Starting phenix.real_space_refine on Fri Feb 23 05:02:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfh_21172/02_2024/6vfh_21172.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfh_21172/02_2024/6vfh_21172.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfh_21172/02_2024/6vfh_21172.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfh_21172/02_2024/6vfh_21172.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfh_21172/02_2024/6vfh_21172.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfh_21172/02_2024/6vfh_21172.pdb" } resolution = 3.86 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 120 5.16 5 C 23556 2.51 5 N 6144 2.21 5 O 7164 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 36984 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "B" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "C" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "D" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "E" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "F" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "G" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "H" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "I" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "J" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "K" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "L" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "M" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "N" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "O" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "P" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "Q" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "R" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "S" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "T" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "U" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "V" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Chain: "W" Number of atoms: 983 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 983 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "X" Number of atoms: 2099 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2099 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 1, 'TRANS': 275} Time building chain proxies: 18.59, per 1000 atoms: 0.50 Number of scatterers: 36984 At special positions: 0 Unit cell: (180.25, 179.22, 174.07, 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 120 16.00 O 7164 8.00 N 6144 7.00 C 23556 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.16 Conformation dependent library (CDL) restraints added in 7.4 seconds 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9336 Finding SS restraints... Secondary structure from input PDB file: 204 helices and 0 sheets defined 90.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.27 Creating SS restraints... Processing helix chain 'A' and resid 1 through 16 Processing helix chain 'A' and resid 18 through 33 Processing helix chain 'A' and resid 36 through 50 Processing helix chain 'A' and resid 52 through 67 Processing helix chain 'A' and resid 70 through 84 Processing helix chain 'A' and resid 86 through 101 Processing helix chain 'A' and resid 104 through 118 Processing helix chain 'B' and resid 2 through 29 Processing helix chain 'B' and resid 32 through 59 Processing helix chain 'B' and resid 63 through 89 Processing helix chain 'B' and resid 91 through 95 Processing helix chain 'B' and resid 97 through 121 Processing helix chain 'B' and resid 125 through 152 Processing helix chain 'B' and resid 159 through 183 Processing helix chain 'B' and resid 187 through 214 Processing helix chain 'B' and resid 218 through 245 Processing helix chain 'B' and resid 250 through 277 Processing helix chain 'C' and resid 1 through 16 Processing helix chain 'C' and resid 18 through 33 Processing helix chain 'C' and resid 36 through 50 Processing helix chain 'C' and resid 52 through 67 Processing helix chain 'C' and resid 70 through 84 Processing helix chain 'C' and resid 86 through 101 Processing helix chain 'C' and resid 104 through 118 Processing helix chain 'D' and resid 2 through 29 Processing helix chain 'D' and resid 32 through 59 Processing helix chain 'D' and resid 63 through 89 Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 97 through 121 Processing helix chain 'D' and resid 125 through 152 Processing helix chain 'D' and resid 159 through 183 Processing helix chain 'D' and resid 187 through 214 Processing helix chain 'D' and resid 218 through 245 Processing helix chain 'D' and resid 250 through 277 Processing helix chain 'E' and resid 1 through 16 Processing helix chain 'E' and resid 18 through 33 Processing helix chain 'E' and resid 36 through 50 Processing helix chain 'E' and resid 52 through 67 Processing helix chain 'E' and resid 70 through 84 Processing helix chain 'E' and resid 86 through 101 Processing helix chain 'E' and resid 104 through 118 Processing helix chain 'F' and resid 2 through 29 Processing helix chain 'F' and resid 32 through 59 Processing helix chain 'F' and resid 63 through 89 Processing helix chain 'F' and resid 91 through 95 Processing helix chain 'F' and resid 97 through 121 Processing helix chain 'F' and resid 125 through 152 Processing helix chain 'F' and resid 159 through 183 Processing helix chain 'F' and resid 187 through 214 Processing helix chain 'F' and resid 218 through 245 Processing helix chain 'F' and resid 250 through 277 Processing helix chain 'G' and resid 1 through 16 Processing helix chain 'G' and resid 18 through 33 Processing helix chain 'G' and resid 36 through 50 Processing helix chain 'G' and resid 52 through 67 Processing helix chain 'G' and resid 70 through 84 Processing helix chain 'G' and resid 86 through 101 Processing helix chain 'G' and resid 104 through 118 Processing helix chain 'H' and resid 2 through 29 Processing helix chain 'H' and resid 32 through 59 Processing helix chain 'H' and resid 63 through 89 Processing helix chain 'H' and resid 91 through 95 Processing helix chain 'H' and resid 97 through 121 Processing helix chain 'H' and resid 125 through 152 Processing helix chain 'H' and resid 159 through 183 Processing helix chain 'H' and resid 187 through 214 Processing helix chain 'H' and resid 218 through 245 Processing helix chain 'H' and resid 250 through 277 Processing helix chain 'I' and resid 1 through 16 Processing helix chain 'I' and resid 18 through 33 Processing helix chain 'I' and resid 36 through 50 Processing helix chain 'I' and resid 52 through 67 Processing helix chain 'I' and resid 70 through 84 Processing helix chain 'I' and resid 86 through 101 Processing helix chain 'I' and resid 104 through 118 Processing helix chain 'J' and resid 2 through 29 Processing helix chain 'J' and resid 32 through 59 Processing helix chain 'J' and resid 63 through 89 Processing helix chain 'J' and resid 91 through 95 Processing helix chain 'J' and resid 97 through 121 Processing helix chain 'J' and resid 125 through 152 Processing helix chain 'J' and resid 159 through 183 Processing helix chain 'J' and resid 187 through 214 Processing helix chain 'J' and resid 218 through 245 Processing helix chain 'J' and resid 250 through 277 Processing helix chain 'K' and resid 1 through 16 Processing helix chain 'K' and resid 18 through 33 Processing helix chain 'K' and resid 36 through 50 Processing helix chain 'K' and resid 52 through 67 Processing helix chain 'K' and resid 70 through 84 Processing helix chain 'K' and resid 86 through 101 Processing helix chain 'K' and resid 104 through 118 Processing helix chain 'L' and resid 2 through 29 Processing helix chain 'L' and resid 32 through 59 Processing helix chain 'L' and resid 63 through 89 Processing helix chain 'L' and resid 91 