REVERT: M 22 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8128 (mp) REVERT: M 135 LYS cc_start: 0.8897 (mmtt) cc_final: 0.8603 (tttp) REVERT: N 22 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8494 (mp) REVERT: N 129 ASP cc_start: 0.7565 (OUTLIER) cc_final: 0.7312 (m-30) REVERT: O 7 PHE cc_start: 0.7977 (OUTLIER) cc_final: 0.7710 (t80) REVERT: O 11 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8244 (tt0) REVERT: P 22 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8360 (mp) REVERT: Q 31 GLN cc_start: 0.8244 (OUTLIER) cc_final: 0.7936 (pt0) REVERT: Q 77 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7932 (mt-10) REVERT: Q 135 LYS cc_start: 0.8227 (tptt) cc_final: 0.7753 (tttm) REVERT: R 135 LYS cc_start: 0.8454 (tptt) cc_final: 0.7755 (ttpp) REVERT: S 22 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8406 (mp) REVERT: V 135 LYS cc_start: 0.8549 (mptt) cc_final: 0.8169 (mttt) REVERT: W 31 GLN cc_start: 0.7820 (OUTLIER) cc_final: 0.7578 (pt0) REVERT: W 135 LYS cc_start: 0.8558 (tptt) cc_final: 0.8265 (ttpp) outliers start: 153 outliers final: 115 residues processed: 538 average time/residue: 0.3285 time to fit residues: 284.0839 Evaluate side-chains 550 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 417 time to evaluate : 2.778 ------------------------------------------------------------------------------- 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 103 ASP 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 103 ASP 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 37 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 8 THR Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain H residue 31 GLN Chi-restraints excluded: chain H residue 64 SER 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 22 LEU Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 37 SER 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 K residue 149 ASN 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 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 74 THR 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 N residue 139 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 22 LEU Chi-restraints excluded: chain P residue 116 LYS 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 64 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 129 ASP Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 37 SER 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 103 ASP 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 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 37 SER Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 64 SER Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 91 VAL 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 U residue 8 THR Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 74 THR 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 139 ASP Chi-restraints excluded: chain U residue 141 MET Chi-restraints excluded: chain U residue 149 ASN 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 V residue 139 ASP 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 82 VAL Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 139 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 104 optimal weight: 9.9990 chunk 280 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 182 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 311 optimal weight: 2.9990 chunk 258 optimal weight: 7.9990 chunk 144 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 103 optimal weight: 1.9990 chunk 163 optimal weight: 2.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 ASN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 87 ASN G 109 GLN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 29 GLN M 109 GLN ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 31 GLN Q 87 ASN T 149 ASN V 31 GLN W 29 GLN W 149 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 24311 Z= 0.223 Angle : 0.462 7.622 33143 Z= 0.249 Chirality : 0.047 0.153 4186 Planarity : 0.003 0.029 4209 Dihedral : 4.162 25.752 3427 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 6.31 % Allowed : 18.39 % Favored : 75.30 % 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: 2.63 (0.15), residues: 3243 helix: 2.30 (0.17), residues: 1081 sheet: 0.97 (0.19), residues: 713 loop : 1.99 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 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 582 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 418 time to evaluate : 2.705 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: B 31 GLN cc_start: 0.8296 (OUTLIER) cc_final: 0.8052 (pt0) REVERT: B 65 LYS cc_start: 0.8432 (mmtt) cc_final: 0.7771 (mttt) REVERT: B 77 GLU cc_start: 0.8329 (mp0) cc_final: 0.8107 (mp0) REVERT: C 22 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8199 (mp) REVERT: C 135 LYS cc_start: 0.8310 (tptt) cc_final: 0.8028 (mptt) REVERT: D 65 LYS cc_start: 0.8725 (mmtt) cc_final: 0.8285 (mmtp) REVERT: E 141 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.8171 (ptt) REVERT: G 85 ASP cc_start: 0.8496 (p0) cc_final: 0.8211 (p0) REVERT: H 31 GLN cc_start: 0.7526 (OUTLIER) cc_final: 0.7221 (pt0) REVERT: I 97 GLU cc_start: 0.8045 (mt-10) cc_final: 0.7808 (mm-30) REVERT: J 13 MET cc_start: 0.8585 (OUTLIER) cc_final: 0.8280 (mmm) REVERT: J 22 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8075 (mp) REVERT: J 129 ASP cc_start: 0.7449 (m-30) cc_final: 0.7058 (t70) REVERT: K 22 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8073 (mp) REVERT: K 31 GLN cc_start: 0.8063 (OUTLIER) cc_final: 0.7693 (pt0) REVERT: L 22 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8303 (mp) REVERT: L 103 ASP cc_start: 0.7836 (p0) cc_final: 0.7366 (p0) REVERT: L 135 LYS cc_start: 0.8321 (tmtt) cc_final: 0.7954 (mtpt) REVERT: M 7 PHE cc_start: 0.7382 (OUTLIER) cc_final: 0.7047 (t80) REVERT: M 22 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8119 (mp) REVERT: M 135 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8578 (tttp) REVERT: N 129 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7279 (m-30) REVERT: O 7 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7763 (t80) REVERT: O 11 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8233 (tt0) REVERT: P 7 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7834 (t80) REVERT: P 22 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8343 (mp) REVERT: Q 31 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7947 (pt0) REVERT: Q 77 GLU cc_start: 0.8211 (mt-10) cc_final: 0.7951 (mt-10) REVERT: Q 135 LYS cc_start: 0.8274 (tptt) cc_final: 0.7758 (tttm) REVERT: R 135 LYS cc_start: 0.8472 (tptt) cc_final: 0.7766 (ttpp) REVERT: R 141 MET cc_start: 0.8636 (OUTLIER) cc_final: 0.8315 (ptm) REVERT: S 22 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8395 (mp) REVERT: V 135 LYS cc_start: 0.8559 (mptt) cc_final: 0.8170 (mttt) REVERT: W 31 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7590 (pt0) REVERT: W 135 LYS cc_start: 0.8566 (tptt) cc_final: 0.8257 (ttpp) outliers start: 164 outliers final: 133 residues processed: 537 average time/residue: 0.3304 time to fit residues: 284.0591 Evaluate side-chains 563 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 410 time to evaluate : 2.844 ------------------------------------------------------------------------------- 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 103 ASP 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 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 103 ASP 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 8 THR Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain H residue 31 GLN Chi-restraints excluded: chain H residue 64 SER 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 22 LEU Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 78 THR 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 J residue 149 ASN Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 149 ASN 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 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 74 THR 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 N residue 139 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 P residue 116 LYS 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 64 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 141 MET Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 37 SER 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 R residue 82 VAL Chi-restraints excluded: chain R residue 103 ASP 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 149 ASN Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 139 ASP 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 37 SER Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 64 SER 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 149 ASN Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 74 THR 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 139 ASP Chi-restraints excluded: chain U residue 141 MET Chi-restraints excluded: chain U residue 149 ASN 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 V residue 139 ASP 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 82 VAL Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 139 ASP 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: 0.9990 chunk 35 optimal weight: 7.9990 chunk 177 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 176 optimal weight: 3.9990 chunk 262 optimal weight: 4.9990 chunk 173 optimal weight: 0.0970 chunk 310 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 189 optimal weight: 8.9990 chunk 143 optimal weight: 0.9980 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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** C 87 ASN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 87 ASN ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 149 ASN V 31 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24311 Z= 0.173 Angle : 0.439 5.875 33143 Z= 0.235 Chirality : 0.046 0.147 4186 Planarity : 0.003 0.028 4209 Dihedral : 3.984 23.446 3427 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.93 % Allowed : 18.62 % Favored : 75.45 % 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: 2.73 (0.15), residues: 3243 helix: 2.42 (0.17), residues: 1081 sheet: 0.97 (0.19), residues: 713 loop : 2.06 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 132 PHE 0.005 0.001 PHE W 108 TYR 0.008 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 584 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 430 time to evaluate : 2.