through 95 Processing helix chain 'L' and resid 97 through 121 Processing helix chain 'L' and resid 125 through 152 Processing helix chain 'L' and resid 159 through 183 Processing helix chain 'L' and resid 187 through 214 Processing helix chain 'L' and resid 218 through 245 Processing helix chain 'L' and resid 250 through 277 Processing helix chain 'M' and resid 1 through 16 Processing helix chain 'M' and resid 18 through 33 Processing helix chain 'M' and resid 36 through 50 Processing helix chain 'M' and resid 52 through 67 Processing helix chain 'M' and resid 70 through 84 Processing helix chain 'M' and resid 86 through 101 Processing helix chain 'M' and resid 104 through 118 Processing helix chain 'N' and resid 2 through 29 Processing helix chain 'N' and resid 32 through 59 Processing helix chain 'N' and resid 63 through 89 Processing helix chain 'N' and resid 91 through 95 Processing helix chain 'N' and resid 97 through 121 Processing helix chain 'N' and resid 125 through 152 Processing helix chain 'N' and resid 159 through 183 Processing helix chain 'N' and resid 187 through 214 Processing helix chain 'N' and resid 218 through 245 Processing helix chain 'N' and resid 250 through 277 Processing helix chain 'O' and resid 1 through 16 Processing helix chain 'O' and resid 18 through 33 Processing helix chain 'O' and resid 36 through 50 Processing helix chain 'O' and resid 52 through 67 Processing helix chain 'O' and resid 70 through 84 Processing helix chain 'O' and resid 86 through 101 Processing helix chain 'O' and resid 104 through 118 Processing helix chain 'P' and resid 2 through 29 Processing helix chain 'P' and resid 32 through 59 Processing helix chain 'P' and resid 63 through 89 Processing helix chain 'P' and resid 91 through 95 Processing helix chain 'P' and resid 97 through 121 Processing helix chain 'P' and resid 125 through 152 Processing helix chain 'P' and resid 159 through 183 Processing helix chain 'P' and resid 187 through 214 Processing helix chain 'P' and resid 218 through 245 Processing helix chain 'P' and resid 250 through 277 Processing helix chain 'Q' and resid 1 through 16 Processing helix chain 'Q' and resid 18 through 33 Processing helix chain 'Q' and resid 36 through 50 Processing helix chain 'Q' and resid 52 through 67 Processing helix chain 'Q' and resid 70 through 84 Processing helix chain 'Q' and resid 86 through 101 Processing helix chain 'Q' and resid 104 through 118 Processing helix chain 'R' and resid 2 through 29 Processing helix chain 'R' and resid 32 through 59 Processing helix chain 'R' and resid 63 through 89 Processing helix chain 'R' and resid 91 through 95 Processing helix chain 'R' and resid 97 through 121 Processing helix chain 'R' and resid 125 through 152 Processing helix chain 'R' and resid 159 through 183 Processing helix chain 'R' and resid 187 through 214 Processing helix chain 'R' and resid 218 through 245 Processing helix chain 'R' and resid 250 through 277 Processing helix chain 'S' and resid 1 through 16 Processing helix chain 'S' and resid 18 through 33 Processing helix chain 'S' and resid 36 through 50 Processing helix chain 'S' and resid 52 through 67 Processing helix chain 'S' and resid 70 through 84 Processing helix chain 'S' and resid 86 through 101 Processing helix chain 'S' and resid 104 through 118 Processing helix chain 'T' and resid 2 through 29 Processing helix chain 'T' and resid 32 through 59 Processing helix chain 'T' and resid 63 through 89 Processing helix chain 'T' and resid 91 through 95 Processing helix chain 'T' and resid 97 through 121 Processing helix chain 'T' and resid 125 through 152 Processing helix chain 'T' and resid 159 through 183 Processing helix chain 'T' and resid 187 through 214 Processing helix chain 'T' and resid 218 through 245 Processing helix chain 'T' and resid 250 through 277 Processing helix chain 'U' and resid 1 through 16 Processing helix chain 'U' and resid 18 through 33 Processing helix chain 'U' and resid 36 through 50 Processing helix chain 'U' and resid 52 through 67 Processing helix chain 'U' and resid 70 through 84 Processing helix chain 'U' and resid 86 through 101 Processing helix chain 'U' and resid 104 through 118 Processing helix chain 'V' and resid 2 through 29 Processing helix chain 'V' and resid 32 through 59 Processing helix chain 'V' and resid 63 through 89 Processing helix chain 'V' and resid 91 through 95 Processing helix chain 'V' and resid 97 through 121 Processing helix chain 'V' and resid 125 through 152 Processing helix chain 'V' and resid 159 through 183 Processing helix chain 'V' and resid 187 through 214 Processing helix chain 'V' and resid 218 through 245 Processing helix chain 'V' and resid 250 through 277 Processing helix chain 'W' and resid 1 through 16 Processing helix chain 'W' and resid 18 through 33 Processing helix chain 'W' and resid 36 through 50 Processing helix chain 'W' and resid 52 through 67 Processing helix chain 'W' and resid 70 through 84 Processing helix chain 'W' and resid 86 through 101 Processing helix chain 'W' and resid 104 through 118 Processing helix chain 'X' and resid 2 through 29 Processing helix chain 'X' and resid 32 through 59 Processing helix chain 'X' and resid 63 through 89 Processing helix chain 'X' and resid 91 through 95 Processing helix chain 'X' and resid 97 through 121 Processing helix chain 'X' and resid 125 through 152 Processing helix chain 'X' and resid 159 through 183 Processing helix chain 'X' and resid 187 through 214 Processing helix chain 'X' and resid 218 through 245 Processing helix chain 'X' and resid 250 through 277 3504 hydrogen bonds defined for protein. 10440 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: 15.15 Time building geometry restraints manager: 16.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8233 1.32 - 1.45: 10435 1.45 - 1.58: 18508 1.58 - 1.70: 12 1.70 - 1.83: 240 Bond restraints: 37428 Sorted by residual: bond pdb=" CB HIS T 92 " pdb=" CG HIS T 92 " ideal model delta sigma weight residual 1.497 1.440 0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" CB HIS P 92 " pdb=" CG HIS P 92 " ideal model delta sigma weight residual 1.497 1.440 0.057 1.40e-02 5.10e+03 1.63e+01 bond pdb=" CB HIS N 92 " pdb=" CG HIS N 92 " ideal model delta sigma weight residual 1.497 1.440 0.057 1.40e-02 5.10e+03 1.63e+01 bond pdb=" CB HIS B 92 " pdb=" CG HIS B 92 " ideal model delta sigma weight residual 1.497 1.440 0.057 1.40e-02 5.10e+03 1.63e+01 bond pdb=" CB HIS X 92 " pdb=" CG HIS X 92 " ideal model delta sigma weight residual 1.497 1.441 0.056 1.40e-02 5.10e+03 1.63e+01 ... (remaining 37423 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.72: 631 106.72 - 113.50: 20365 113.50 - 120.28: 17382 120.28 - 127.06: 12010 127.06 - 133.84: 180 Bond angle restraints: 50568 Sorted by residual: angle pdb=" C ASP M 67 " pdb=" N PRO M 68 " pdb=" CA PRO M 68 " ideal model delta sigma weight residual 119.82 127.54 -7.72 9.80e-01 1.04e+00 6.20e+01 angle pdb=" C ASP G 67 " pdb=" N PRO G 68 " pdb=" CA PRO G 68 " ideal model delta sigma weight residual 119.82 127.53 -7.71 9.80e-01 1.04e+00 6.19e+01 angle pdb=" C ASP C 67 " pdb=" N PRO C 68 " pdb=" CA PRO C 68 " ideal model delta sigma weight residual 119.82 127.53 -7.71 9.80e-01 1.04e+00 6.19e+01 angle pdb=" C ASP A 67 " pdb=" N PRO A 68 " pdb=" CA PRO A 68 " ideal model delta sigma weight residual 119.82 127.52 -7.70 9.80e-01 1.04e+00 6.17e+01 angle pdb=" C ASP I 67 " pdb=" N PRO I 68 " pdb=" CA PRO I 68 " ideal model delta sigma weight residual 119.82 127.51 -7.69 9.80e-01 1.04e+00 6.16e+01 ... (remaining 50563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.37: 21651 12.37 - 24.75: 1389 24.75 - 37.12: 84 37.12 - 49.50: 63 49.50 - 61.87: 81 Dihedral angle restraints: 23268 sinusoidal: 8952 harmonic: 