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 GLN cc_start: 0.8258 (OUTLIER) cc_final: 0.8010 (pt0) REVERT: B 65 LYS cc_start: 0.8430 (mmtt) cc_final: 0.7772 (mttt) REVERT: B 77 GLU cc_start: 0.8303 (mp0) cc_final: 0.8099 (mp0) REVERT: C 22 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8213 (mp) REVERT: C 135 LYS cc_start: 0.8319 (tptt) cc_final: 0.8040 (mptt) REVERT: D 65 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8281 (mmtp) REVERT: G 85 ASP cc_start: 0.8507 (p0) cc_final: 0.8222 (p0) REVERT: H 31 GLN cc_start: 0.7441 (OUTLIER) cc_final: 0.7158 (pt0) REVERT: I 97 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7813 (mm-30) REVERT: J 13 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8326 (mmm) REVERT: J 129 ASP cc_start: 0.7447 (m-30) cc_final: 0.7071 (t70) REVERT: K 22 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8068 (mp) REVERT: K 31 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7684 (pt0) REVERT: K 91 VAL cc_start: 0.8952 (m) cc_final: 0.8720 (t) REVERT: L 22 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8306 (mp) REVERT: L 103 ASP cc_start: 0.7787 (p0) cc_final: 0.7314 (p0) REVERT: L 135 LYS cc_start: 0.8331 (tmtt) cc_final: 0.7956 (mtpt) REVERT: M 7 PHE cc_start: 0.7394 (OUTLIER) cc_final: 0.7028 (t80) REVERT: M 22 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8088 (mp) REVERT: N 129 ASP cc_start: 0.7557 (m-30) cc_final: 0.7296 (m-30) REVERT: O 7 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7758 (t80) REVERT: P 7 PHE cc_start: 0.8154 (OUTLIER) cc_final: 0.7852 (t80) REVERT: P 22 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8315 (mp) REVERT: Q 31 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.7922 (pt0) REVERT: Q 77 GLU cc_start: 0.8226 (mt-10) cc_final: 0.7977 (mt-10) REVERT: R 135 LYS cc_start: 0.8457 (tptt) cc_final: 0.7749 (ttpp) REVERT: S 22 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8433 (mp) REVERT: T 22 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8432 (mp) REVERT: V 22 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8578 (mp) REVERT: V 135 LYS cc_start: 0.8575 (mptt) cc_final: 0.8169 (mttt) REVERT: W 31 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7561 (pt0) REVERT: W 135 LYS cc_start: 0.8597 (tptt) cc_final: 0.8346 (mtpp) outliers start: 154 outliers final: 126 residues processed: 542 average time/residue: 0.3297 time to fit residues: 286.4468 Evaluate side-chains 565 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 422 time to evaluate : 2.610 ------------------------------------------------------------------------------- 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 52 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 103 ASP 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 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 103 ASP 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 F residue 8 THR Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain H residue 31 GLN Chi-restraints excluded: chain H residue 64 SER 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 92 ILE Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 141 MET Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 149 ASN 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 110 THR 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 74 THR Chi-restraints excluded: chain N residue 92 ILE Chi-restraints excluded: chain N residue 103 ASP Chi-restraints excluded: chain N residue 139 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 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 31 GLN Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 64 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 141 MET Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 37 SER 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 R residue 82 VAL Chi-restraints excluded: chain R residue 103 ASP 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 74 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 139 ASP 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 64 SER 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 U residue 8 THR Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 125 ASN Chi-restraints excluded: chain U residue 139 ASP Chi-restraints excluded: chain U residue 141 MET Chi-restraints excluded: chain U residue 149 ASN Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 85 ASP Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 139 ASP 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 82 VAL Chi-restraints excluded: chain W residue 112 THR Chi-restraints excluded: chain W residue 139 ASP Chi-restraints excluded: chain W residue 148 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 192 optimal weight: 0.0770 chunk 123 optimal weight: 4.9990 chunk 185 optimal weight: 0.9980 chunk 93 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 197 optimal weight: 5.9990 chunk 211 optimal weight: 6.9990 chunk 153 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 243 optimal weight: 3.9990 chunk 282 optimal weight: 3.9990 overall best weight: 1.9942 ------------------------------------------------------------------------------- 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** C 87 ASN D 125 ASN E 87 ASN E 149 ASN G 109 GLN ** H 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 149 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24311 Z= 0.222 Angle : 0.463 5.682 33143 Z= 0.249 Chirality : 0.047 0.154 4186 Planarity : 0.003 0.031 4209 Dihedral : 4.130 24.879 3427 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 6.46 % Allowed : 18.12 % Favored : 75.41 % 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: 2.64 (0.15), residues: 3243 helix: 2.34 (0.17), residues: 1081 sheet: 0.93 (0.19), residues: 713 loop : 1.99 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 132 PHE 0.006 0.001 PHE E 142 TYR 0.010 0.001 TYR G 33 ARG 0.007 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 589 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 421 time to evaluate : 2.566 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: A 125 ASN cc_start: 0.8166 (t0) cc_final: 0.7893 (t0) REVERT: B 31 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.8056 (pt0) REVERT: B 65 LYS cc_start: 0.8436 (mmtt) cc_final: 0.7777 (mttt) REVERT: B 77 GLU cc_start: 0.8306 (mp0) cc_final: 0.8105 (mp0) REVERT: C 22 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8192 (mp) REVERT: C 77 GLU cc_start: 0.8192 (mp0) cc_final: 0.7953 (mp0) REVERT: C 135 LYS cc_start: 0.8338 (tptt) cc_final: 0.7941 (mttp) REVERT: D 65 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8346 (mmtp) REVERT: G 85 ASP cc_start: 0.8496 (p0) cc_final: 0.8206 (p0) REVERT: H 31 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7287 (pt0) REVERT: I 97 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7817 (mm-30) REVERT: J 13 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8292 (mmm) REVERT: J 22 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8069 (mp) REVERT: J 129 ASP cc_start: 0.7448 (m-30) cc_final: 0.7042 (t0) REVERT: K 22 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8055 (mp) REVERT: K 31 GLN cc_start: 0.8070 (OUTLIER) cc_final: 0.7701 (pt0) REVERT: L 22 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8284 (mp) REVERT: L 103 ASP cc_start: 0.7798 (p0) cc_final: 0.7348 (p0) REVERT: L 135 LYS cc_start: 0.8319 (tmtt) cc_final: 0.7956 (mtpt) REVERT: M 7 PHE cc_start: 0.7385 (OUTLIER) cc_final: 0.7033 (t80) REVERT: M 22 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8121 (mp) REVERT: M 135 LYS cc_start: 0.8918 (mmtt) cc_final: 0.8601 (tttp) REVERT: N 129 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7256 (m-30) REVERT: P 7 PHE cc_start: 0.8125 (OUTLIER) cc_final: 0.7868 (t80) REVERT: P 22 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8330 (mp) REVERT: Q 31 GLN cc_start: 0.8256 (OUTLIER) cc_final: 0.7950 (pt0) REVERT: Q 77 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7995 (mt-10) REVERT: R 135 LYS cc_start: 0.8479 (tptt) cc_final: 0.7780 (ttpp) REVERT: R 141 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8299 (ptm) REVERT: S 22 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8410 (mp) REVERT: V 22 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8561 (mp) REVERT: V 135 LYS cc_start: 0.8544 (mptt) cc_final: 0.8156 (mttt) REVERT: W 31 GLN cc_start: 0.7825 (OUTLIER) cc_final: 0.7582 (pt0) REVERT: W 135 LYS cc_start: 0.8601 (tptt) cc_final: 0.8334 (mtpp) outliers start: 168 outliers final: 140 residues processed: 542 average time/residue: 0.3253 time to fit residues: 283.7407 Evaluate side-chains 572 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 414 time to evaluate : 2.588 ------------------------------------------------------------------------------- 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 52 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 103 ASP 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 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 103 ASP 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 F residue 8 THR Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain H residue 31 GLN Chi-restraints excluded: chain H residue 64 SER 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 I residue 124 LEU Chi-restraints excluded: chain J residue 8 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 92 ILE Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 141 MET Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 22 LEU 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 98 ASP Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 149 ASN 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 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 110 THR 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 74 THR 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 N residue 139 ASP 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 P residue 22 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 116 LYS 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 