14316 Sorted by residual: dihedral pdb=" C THR N 94 " pdb=" N THR N 94 " pdb=" CA THR N 94 " pdb=" CB THR N 94 " ideal model delta harmonic sigma weight residual -122.00 -130.90 8.90 0 2.50e+00 1.60e-01 1.27e+01 dihedral pdb=" C THR L 94 " pdb=" N THR L 94 " pdb=" CA THR L 94 " pdb=" CB THR L 94 " ideal model delta harmonic sigma weight residual -122.00 -130.90 8.90 0 2.50e+00 1.60e-01 1.27e+01 dihedral pdb=" C THR F 94 " pdb=" N THR F 94 " pdb=" CA THR F 94 " pdb=" CB THR F 94 " ideal model delta harmonic sigma weight residual -122.00 -130.89 8.89 0 2.50e+00 1.60e-01 1.27e+01 ... (remaining 23265 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4035 0.076 - 0.152: 1518 0.152 - 0.228: 351 0.228 - 0.304: 24 0.304 - 0.380: 36 Chirality restraints: 5964 Sorted by residual: chirality pdb=" CA ASP F 152 " pdb=" N ASP F 152 " pdb=" C ASP F 152 " pdb=" CB ASP F 152 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.60e+00 chirality pdb=" CA ASP V 152 " pdb=" N ASP V 152 " pdb=" C ASP V 152 " pdb=" CB ASP V 152 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CA ASP X 152 " pdb=" N ASP X 152 " pdb=" C ASP X 152 " pdb=" CB ASP X 152 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.58e+00 ... (remaining 5961 not shown) Planarity restraints: 6432 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 93 " -0.062 2.00e-02 2.50e+03 3.22e-02 2.08e+01 pdb=" CG TYR Q 93 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 93 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 93 " 0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 93 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 93 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR Q 93 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR Q 93 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR U 93 " -0.062 2.00e-02 2.50e+03 3.21e-02 2.06e+01 pdb=" CG TYR U 93 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR U 93 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR U 93 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR U 93 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR U 93 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR U 93 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR U 93 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 93 " -0.062 2.00e-02 2.50e+03 3.21e-02 2.06e+01 pdb=" CG TYR G 93 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR G 93 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR G 93 " 0.024 2.00e-02 2.50e+03 pdb=" CE1 TYR G 93 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR G 93 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR G 93 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR G 93 " -0.044 2.00e-02 2.50e+03 ... (remaining 6429 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 20522 2.98 - 3.46: 40952 3.46 - 3.94: 61187 3.94 - 4.42: 75458 4.42 - 4.90: 113052 Nonbonded interactions: 311171 Sorted by model distance: nonbonded pdb=" NZ LYS L 235 " pdb=" OE2 GLU V 7 " model vdw 2.497 2.520 nonbonded pdb=" NZ LYS F 235 " pdb=" OE2 GLU P 7 " model vdw 2.497 2.520 nonbonded pdb=" OE2 GLU H 7 " pdb=" NZ LYS V 235 " model vdw 2.497 2.520 nonbonded pdb=" NZ LYS B 235 " pdb=" OE2 GLU J 7 " model vdw 2.497 2.520 nonbonded pdb=" OE2 GLU D 7 " pdb=" NZ LYS X 235 " model vdw 2.497 2.520 ... (remaining 311166 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 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: 0.040 Extract box with map and model: 8.160 Check model and map are aligned: 0.660 Set scattering table: 0.390 Process input model: 98.900 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 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 : 0.019 0.083 37428 Z= 1.199 Angle : 1.388 8.973 50568 Z= 0.949 Chirality : 0.084 0.380 5964 Planarity : 0.008 0.032 6432 Dihedral : 9.310 61.873 13932 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 2.06 (0.10), residues: 4704 helix: 1.51 (0.06), residues: 4236 sheet: None (None), residues: 0 loop : 0.57 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.008 TRP K 74 HIS 0.011 0.004 HIS T 185 PHE 0.019 0.007 PHE T 66 TYR 0.062 0.009 TYR Q 93 ARG 0.003 0.000 ARG L 234 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1526 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1526 time to evaluate : 4.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.8429 (m-30) cc_final: 0.8146 (m-30) REVERT: A 94 TYR cc_start: 0.8614 (m-80) cc_final: 0.8283 (m-80) REVERT: B 45 ARG cc_start: 0.8049 (ttp80) cc_final: 0.7808 (ttm-80) REVERT: B 80 LYS cc_start: 0.8906 (mmtt) cc_final: 0.8677 (mmtt) REVERT: B 226 ILE cc_start: 0.8847 (mt) cc_final: 0.8593 (mm) REVERT: C 33 ASP cc_start: 0.8124 (t0) cc_final: 0.7522 (t0) REVERT: C 52 ASP cc_start: 0.8432 (m-30) cc_final: 0.8174 (m-30) REVERT: C 96 LYS cc_start: 0.8604 (mttp) cc_final: 0.8160 (mtpp) REVERT: D 8 MET cc_start: 0.8641 (mtp) cc_final: 0.8394 (mtm) REVERT: D 80 LYS cc_start: 0.8831 (mmtt) cc_final: 0.8551 (mmtt) REVERT: D 129 MET cc_start: 0.8608 (mtm) cc_final: 0.8367 (ttm) REVERT: E 33 ASP cc_start: 0.8219 (t0) cc_final: 0.7725 (t0) REVERT: E 52 ASP cc_start: 0.8305 (m-30) cc_final: 0.8070 (m-30) REVERT: E 96 LYS cc_start: 0.8416 (mttp) cc_final: 0.8151 (mtpt) REVERT: F 67 MET cc_start: 0.8061 (mtm) cc_final: 0.7771 (mtp) REVERT: F 80 LYS cc_start: 0.8800 (mmtt) cc_final: 0.8573 (mmtt) REVERT: G 52 ASP cc_start: 0.8355 (m-30) cc_final: 0.8093 (m-30) REVERT: G 96 LYS cc_start: 0.8536 (mttp) cc_final: 0.8229 (mtpp) REVERT: H 226 ILE cc_start: 0.8781 (mt) cc_final: 0.8432 (mm) REVERT: I 33 ASP cc_start: 0.8059 (t0) cc_final: 0.7515 (t0) REVERT: J 63 SER cc_start: 0.8418 (m) cc_final: 0.8216 (p) REVERT: J 67 MET cc_start: 0.8167 (mtm) cc_final: 0.7724 (mtp) REVERT: J 86 TYR cc_start: 0.8682 (t80) cc_final: 0.8456 (t80) REVERT: J 129 MET cc_start: 0.8469 (mtm) cc_final: 0.8219 (mtp) REVERT: J 226 ILE cc_start: 0.8875 (mt) cc_final: 0.8446 (mm) REVERT: K 35 ASN cc_start: 0.7911 (m-40) cc_final: 0.7630 (t0) REVERT: K 52 ASP cc_start: 0.8417 (m-30) cc_final: 0.8201 (m-30) REVERT: K 94 TYR cc_start: 0.8453 (m-80) cc_final: 0.8154 (m-80) REVERT: L 129 MET cc_start: 0.8601 (mtm) cc_final: 0.8263 (mtp) REVERT: L 226 ILE cc_start: 0.8816 (mt) cc_final: 0.8446 (mm) REVERT: M 33 ASP cc_start: 0.8201 (t0) cc_final: 0.7730 (t0) REVERT: M 67 ASP cc_start: 0.8592 (t0) cc_final: 0.8305 (t0) REVERT: N 45 ARG cc_start: 0.7950 (ttp80) cc_final: 0.7731 (ttm-80) REVERT: N 63 SER cc_start: 0.8392 (m) cc_final: 0.8134 (p) REVERT: N 67 MET cc_start: 0.8018 (mtm) cc_final: 0.7631 (mtp) REVERT: N 80 LYS cc_start: 0.8846 (mmtt) cc_final: 0.8624 (mmtt) REVERT: N 149 ARG cc_start: 0.7579 (mtt180) cc_final: 0.7362 (mtm180) REVERT: N 226 ILE cc_start: 0.8818 (mt) cc_final: 0.8509 (mm) REVERT: O 35 ASN cc_start: 0.7968 (m-40) cc_final: 0.7735 (t0) REVERT: O 48 TYR cc_start: 0.8412 (t80) cc_final: 0.8152 (t80) REVERT: O 96 LYS cc_start: 0.8330 (mttp) cc_final: 0.8000 (mtpp) REVERT: P 8 MET cc_start: 0.8709 (mtp) cc_final: 0.8477 (mtm) REVERT: P 67 MET cc_start: 0.8173 (mtm) cc_final: 0.7840 (mtp) REVERT: P 129 MET cc_start: 0.8420 (mtm) cc_final: 0.8144 (mtp) REVERT: P 226 ILE cc_start: 0.8734 (mt) cc_final: 0.8491 (mm) REVERT: Q 33 ASP cc_start: 0.8195 (t0) cc_final: 0.7687 (t0) REVERT: Q 52 ASP cc_start: 0.8355 (m-30) cc_final: 0.8052 (m-30) REVERT: Q 67 ASP cc_start: 0.8549 (t0) cc_final: 0.8293 (t0) REVERT: R 63 SER cc_start: 0.8554 (m) cc_final: 0.8247 (p) REVERT: R 67 MET cc_start: 0.8247 (mtm) cc_final: 0.7771 (mtp) REVERT: S 33 ASP cc_start: 0.8217 (t0) cc_final: 0.7761 (t0) REVERT: S 48 TYR cc_start: 0.8415 (t80) cc_final: 0.8074 (t80) REVERT: S 52 ASP cc_start: 0.8338 (m-30) cc_final: 0.8017 (m-30) REVERT: T 45 ARG cc_start: 0.7988 (ttp80) cc_final: 0.7718 (ttm-80) REVERT: T 67 MET cc_start: 0.8052 (mtm) cc_final: 0.7828 (mtp) REVERT: T 129 MET cc_start: 0.8540 (mtm) cc_final: 0.8319 (mtp) REVERT: T 226 ILE cc_start: 0.8859 (mt) cc_final: 0.8617 (mm) REVERT: U 33 ASP cc_start: 0.8090 (t0) cc_final: 0.7661 (t0) REVERT: U 52 ASP cc_start: 0.8328 (m-30) cc_final: 0.8085 (m-30) REVERT: V 63 SER cc_start: 0.8501 (m) cc_final: 0.8229 (p) REVERT: V 67 MET cc_start: 0.8037 (mtm) cc_final: 0.7698 (mtp) REVERT: V 80 LYS cc_start: 0.8820 (mmtt) cc_final: 0.8532 (mmtt) REVERT: V 129 MET cc_start: 0.8569 (mtm) cc_final: 0.8339 (mtm) REVERT: W 52 ASP cc_start: 0.8340 (m-30) cc_final: 0.8116 (m-30) REVERT: W 67 ASP cc_start: 0.8535 (t0) cc_final: 0.8290 (t0) REVERT: W 94 TYR cc_start: 0.8467 (m-80) cc_final: 0.8229 (m-80) REVERT: X 67 MET cc_start: 0.8071 (mtm) cc_final: 0.7818 (mtp) REVERT: X 80 LYS cc_start: 0.8762 (mmtt) cc_final: 0.8533 (mmtt) REVERT: X 129 MET cc_start: 0.8628 (mtm) cc_final: 0.8291 (mtp) outliers start: 0 outliers final: 0 residues processed: 1526 average time/residue: 0.5866 time to fit residues: 1344.8271 Evaluate side-chains 743 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 743 time to evaluate : 4.