64 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 141 MET Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 37 SER 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 R residue 82 VAL Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain R residue 141 MET Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 139 ASP Chi-restraints excluded: chain S residue 141 MET Chi-restraints excluded: chain S residue 149 ASN 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 64 SER Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 91 VAL 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 149 ASN Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 125 ASN Chi-restraints excluded: chain U residue 139 ASP Chi-restraints excluded: chain U residue 141 MET Chi-restraints excluded: chain U residue 149 ASN Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain V residue 139 ASP 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 139 ASP Chi-restraints excluded: chain W residue 148 ASP Chi-restraints excluded: chain W residue 149 ASN 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: 0.7980 chunk 174 optimal weight: 6.9990 chunk 125 optimal weight: 0.0870 chunk 227 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 261 optimal weight: 7.9990 chunk 273 optimal weight: 6.9990 chunk 288 optimal weight: 6.9990 chunk 189 optimal weight: 7.9990 overall best weight: 1.7764 ------------------------------------------------------------------------------- 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** C 87 ASN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 87 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 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 109 GLN ** O 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 87 ASN T 149 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 24311 Z= 0.203 Angle : 0.455 5.175 33143 Z= 0.244 Chirality : 0.046 0.152 4186 Planarity : 0.003 0.033 4209 Dihedral : 4.076 24.409 3427 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 6.54 % Allowed : 18.20 % Favored : 75.26 % 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: 2.66 (0.15), residues: 3243 helix: 2.37 (0.17), residues: 1081 sheet: 0.92 (0.19), residues: 713 loop : 2.01 (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 N 108 TYR 0.009 0.001 TYR I 33 ARG 0.006 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 590 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 420 time to evaluate : 2.819 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 125 ASN cc_start: 0.8182 (t0) cc_final: 0.7906 (t0) REVERT: B 31 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.8035 (pt0) REVERT: B 65 LYS cc_start: 0.8434 (mmtt) cc_final: 0.7773 (mttt) REVERT: C 22 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8195 (mp) REVERT: C 77 GLU cc_start: 0.8199 (mp0) cc_final: 0.7953 (mp0) REVERT: C 135 LYS cc_start: 0.8328 (tptt) cc_final: 0.8003 (mptt) REVERT: D 65 LYS cc_start: 0.8723 (mmtt) cc_final: 0.8345 (mmtp) REVERT: G 85 ASP cc_start: 0.8517 (p0) cc_final: 0.8225 (p0) REVERT: H 31 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7199 (pt0) REVERT: I 97 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7835 (mm-30) REVERT: J 13 MET cc_start: 0.8598 (OUTLIER) cc_final: 0.8316 (mmm) REVERT: J 22 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8124 (mp) REVERT: J 129 ASP cc_start: 0.7447 (m-30) cc_final: 0.7087 (t70) REVERT: K 22 LEU cc_start: 0.8339 (OUTLIER) cc_final: 0.8072 (mp) REVERT: K 31 GLN cc_start: 0.8061 (OUTLIER) cc_final: 0.7690 (pt0) REVERT: L 22 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8282 (mp) REVERT: L 135 LYS cc_start: 0.8324 (tmtt) cc_final: 0.7932 (mtpt) REVERT: M 7 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.7072 (t80) REVERT: M 22 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8118 (mp) REVERT: N 129 ASP cc_start: 0.7524 (OUTLIER) cc_final: 0.7272 (m-30) REVERT: P 7 PHE cc_start: 0.8104 (OUTLIER) cc_final: 0.7850 (t80) REVERT: P 22 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8346 (mp) REVERT: Q 31 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7946 (pt0) REVERT: Q 77 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7969 (mt-10) REVERT: R 135 LYS cc_start: 0.8476 (tptt) cc_final: 0.7780 (ttpp) REVERT: R 141 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8284 (ptm) REVERT: S 22 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8427 (mp) REVERT: T 22 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8443 (mp) REVERT: V 22 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8579 (mp) REVERT: V 135 LYS cc_start: 0.8549 (mptt) cc_final: 0.8151 (mttt) REVERT: W 31 GLN cc_start: 0.7811 (OUTLIER) cc_final: 0.7567 (pt0) REVERT: W 135 LYS cc_start: 0.8625 (tptt) cc_final: 0.8346 (mtpp) outliers start: 170 outliers final: 143 residues processed: 544 average time/residue: 0.3292 time to fit residues: 288.0813 Evaluate side-chains 579 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 417 time to evaluate : 2.741 ------------------------------------------------------------------------------- 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 