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 385 optimal weight: 5.9990 chunk 345 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 233 optimal weight: 2.9990 chunk 184 optimal weight: 0.0050 chunk 357 optimal weight: 0.9990 chunk 138 optimal weight: 1.9990 chunk 217 optimal weight: 0.9990 chunk 266 optimal weight: 0.8980 chunk 414 optimal weight: 0.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 GLN B 216 HIS ** C 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN D 216 HIS E 118 GLN F 184 ASN H 184 ASN I 118 GLN J 184 ASN J 216 HIS K 118 GLN L 184 ASN L 216 HIS N 184 ASN N 216 HIS ** O 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 118 GLN P 184 ASN P 216 HIS ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 184 ASN S 118 GLN T 184 ASN T 216 HIS ** U 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 118 GLN V 184 ASN V 216 HIS ** W 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 118 GLN X 184 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37428 Z= 0.197 Angle : 0.537 9.136 50568 Z= 0.299 Chirality : 0.038 0.238 5964 Planarity : 0.004 0.029 6432 Dihedral : 3.423 15.796 5160 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.88 % Allowed : 8.97 % Favored : 89.15 % 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: 4.49 (0.11), residues: 4704 helix: 3.16 (0.07), residues: 4272 sheet: None (None), residues: 0 loop : 0.48 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP S 40 HIS 0.006 0.002 HIS N 185 PHE 0.023 0.002 PHE H 97 TYR 0.018 0.002 TYR E 94 ARG 0.008 0.001 ARG J 234 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1115 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1047 time to evaluate : 4.722 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 80 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8478 (mmtp) REVERT: B 150 LEU cc_start: 0.8655 (mt) cc_final: 0.8276 (mt) REVERT: B 237 ILE cc_start: 0.9031 (mt) cc_final: 0.8680 (mm) REVERT: D 8 MET cc_start: 0.8618 (mtp) cc_final: 0.7789 (mtm) REVERT: D 80 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8504 (mmtp) REVERT: D 129 MET cc_start: 0.8426 (mtm) cc_final: 0.8091 (mtp) REVERT: D 150 LEU cc_start: 0.8740 (mt) cc_final: 0.8365 (mt) REVERT: E 48 TYR cc_start: 0.8384 (t80) cc_final: 0.8049 (t80) REVERT: F 67 MET cc_start: 0.7934 (mtm) cc_final: 0.7706 (mtp) REVERT: F 80 LYS cc_start: 0.8839 (mmtt) cc_final: 0.8560 (mmtp) REVERT: F 150 LEU cc_start: 0.8851 (mt) cc_final: 0.8456 (mt) REVERT: F 226 ILE cc_start: 0.8828 (mm) cc_final: 0.8510 (mm) REVERT: F 261 ASP cc_start: 0.7757 (m-30) cc_final: 0.7557 (m-30) REVERT: H 150 LEU cc_start: 0.8847 (mt) cc_final: 0.8530 (mt) REVERT: H 237 ILE cc_start: 0.9022 (mt) cc_final: 0.8803 (mm) REVERT: J 36 VAL cc_start: 0.6658 (t) cc_final: 0.6443 (p) REVERT: J 67 MET cc_start: 0.8139 (mtm) cc_final: 0.7580 (mtp) REVERT: J 129 MET cc_start: 0.8317 (mtm) cc_final: 0.8095 (mtp) REVERT: J 150 LEU cc_start: 0.8760 (mt) cc_final: 0.8525 (mt) REVERT: J 237 ILE cc_start: 0.9169 (mt) cc_final: 0.8917 (mm) REVERT: K 52 ASP cc_start: 0.8097 (m-30) cc_final: 0.7812 (m-30) REVERT: L 129 MET cc_start: 0.8471 (mtm) cc_final: 0.8154 (mtp) REVERT: L 237 ILE cc_start: 0.9073 (mt) cc_final: 0.8788 (mm) REVERT: N 67 MET cc_start: 0.8011 (mtm) cc_final: 0.7452 (mtp) REVERT: N 80 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8563 (mmtt) REVERT: N 150 LEU cc_start: 0.8938 (mt) cc_final: 0.8597 (mt) REVERT: O 110 ASN cc_start: 0.8986 (m110) cc_final: 0.8775 (m-40) REVERT: P 67 MET cc_start: 0.8065 (mtm) cc_final: 0.7611 (mtp) REVERT: P 129 MET cc_start: 0.8441 (mtm) cc_final: 0.8105 (mtp) REVERT: P 150 LEU cc_start: 0.8844 (mt) cc_final: 0.8402 (mt) REVERT: P 237 ILE cc_start: 0.8932 (mt) cc_final: 0.8625 (mm) REVERT: R 63 SER cc_start: 0.8389 (m) cc_final: 0.8171 (m) REVERT: R 67 MET cc_start: 0.8250 (mtm) cc_final: 0.7635 (mtp) REVERT: R 150 LEU cc_start: 0.8836 (mt) cc_final: 0.8584 (mt) REVERT: R 157 ASP cc_start: 0.7238 (p0) cc_final: 0.7033 (p0) REVERT: S 48 TYR cc_start: 0.8431 (t80) cc_final: 0.8075 (t80) REVERT: S 52 ASP cc_start: 0.8080 (m-30) cc_final: 0.7678 (m-30) REVERT: T 60 ASN cc_start: 0.7972 (m-40) cc_final: 0.7610 (t0) REVERT: T 67 MET cc_start: 0.7865 (mtm) cc_final: 0.7540 (mtp) REVERT: T 98 MET cc_start: 0.5163 (mmt) cc_final: 0.4691 (mmt) REVERT: T 129 MET cc_start: 0.8544 (mtm) cc_final: 0.8196 (mtp) REVERT: T 237 ILE cc_start: 0.9151 (mt) cc_final: 0.8860 (mm) REVERT: V 63 SER cc_start: 0.8369 (m) cc_final: 0.8140 (m) REVERT: V 67 MET cc_start: 0.8073 (mtm) cc_final: 0.7529 (mtp) REVERT: V 80 LYS cc_start: 0.8823 (mmtt) cc_final: 0.8456 (mmtp) REVERT: V 129 MET cc_start: 0.8444 (mtm) cc_final: 0.8187 (mtp) REVERT: V 150 LEU cc_start: 0.8641 (mt) cc_final: 0.8264 (mt) REVERT: X 67 MET cc_start: 0.8069 (mtm) cc_final: 0.7865 (mtp) REVERT: X 80 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8401 (mmtp) REVERT: X 129 MET cc_start: 0.8577 (mtm) cc_final: 0.8160 (mtp) REVERT: X 145 GLU cc_start: 0.8160 (tp30) cc_final: 0.7844 (tp30) REVERT: X 148 TYR cc_start: 0.8990 (t80) cc_final: 0.8775 (t80) REVERT: X 150 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8264 (mp) REVERT: X 207 GLU cc_start: 0.7698 (tt0) cc_final: 0.7457 (tt0) REVERT: X 226 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8476 (mm) REVERT: X 237 ILE cc_start: 0.9090 (mt) cc_final: 0.8835 (mm) outliers start: 68 outliers final: 32 residues processed: 1076 average time/residue: 0.4888 time to fit residues: 844.2121 Evaluate side-chains 732 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 698 time to evaluate : 4.