52 THR Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 103 ASP 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 109 GLN Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 82 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 103 ASP 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 F residue 8 THR Chi-restraints excluded: chain F residue 29 GLN Chi-restraints excluded: chain F residue 76 THR Chi-restraints excluded: chain F residue 103 ASP Chi-restraints excluded: chain F residue 112 THR Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 31 GLN Chi-restraints excluded: chain G residue 103 ASP Chi-restraints excluded: chain G residue 112 THR Chi-restraints excluded: chain G residue 129 ASP Chi-restraints excluded: chain H residue 31 GLN Chi-restraints excluded: chain H residue 64 SER 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 I residue 124 LEU Chi-restraints excluded: chain J residue 8 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 92 ILE Chi-restraints excluded: chain J residue 103 ASP Chi-restraints excluded: chain J residue 141 MET Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 8 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 31 GLN Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 52 THR Chi-restraints excluded: chain K residue 73 SER Chi-restraints excluded: chain K residue 98 ASP Chi-restraints excluded: chain K residue 112 THR Chi-restraints excluded: chain K residue 149 ASN 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 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 110 THR 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 74 THR 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 N residue 139 ASP 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 P residue 22 LEU Chi-restraints excluded: chain P residue 74 THR Chi-restraints excluded: chain P residue 116 LYS 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 64 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 141 MET Chi-restraints excluded: chain R residue 8 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 37 SER 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 R residue 82 VAL Chi-restraints excluded: chain R residue 103 ASP Chi-restraints excluded: chain R residue 110 THR Chi-restraints excluded: chain R residue 139 ASP Chi-restraints excluded: chain R residue 141 MET Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 139 ASP Chi-restraints excluded: chain S residue 141 MET Chi-restraints excluded: chain S residue 149 ASN Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 37 SER Chi-restraints excluded: chain T residue 52 THR Chi-restraints excluded: chain T residue 64 SER Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 91 VAL 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 149 ASN Chi-restraints excluded: chain U residue 8 THR Chi-restraints excluded: chain U residue 73 SER Chi-restraints excluded: chain U residue 74 THR Chi-restraints excluded: chain U residue 78 THR Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain U residue 110 THR Chi-restraints excluded: chain U residue 125 ASN Chi-restraints excluded: chain U residue 139 ASP Chi-restraints excluded: chain U residue 141 MET Chi-restraints excluded: chain U residue 149 ASN Chi-restraints excluded: chain V residue 7 PHE Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 103 ASP Chi-restraints excluded: chain V residue 112 THR Chi-restraints excluded: chain V residue 139 ASP 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 139 ASP Chi-restraints excluded: chain W residue 148 ASP Chi-restraints excluded: chain W residue 149 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 322 random chunks: chunk 305 optimal weight: 9.9990 chunk 186 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 212 optimal weight: 0.0870 chunk 320 optimal weight: 8.9990 chunk 295 optimal weight: 0.1980 chunk 255 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 197 optimal weight: 0.5980 chunk 156 optimal weight: 0.9980 chunk 202 optimal weight: 10.0000 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 87 ASN C 149 ASN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 87 ASN G 29 GLN G 109 GLN L 29 GLN M 109 GLN O 31 GLN O 149 ASN Q 87 ASN T 149 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 24311 Z= 0.112 Angle : 0.410 4.700 33143 Z= 0.217 Chirality : 0.045 0.141 4186 Planarity : 0.003 0.028 4209 Dihedral : 3.634 20.731 3427 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 3.50 % Allowed : 21.32 % 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: 2.95 (0.15), residues: 3243 helix: 2.65 (0.17), residues: 1081 sheet: 1.07 (0.19), residues: 713 loop : 2.15 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 132 PHE 0.005 0.001 PHE N 108 TYR 0.008 0.001 TYR I 33 ARG 0.007 0.000 ARG S 126 ********************** 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 559 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 468 time to evaluate : 2.671 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: B 65 LYS cc_start: 0.8414 (mmtt) cc_final: 0.7755 (mttt) REVERT: C 77 GLU cc_start: 0.8197 (mp0) cc_final: 