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 243 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain F residue 155 THR Chi-restraints excluded: chain F residue 246 ASN Chi-restraints excluded: chain I residue 16 LEU Chi-restraints excluded: chain J residue 16 SER Chi-restraints excluded: chain J residue 134 SER Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 173 LEU Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain P residue 46 LEU Chi-restraints excluded: chain Q residue 16 LEU Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 155 THR Chi-restraints excluded: chain R residue 246 ASN Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain U residue 54 ASP Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain X residue 16 SER Chi-restraints excluded: chain X residue 134 SER Chi-restraints excluded: chain X residue 150 LEU Chi-restraints excluded: chain X residue 226 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 230 optimal weight: 6.9990 chunk 128 optimal weight: 0.0030 chunk 344 optimal weight: 5.9990 chunk 281 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 414 optimal weight: 0.9990 chunk 448 optimal weight: 2.9990 chunk 369 optimal weight: 3.9990 chunk 411 optimal weight: 0.0970 chunk 141 optimal weight: 0.9980 chunk 332 optimal weight: 0.9990 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 107 ASN C 118 GLN D 60 ASN D 123 HIS H 216 HIS M 118 GLN N 123 HIS ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 123 HIS R 184 ASN S 61 GLN ** V 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 GLN W 118 GLN X 216 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 37428 Z= 0.162 Angle : 0.471 11.465 50568 Z= 0.262 Chirality : 0.035 0.164 5964 Planarity : 0.003 0.027 6432 Dihedral : 3.270 15.374 5160 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.05 % Allowed : 12.54 % Favored : 85.41 % 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: 4.45 (0.11), residues: 4704 helix: 3.14 (0.07), residues: 4284 sheet: None (None), residues: 0 loop : 0.27 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 40 HIS 0.004 0.001 HIS P 185 PHE 0.013 0.001 PHE F 97 TYR 0.019 0.001 TYR P 210 ARG 0.004 0.000 ARG L 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 963 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 889 time to evaluate : 4.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 ASN cc_start: 0.7898 (m-40) cc_final: 0.7495 (t0) REVERT: B 80 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8489 (mmtm) REVERT: B 98 MET cc_start: 0.5484 (mmt) cc_final: 0.4653 (mmt) REVERT: B 157 ASP cc_start: 0.6832 (p0) cc_final: 0.6373 (p0) REVERT: D 8 MET cc_start: 0.8523 (mtp) cc_final: 0.8052 (mtm) REVERT: D 61 LEU cc_start: 0.8340 (mt) cc_final: 0.7947 (mt) REVERT: D 80 LYS cc_start: 0.8775 (mmtt) cc_final: 0.8468 (mmtp) REVERT: D 114 LEU cc_start: 0.8256 (mt) cc_final: 0.8023 (mt) REVERT: D 129 MET cc_start: 0.8391 (mtm) cc_final: 0.8084 (mtp) REVERT: D 152 ASP cc_start: 0.7848 (t0) cc_final: 0.7453 (t70) REVERT: E 48 TYR cc_start: 0.8407 (t80) cc_final: 0.8151 (t80) REVERT: F 61 LEU cc_start: 0.8452 (mt) cc_final: 0.8062 (mt) REVERT: F 67 MET cc_start: 0.8071 (mtm) cc_final: 0.7760 (mtp) REVERT: F 80 LYS cc_start: 0.8848 (mmtt) cc_final: 0.8502 (mmtp) REVERT: F 129 MET cc_start: 0.8172 (mtm) cc_final: 0.7813 (mtp) REVERT: F 165 GLU cc_start: 0.8557 (mp0) cc_final: 0.8356 (mp0) REVERT: H 157 ASP cc_start: 0.7251 (p0) cc_final: 0.6984 (p0) REVERT: J 36 VAL cc_start: 0.6932 (t) cc_final: 0.6511 (p) REVERT: J 60 ASN cc_start: 0.8036 (m-40) cc_final: 0.7566 (t0) REVERT: J 67 MET cc_start: 0.8208 (mtm) cc_final: 0.7598 (mtp) REVERT: J 129 MET cc_start: 0.8303 (mtm) cc_final: 0.8101 (mtp) REVERT: J 226 ILE cc_start: 0.8640 (mm) cc_final: 0.8360 (mm) REVERT: L 60 ASN cc_start: 0.7910 (m-40) cc_final: 0.7661 (t0) REVERT: L 129 MET cc_start: 0.8474 (mtm) cc_final: 0.8090 (mtp) REVERT: L 150 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8419 (mp) REVERT: N 67 MET cc_start: 0.8063 (mtm) cc_final: 0.7523 (mtp) REVERT: N 157 ASP cc_start: 0.6775 (p0) cc_final: 0.6458 (p0) REVERT: N 227 GLU cc_start: 0.7691 (tp30) cc_final: 0.7197 (tp30) REVERT: P 60 ASN cc_start: 0.7936 (m-40) cc_final: 0.7663 (t0) REVERT: P 67 MET cc_start: 0.8052 (mtm) cc_final: 0.7655 (mtp) REVERT: P 129 MET cc_start: 0.8323 (mtm) cc_final: 0.8035 (mtp) REVERT: P 157 ASP cc_start: 0.6884 (p0) cc_final: 0.6516 (p0) REVERT: R 60 ASN cc_start: 0.8015 (m-40) cc_final: 0.7767 (t0) REVERT: R 67 MET cc_start: 0.8283 (mtm) cc_final: 0.7792 (mtp) REVERT: S 48 TYR cc_start: 0.8509 (t80) cc_final: 0.8238 (t80) REVERT: T 60 ASN cc_start: 0.7973 (m-40) cc_final: 0.7756 (t0) REVERT: T 67 MET cc_start: 0.7927 (mtm) cc_final: 0.7678 (mtp) REVERT: T 129 MET cc_start: 0.8527 (mtm) cc_final: 0.8303 (mtp) REVERT: T 150 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8117 (mp) REVERT: T 153 ASN cc_start: 0.7610 (m-40) cc_final: 0.7272 (p0) REVERT: T 157 ASP cc_start: 0.7355 (p0) cc_final: 0.6935 (p0) REVERT: V 63 SER cc_start: 0.8233 (m) cc_final: 0.7958 (m) REVERT: V 67 MET cc_start: 0.8129 (mtm) cc_final: 0.7486 (mtp) REVERT: V 80 LYS cc_start: 0.8821 (mmtt) cc_final: 0.8416 (mmtp) REVERT: V 129 MET cc_start: 0.8435 (mtm) cc_final: 0.8166 (mtp) REVERT: V 157 ASP cc_start: 0.7515 (p0) cc_final: 0.7193 (p0) REVERT: X 67 MET cc_start: 0.8170 (mtm) cc_final: 0.7855 (mtp) REVERT: X 80 LYS cc_start: 0.8655 (mmtt) cc_final: 0.8322 (mmtp) REVERT: X 129 MET cc_start: 0.8536 (mtm) cc_final: 0.8113 (mtp) REVERT: X 145 GLU cc_start: 0.8073 (tp30) cc_final: 0.7803 (tp30) REVERT: X 157 ASP cc_start: 0.7264 (p0) cc_final: 0.6851 (p0) outliers start: 74 outliers final: 45 residues processed: 922 average time/residue: 0.4748 time to fit residues: 710.1385 Evaluate side-chains 745 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 698 time to evaluate : 4.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 16 SER Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain L residue 150 LEU Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain N residue 16 SER Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain P residue 165 GLU Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 246 ASN Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain T residue 119 LEU Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain U residue 54 ASP Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain W residue 16 LEU Chi-restraints excluded: chain W residue 54 ASP Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 105 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 409 optimal weight: 9.9990 chunk 311 optimal weight: 10.0000 chunk 215 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 278 optimal weight: 2.9990 chunk 416 optimal weight: 0.9990 chunk 440 optimal weight: 0.8980 chunk 217 optimal weight: 0.0070 chunk 394 optimal weight: 0.9990 chunk 118 optimal weight: 5.9990 overall best weight: 0.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 123 HIS ** H 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 123 HIS P 123 HIS S 84 GLN ** V 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 37428 Z= 0.157 Angle : 0.475 12.635 50568 Z= 0.254 Chirality : 0.035 0.176 5964 Planarity : 0.003 0.026 6432 Dihedral : 3.204 14.571 5160 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.30 % Allowed : 14.42 % Favored : 83.28 % 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: 4.36 (0.11), residues: 4704 helix: 3.10 (0.07), residues: 4284 sheet: None (None), residues: 0 loop : -0.03 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP U 40 HIS 0.004 0.001 HIS T 185 PHE 0.010 0.001 PHE F 97 TYR 0.022 0.001 TYR P 210 ARG 0.004 0.000 ARG T 211 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 930 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 847 time to evaluate : 4.449 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 80 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8449 (mmtm) REVERT: B 98 MET cc_start: 0.5482 (mmt) cc_final: 0.4711 (mmt) REVERT: B 150 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8138 (mp) REVERT: B 157 ASP cc_start: 0.6826 (p0) cc_final: 0.6519 (p0) REVERT: D 8 MET cc_start: 0.8562 (mtp) cc_final: 0.8011 (mtm) REVERT: D 80 LYS cc_start: 0.8782 (mmtt) cc_final: 0.8440 (mmtp) REVERT: D 114 LEU cc_start: 0.8244 (mt) cc_final: 0.8012 (mt) REVERT: D 129 MET cc_start: 0.8421 (mtm) cc_final: 0.8105 (mtp) REVERT: D 150 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8081 (mp) REVERT: D 157 ASP cc_start: 0.6898 (p0) cc_final: 0.6556 (p0) REVERT: E 48 TYR cc_start: 0.8404 (t80) cc_final: 0.8175 (t80) REVERT: F 67 MET cc_start: 0.8138 (mtm) cc_final: 0.7851 (mtp) REVERT: F 80 LYS cc_start: 0.8833 (mmtt) cc_final: 0.8409 (mmtp) REVERT: H 23 LEU cc_start: 0.9049 (mm) cc_final: 0.8808 (mm) REVERT: J 36 VAL cc_start: 0.6989 (t) cc_final: 0.6562 (p) REVERT: J 60 ASN cc_start: 0.8064 (m-40) cc_final: 0.7753 (t0) REVERT: J 67 MET cc_start: 0.8211 (mtm) cc_final: 0.7614 (mtp) REVERT: J 129 MET cc_start: 0.8323 (mtm) cc_final: 0.8087 (mtp) REVERT: J 150 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8178 (mp) REVERT: L 23 LEU cc_start: 0.9004 (mm) cc_final: 0.8785 (mm) REVERT: L 129 MET cc_start: 0.8490 (mtm) cc_final: 0.8154 (mtp) REVERT: L 157 ASP cc_start: 0.6915 (p0) cc_final: 0.6569 (p0) REVERT: N 67 MET cc_start: 0.8085 (mtm) cc_final: 0.7580 (mtp) REVERT: N 114 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8583 (mt) REVERT: P 23 LEU cc_start: 0.8981 (mm) cc_final: 0.8711 (mm) REVERT: P 67 MET cc_start: 0.8097 (mtm) cc_final: 0.7685 (mtp) REVERT: P 129 MET cc_start: 0.8324 (mtm) cc_final: 0.8039 (mtp) REVERT: P 157 ASP cc_start: 0.7042 (p0) cc_final: 0.6826 (p0) REVERT: R 67 MET cc_start: 0.8323 (mtm) cc_final: 0.7854 (mtp) REVERT: S 48 TYR cc_start: 0.8508 (t80) cc_final: 0.8306 (t80) REVERT: T 67 MET cc_start: 0.8046 (mtm) cc_final: 0.7749 (mtp) REVERT: T 98 MET cc_start: 0.5175 (mmt) cc_final: 0.4908 (mmt) REVERT: T 129 MET cc_start: 0.8520 (mtm) cc_final: 0.8280 (mtp) REVERT: T 150 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8427 (mp) REVERT: U 54 ASP cc_start: 0.8873 (OUTLIER) cc_final: 0.8547 (m-30) REVERT: V 23 LEU cc_start: 0.8898 (mm) cc_final: 0.8633 (mm) REVERT: V 63 SER cc_start: 0.8283 (m) cc_final: 0.8017 (m) REVERT: V 67 MET cc_start: 0.8189 (mtm) cc_final: 0.7557 (mtp) REVERT: V 129 MET cc_start: 0.8431 (mtm) cc_final: 0.8175 (mtp) REVERT: V 157 ASP cc_start: 0.7611 (p0) cc_final: 0.6964 (p0) REVERT: V 266 LEU cc_start: 0.8573 (mt) cc_final: 0.8269 (mt) REVERT: X 67 MET cc_start: 0.8156 (mtm) cc_final: 0.7868 (mtp) REVERT: X 80 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8360 (mmtp) REVERT: X 129 MET cc_start: 0.8552 (mtm) cc_final: 0.8078 (mtp) REVERT: X 145 GLU cc_start: 0.8121 (tp30) cc_final: 0.7864 (tp30) outliers start: 83 outliers final: 44 residues processed: 889 average time/residue: 0.5060 time to fit residues: 732.9837 Evaluate side-chains 747 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 697 time to evaluate : 4.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain J residue 150 LEU Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain N residue 76 GLU Chi-restraints excluded: chain N residue 114 LEU Chi-restraints excluded: chain N residue 248 THR Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain Q residue 54 ASP Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 119 LEU Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain U residue 54 ASP Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 173 LEU Chi-restraints excluded: chain W residue 54 ASP Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 105 LEU Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain X residue 248 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 367 optimal weight: 1.9990 chunk 250 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 328 optimal weight: 0.5980 chunk 181 optimal weight: 9.9990 chunk 376 optimal weight: 0.9980 chunk 304 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 225 optimal weight: 6.9990 chunk 395 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN B 123 HIS F 60 ASN H 123 HIS ** H 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN M 110 ASN P 60 ASN S 84 GLN ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 107 ASN V 123 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.5231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37428 Z= 0.166 Angle : 0.492 12.896 50568 Z= 0.263 Chirality : 0.037 0.249 5964 Planarity : 0.003 0.027 6432 Dihedral : 3.192 13.845 5160 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.63 % Allowed : 15.67 % Favored : 81.70 % 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: 4.28 (0.11), residues: 4704 helix: 3.06 (0.07), residues: 4272 sheet: None (None), residues: 0 loop : -0.07 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP I 40 HIS 0.004 0.001 HIS X 185 PHE 0.008 0.001 PHE X 190 TYR 0.021 0.001 TYR P 210 ARG 0.003 0.000 ARG B 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 810 time to evaluate : 4.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 LYS cc_start: 0.8775 (mmtt) cc_final: 0.8389 (mmtm) REVERT: B 98 MET cc_start: 0.5479 (mmt) cc_final: 0.4711 (mmt) REVERT: B 150 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8326 (mp) REVERT: B 157 ASP cc_start: 0.6835 (p0) cc_final: 0.6548 (p0) REVERT: C 32 ARG cc_start: 0.8675 (tpp80) cc_final: 0.8139 (mpt-90) REVERT: D 80 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8362 (mmtp) REVERT: D 129 MET cc_start: 0.8411 (mtm) cc_final: 0.8121 (mtp) REVERT: D 150 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8189 (mp) REVERT: D 157 ASP cc_start: 0.7133 (p0) cc_final: 0.6895 (p0) REVERT: D 165 GLU cc_start: 0.8505 (mp0) cc_final: 0.8304 (mp0) REVERT: E 54 ASP cc_start: 0.8707 (OUTLIER) cc_final: 0.8432 (m-30) REVERT: F 67 MET cc_start: 0.8219 (mtm) cc_final: 0.7896 (mtp) REVERT: F 80 LYS cc_start: 0.8828 (mmtt) cc_final: 0.8355 (mmtp) REVERT: F 150 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8459 (mp) REVERT: F 230 GLU cc_start: 0.7103 (pt0) cc_final: 0.6847 (pt0) REVERT: H 23 LEU cc_start: 0.9077 (mm) cc_final: 0.8741 (mm) REVERT: J 36 VAL cc_start: 0.7012 (t) cc_final: 0.6612 (p) REVERT: J 60 ASN cc_start: 0.8086 (m-40) cc_final: 0.7801 (t0) REVERT: J 67 MET cc_start: 0.8237 (mtm) cc_final: 0.7653 (mtp) REVERT: J 129 MET cc_start: 0.8353 (mtm) cc_final: 0.8131 (mtp) REVERT: L 23 LEU cc_start: 0.9029 (mm) cc_final: 0.8685 (mm) REVERT: L 129 MET cc_start: 0.8513 (mtm) cc_final: 0.8204 (mtp) REVERT: N 67 MET cc_start: 0.8178 (mtm) cc_final: 0.7649 (mtp) REVERT: N 114 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8574 (mt) REVERT: N 207 GLU cc_start: 0.8103 (tt0) cc_final: 0.7851 (tt0) REVERT: P 23 LEU cc_start: 0.9013 (mm) cc_final: 0.8619 (mm) REVERT: P 67 MET cc_start: 0.8067 (mtm) cc_final: 0.7696 (mtp) REVERT: P 98 MET cc_start: 0.5485 (mmt) cc_final: 0.4790 (mmt) REVERT: P 129 MET cc_start: 0.8339 (mtm) cc_final: 0.8071 (mtp) REVERT: R 67 MET cc_start: 0.8338 (mtm) cc_final: 0.7769 (mtp) REVERT: T 42 GLU cc_start: 0.7862 (mm-30) cc_final: 0.7543 (mm-30) REVERT: T 67 MET cc_start: 0.8089 (mtm) cc_final: 0.7767 (mtp) REVERT: T 129 MET cc_start: 0.8511 (mtm) cc_final: 0.8300 (mtp) REVERT: T 150 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8237 (mp) REVERT: T 153 ASN cc_start: 0.7796 (m-40) cc_final: 0.7362 (p0) REVERT: U 54 ASP cc_start: 0.8857 (OUTLIER) cc_final: 0.8549 (m-30) REVERT: V 23 LEU cc_start: 0.8876 (OUTLIER) cc_final: 0.8499 (mm) REVERT: V 63 SER cc_start: 0.8277 (m) cc_final: 0.7975 (m) REVERT: V 67 MET cc_start: 0.8233 (mtm) cc_final: 0.7611 (mtp) REVERT: V 129 MET cc_start: 0.8468 (mtm) cc_final: 0.8222 (mtp) REVERT: V 266 LEU cc_start: 0.8622 (mt) cc_final: 0.8331 (mt) REVERT: W 32 ARG cc_start: 0.8620 (tpp80) cc_final: 0.8248 (mmm-85) REVERT: W 48 TYR cc_start: 0.8514 (t80) cc_final: 0.8299 (t80) REVERT: X 67 MET cc_start: 0.8241 (mtm) cc_final: 0.7907 (mtp) REVERT: X 80 LYS cc_start: 0.8775 (mmtt) cc_final: 0.8381 (mmtp) REVERT: X 129 MET cc_start: 0.8615 (mtm) cc_final: 0.8025 (mtp) REVERT: X 145 GLU cc_start: 0.8075 (tp30) cc_final: 0.7806 (tp30) outliers start: 95 outliers final: 60 residues processed: 853 average time/residue: 0.5019 time to fit residues: 702.3850 Evaluate side-chains 754 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 686 time to evaluate : 4.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 87 ARG Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 266 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 248 THR Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 84 GLN Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 246 ASN Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain N residue 7 GLU Chi-restraints excluded: chain N residue 76 GLU Chi-restraints excluded: chain N residue 114 LEU Chi-restraints excluded: chain N residue 227 GLU Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 246 ASN Chi-restraints excluded: chain R residue 248 THR Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain T residue 16 SER Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 119 LEU Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 152 ASP Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain U residue 54 ASP Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain W residue 16 LEU Chi-restraints excluded: chain W residue 54 ASP Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain X residue 16 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 148 optimal weight: 2.9990 chunk 396 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 258 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 441 optimal weight: 4.9990 chunk 366 optimal weight: 0.9980 chunk 204 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 231 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN F 60 ASN F 185 HIS ** H 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 185 HIS ** H 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 123 HIS ** N 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 185 HIS T 107 ASN X 123 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 37428 Z= 0.167 Angle : 0.506 14.321 50568 Z= 0.268 Chirality : 0.037 0.289 5964 Planarity : 0.003 0.027 6432 Dihedral : 3.184 13.094 5160 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.85 % Allowed : 16.81 % Favored : 80.34 % 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: 4.25 (0.11), residues: 4704 helix: 3.05 (0.07), residues: 4272 sheet: None (None), residues: 0 loop : -0.10 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 40 HIS 0.004 0.001 HIS X 123 PHE 0.007 0.001 PHE F 97 TYR 0.019 0.001 TYR P 210 ARG 0.003 0.000 ARG P 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 880 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 777 time to evaluate : 4.380 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 80 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8334 (mmtm) REVERT: B 98 MET cc_start: 0.5422 (mmt) cc_final: 0.4716 (mmt) REVERT: D 80 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8366 (mmtp) REVERT: D 129 MET cc_start: 0.8425 (mtm) cc_final: 0.8167 (mtp) REVERT: D 150 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8171 (mp) REVERT: D 157 ASP cc_start: 0.7084 (p0) cc_final: 0.6847 (p0) REVERT: D 165 GLU cc_start: 0.8604 (mp0) cc_final: 0.8281 (mp0) REVERT: E 54 ASP cc_start: 0.8689 (OUTLIER) cc_final: 0.8402 (m-30) REVERT: F 67 MET cc_start: 0.8270 (mtm) cc_final: 0.7927 (mtp) REVERT: F 80 LYS cc_start: 0.8823 (mmtt) cc_final: 0.8309 (mmtp) REVERT: F 98 MET cc_start: 0.5883 (mmt) cc_final: 0.5103 (mmt) REVERT: H 23 LEU cc_start: 0.9085 (mm) cc_final: 0.8601 (mm) REVERT: H 210 TYR cc_start: 0.8217 (t80) cc_final: 0.8012 (t80) REVERT: J 60 ASN cc_start: 0.8058 (m-40) cc_final: 0.7830 (t0) REVERT: J 67 MET cc_start: 0.8243 (mtm) cc_final: 0.7661 (mtp) REVERT: J 129 MET cc_start: 0.8376 (mtm) cc_final: 0.8173 (mtp) REVERT: L 23 LEU cc_start: 0.9045 (mm) cc_final: 0.8695 (mm) REVERT: L 129 MET cc_start: 0.8498 (mtm) cc_final: 0.8202 (mtp) REVERT: N 67 MET cc_start: 0.8207 (mtm) cc_final: 0.7726 (mtp) REVERT: N 114 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8566 (mt) REVERT: O 48 TYR cc_start: 0.8427 (t80) cc_final: 0.8149 (t80) REVERT: O 61 GLN cc_start: 0.8466 (mt0) cc_final: 0.8265 (mt0) REVERT: P 23 LEU cc_start: 0.9034 (mm) cc_final: 0.8732 (mm) REVERT: P 67 MET cc_start: 0.8135 (mtm) cc_final: 0.7761 (mtp) REVERT: P 98 MET cc_start: 0.5541 (mmt) cc_final: 0.5022 (mmt) REVERT: P 129 MET cc_start: 0.8344 (mtm) cc_final: 0.8050 (mtp) REVERT: P 150 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8380 (mp) REVERT: R 67 MET cc_start: 0.8374 (mtm) cc_final: 0.7816 (mtp) REVERT: T 42 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7522 (mm-30) REVERT: T 60 ASN cc_start: 0.7899 (t0) cc_final: 0.7660 (t0) REVERT: T 129 MET cc_start: 0.8503 (mtm) cc_final: 0.8294 (mtp) REVERT: T 150 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8180 (mp) REVERT: T 153 ASN cc_start: 0.7999 (m-40) cc_final: 0.7468 (p0) REVERT: V 23 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8471 (mm) REVERT: V 63 SER cc_start: 0.8301 (m) cc_final: 0.7999 (m) REVERT: V 67 MET cc_start: 0.8253 (mtm) cc_final: 0.7641 (mtp) REVERT: V 76 GLU cc_start: 0.7790 (OUTLIER) cc_final: 0.7557 (mp0) REVERT: V 98 MET cc_start: 0.5467 (mmt) cc_final: 0.4798 (mmt) REVERT: V 129 MET cc_start: 0.8432 (mtm) cc_final: 0.8210 (mtp) REVERT: V 150 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8233 (mp) REVERT: V 246 ASN cc_start: 0.7604 (m110) cc_final: 0.7398 (t0) REVERT: V 266 LEU cc_start: 0.8653 (mt) cc_final: 0.8416 (mt) REVERT: W 48 TYR cc_start: 0.8496 (t80) cc_final: 0.8287 (t80) REVERT: X 67 MET cc_start: 0.8317 (mtm) cc_final: 0.7966 (mtp) REVERT: X 80 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8350 (mmtp) REVERT: X 129 MET cc_start: 0.8601 (mtm) cc_final: 0.8048 (mtp) REVERT: X 145 GLU cc_start: 0.8092 (tp30) cc_final: 0.7857 (tp30) outliers start: 103 outliers final: 68 residues processed: 827 average time/residue: 0.4982 time to fit residues: 670.5425 Evaluate side-chains 769 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 693 time to evaluate : 4.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 54 ASP Chi-restraints excluded: chain E residue 84 GLN Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain I residue 84 GLN Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain K residue 84 GLN Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 115 MET Chi-restraints excluded: chain N residue 76 GLU Chi-restraints excluded: chain N residue 114 LEU Chi-restraints excluded: chain N residue 227 GLU Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain O residue 84 GLN Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 54 ASP Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 246 ASN Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 54 ASP Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain T residue 16 SER Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 107 ASN Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 119 LEU Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 152 ASP Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain V residue 7 GLU Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 76 GLU Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 248 THR Chi-restraints excluded: chain W residue 16 LEU Chi-restraints excluded: chain W residue 54 ASP Chi-restraints excluded: chain W residue 84 GLN Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain X residue 16 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 425 optimal weight: 8.9990 chunk 49 optimal weight: 0.9980 chunk 251 optimal weight: 6.9990 chunk 322 optimal weight: 3.9990 chunk 249 optimal weight: 0.9980 chunk 371 optimal weight: 0.8980 chunk 246 optimal weight: 2.9990 chunk 439 optimal weight: 0.6980 chunk 275 optimal weight: 4.9990 chunk 267 optimal weight: 7.9990 chunk 202 optimal weight: 0.1980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN H 184 ASN ** H 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 185 HIS N 60 ASN ** N 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 216 HIS ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 246 ASN ** X 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.5647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 