0.7897 (mp0) REVERT: C 135 LYS cc_start: 0.8322 (tptt) cc_final: 0.8001 (mptt) REVERT: D 65 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8319 (mmtp) REVERT: G 85 ASP cc_start: 0.8512 (p0) cc_final: 0.8281 (p0) REVERT: G 141 MET cc_start: 0.8355 (ptp) cc_final: 0.8144 (ptm) REVERT: H 31 GLN cc_start: 0.7344 (OUTLIER) cc_final: 0.7099 (pt0) REVERT: I 97 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7851 (mm-30) REVERT: J 129 ASP cc_start: 0.7458 (m-30) cc_final: 0.7032 (t0) REVERT: K 31 GLN cc_start: 0.7984 (OUTLIER) cc_final: 0.7596 (pt0) REVERT: L 22 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8256 (mp) REVERT: L 135 LYS cc_start: 0.8271 (tmtt) cc_final: 0.7914 (mtpt) REVERT: M 7 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.6997 (t80) REVERT: M 22 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.8033 (mp) REVERT: O 43 LEU cc_start: 0.9115 (tp) cc_final: 0.8830 (tp) REVERT: O 91 VAL cc_start: 0.8739 (m) cc_final: 0.8502 (t) REVERT: P 7 PHE cc_start: 0.8087 (OUTLIER) cc_final: 0.7840 (t80) REVERT: Q 7 PHE cc_start: 0.7773 (OUTLIER) cc_final: 0.7168 (t80) REVERT: Q 77 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7979 (mt-10) REVERT: R 135 LYS cc_start: 0.8448 (tptt) cc_final: 0.7747 (ttpp) REVERT: S 22 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8432 (mp) REVERT: V 135 LYS cc_start: 0.8541 (mptt) cc_final: 0.8131 (mttt) REVERT: W 135 LYS cc_start: 0.8602 (tptt) cc_final: 0.8283 (mtpp) outliers start: 91 outliers final: 66 residues processed: 530 average time/residue: 0.3338 time to fit residues: 282.2503 Evaluate side-chains 522 residues out of total 2599 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 448 time to evaluate : 2.769 ------------------------------------------------------------------------------- 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 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 82 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 76 THR Chi-restraints excluded: chain D residue 136 SER Chi-restraints excluded: chain E residue 73 SER 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 I residue 8 THR Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain J residue 73 SER Chi-restraints excluded: chain J residue 78 THR 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 22 LEU Chi-restraints excluded: chain L residue 29 GLN 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 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 8 THR Chi-restraints excluded: chain O residue 73 SER Chi-restraints excluded: chain O residue 82 VAL Chi-restraints excluded: chain O residue 141 MET Chi-restraints excluded: chain P residue 7 PHE Chi-restraints excluded: chain Q residue 7 PHE Chi-restraints excluded: chain Q residue 41 SER Chi-restraints excluded: chain Q residue 78 THR Chi-restraints excluded: chain Q residue 141 MET 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 R residue 103 ASP Chi-restraints excluded: chain R residue 141 MET Chi-restraints excluded: chain R residue 149 ASN Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 73 SER Chi-restraints excluded: chain S residue 74 THR Chi-restraints excluded: chain S residue 78 THR Chi-restraints excluded: chain S residue 112 THR Chi-restraints excluded: chain S residue 149 ASN Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 64 SER Chi-restraints excluded: chain T residue 78 THR Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 149 ASN 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 103 ASP 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: 5.9990 chunk 78 optimal weight: 2.9990 chunk 235 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 255 optimal weight: 0.9990 chunk 107 optimal weight: 0.6980 chunk 262 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 224 optimal weight: 4.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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** C 87 ASN ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 125 ASN E 29 GLN E 87 ASN G 29 GLN G 109 GLN M 29 GLN ** M 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 149 ASN ** V 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.096040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.087239 restraints weight = 32843.093| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.22 r_work: 0.2810 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2701 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.2732 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= 0.184 Angle : 0.447 6.935 33143 Z= 0.237 Chirality : 0.046 0.148 4186 Planarity : 0.003 0.027 4209 Dihedral : 3.832 20.124 3427 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.35 % Allowed : 21.66 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.15), residues: 3243 helix: 2.58 (0.17), residues: 1081 sheet: 1.04 (0.19), residues: 713 loop : 2.13 (0.16), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 132 PHE 0.006 0.001 PHE W 7 TYR 0.010 0.001 TYR L 30 ARG 0.005 0.000 ARG P 59 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5864.38 seconds wall clock time: 108 minutes 26.92 seconds (6506.92 seconds total)