37428 Z= 0.162 Angle : 0.526 14.318 50568 Z= 0.276 Chirality : 0.037 0.287 5964 Planarity : 0.003 0.028 6432 Dihedral : 3.172 14.586 5160 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.18 % Allowed : 17.55 % Favored : 79.26 % 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: 4.19 (0.11), residues: 4704 helix: 3.01 (0.07), residues: 4272 sheet: None (None), residues: 0 loop : -0.18 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 40 HIS 0.004 0.001 HIS X 185 PHE 0.007 0.001 PHE X 97 TYR 0.015 0.001 TYR P 210 ARG 0.007 0.000 ARG N 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 911 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 796 time to evaluate : 4.509 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 32 ARG cc_start: 0.8361 (mmm-85) cc_final: 0.8161 (mmm-85) REVERT: B 80 LYS cc_start: 0.8763 (mmtt) cc_final: 0.8316 (mmtm) REVERT: B 98 MET cc_start: 0.5498 (mmt) cc_final: 0.4788 (mmt) REVERT: B 150 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8252 (mp) REVERT: C 32 ARG cc_start: 0.8530 (mpt-90) cc_final: 0.8192 (mpt-90) REVERT: D 8 MET cc_start: 0.8518 (mtp) cc_final: 0.8089 (mtm) REVERT: D 98 MET cc_start: 0.5796 (mmt) cc_final: 0.5147 (mmt) REVERT: D 129 MET cc_start: 0.8457 (mtm) cc_final: 0.8201 (mtp) REVERT: D 150 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8068 (mp) REVERT: F 67 MET cc_start: 0.8285 (mtm) cc_final: 0.7930 (mtp) REVERT: F 80 LYS cc_start: 0.8808 (mmtt) cc_final: 0.8305 (mmtp) REVERT: F 98 MET cc_start: 0.5835 (mmt) cc_final: 0.5271 (mmt) REVERT: F 150 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8305 (mp) REVERT: H 23 LEU cc_start: 0.9007 (mm) cc_final: 0.8627 (mm) REVERT: J 67 MET cc_start: 0.8301 (mtm) cc_final: 0.7718 (mtp) REVERT: L 23 LEU cc_start: 0.9063 (mm) cc_final: 0.8434 (mm) REVERT: L 129 MET cc_start: 0.8443 (mtm) cc_final: 0.8202 (mtp) REVERT: N 67 MET cc_start: 0.8230 (mtm) cc_final: 0.7724 (mtp) REVERT: N 98 MET cc_start: 0.5722 (mmt) cc_final: 0.4662 (mmt) REVERT: O 48 TYR cc_start: 0.8446 (t80) cc_final: 0.8155 (t80) REVERT: O 61 GLN cc_start: 0.8450 (mt0) cc_final: 0.8227 (mt0) REVERT: P 23 LEU cc_start: 0.9044 (mm) cc_final: 0.8715 (mm) REVERT: P 67 MET cc_start: 0.8168 (mtm) cc_final: 0.7746 (mtp) REVERT: P 98 MET cc_start: 0.5456 (mmt) cc_final: 0.5185 (mmt) REVERT: P 129 MET cc_start: 0.8361 (mtm) cc_final: 0.8093 (mtp) REVERT: P 150 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8385 (mp) REVERT: P 260 ILE cc_start: 0.8319 (mt) cc_final: 0.7954 (mt) REVERT: R 34 LYS cc_start: 0.8075 (mmpt) cc_final: 0.7875 (mptt) REVERT: R 67 MET cc_start: 0.8391 (mtm) cc_final: 0.7916 (mtp) REVERT: T 129 MET cc_start: 0.8502 (mtm) cc_final: 0.8301 (mtp) REVERT: T 150 LEU cc_start: 0.8729 (OUTLIER) cc_final: 0.8184 (mp) REVERT: T 153 ASN cc_start: 0.7950 (m-40) cc_final: 0.7552 (p0) REVERT: U 32 ARG cc_start: 0.8341 (mmm-85) cc_final: 0.7712 (mpt-90) REVERT: V 23 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8313 (mm) REVERT: V 63 SER cc_start: 0.8344 (m) cc_final: 0.8086 (m) REVERT: V 67 MET cc_start: 0.8264 (mtm) cc_final: 0.7660 (mtp) REVERT: V 98 MET cc_start: 0.5433 (mmt) cc_final: 0.4790 (mmt) REVERT: V 129 MET cc_start: 0.8454 (mtm) cc_final: 0.8212 (mtp) REVERT: V 150 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8256 (mp) REVERT: V 246 ASN cc_start: 0.7564 (m110) cc_final: 0.7349 (t0) REVERT: V 266 LEU cc_start: 0.8714 (mt) cc_final: 0.8471 (mt) REVERT: X 67 MET cc_start: 0.8331 (mtm) cc_final: 0.8049 (mtp) REVERT: X 80 LYS cc_start: 0.8749 (mmtt) cc_final: 0.8333 (mmtp) REVERT: X 129 MET cc_start: 0.8615 (mtm) cc_final: 0.8091 (mtp) outliers start: 115 outliers final: 78 residues processed: 848 average time/residue: 0.4740 time to fit residues: 650.1468 Evaluate side-chains 791 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 706 time to evaluate : 4.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 150 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 84 GLN Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 231 LYS Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain I residue 84 GLN Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 246 ASN Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain K residue 84 GLN Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 170 LEU Chi-restraints excluded: chain L residue 246 ASN Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 115 MET Chi-restraints excluded: chain N residue 76 GLU Chi-restraints excluded: chain N residue 227 GLU Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 54 ASP Chi-restraints excluded: chain Q residue 84 GLN Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 7 GLU Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 246 ASN Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain T residue 16 SER Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 119 LEU Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain T residue 246 ASN Chi-restraints excluded: chain U residue 84 GLN Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 76 GLU Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 248 THR Chi-restraints excluded: chain W residue 16 LEU Chi-restraints excluded: chain W residue 54 ASP Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain X residue 16 SER Chi-restraints excluded: chain X residue 196 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 271 optimal weight: 1.9990 chunk 175 optimal weight: 0.9980 chunk 262 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 86 optimal weight: 9.9990 chunk 85 optimal weight: 0.1980 chunk 279 optimal weight: 6.9990 chunk 299 optimal weight: 2.9990 chunk 217 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 345 optimal weight: 0.8980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 184 ASN ** H 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 60 ASN ** N 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 37428 Z= 0.178 Angle : 0.546 14.538 50568 Z= 0.290 Chirality : 0.039 0.380 5964 Planarity : 0.003 0.029 6432 Dihedral : 3.202 13.433 5160 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.93 % Allowed : 18.05 % Favored : 79.01 % 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: 4.08 (0.11), residues: 4704 helix: 2.94 (0.07), residues: 4272 sheet: None (None), residues: 0 loop : -0.26 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 40 HIS 0.003 0.001 HIS P 185 PHE 0.007 0.001 PHE X 190 TYR 0.015 0.001 TYR J 86 ARG 0.006 0.000 ARG N 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 762 time to evaluate : 4.276 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: B 80 LYS cc_start: 0.8751 (mmtt) cc_final: 0.8290 (mmtm) REVERT: B 98 MET cc_start: 0.5516 (mmt) cc_final: 0.4845 (mmt) REVERT: B 150 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8333 (mp) REVERT: D 8 MET cc_start: 0.8487 (mtp) cc_final: 0.8098 (mtm) REVERT: D 98 MET cc_start: 0.5648 (mmt) cc_final: 0.5119 (mmt) REVERT: D 207 GLU cc_start: 0.8172 (tt0) cc_final: 0.7680 (tt0) REVERT: F 67 MET cc_start: 0.8313 (mtm) cc_final: 0.7951 (mtp) REVERT: F 80 LYS cc_start: 0.8818 (mmtt) cc_final: 0.8304 (mmtp) REVERT: F 98 MET cc_start: 0.5719 (mmt) cc_final: 0.5185 (mmt) REVERT: F 150 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8285 (mp) REVERT: H 23 LEU cc_start: 0.9024 (mm) cc_final: 0.8634 (mm) REVERT: J 67 MET cc_start: 0.8246 (mtm) cc_final: 0.7983 (mtm) REVERT: K 32 ARG cc_start: 0.8580 (mmm-85) cc_final: 0.7937 (mmm-85) REVERT: L 23 LEU cc_start: 0.8860 (mm) cc_final: 0.8460 (mm) REVERT: L 129 MET cc_start: 0.8462 (mtm) cc_final: 0.8124 (mtp) REVERT: N 67 MET cc_start: 0.8250 (mtm) cc_final: 0.7758 (mtp) REVERT: N 98 MET cc_start: 0.5883 (mmt) cc_final: 0.4826 (mmt) REVERT: O 48 TYR cc_start: 0.8461 (t80) cc_final: 0.8177 (t80) REVERT: O 61 GLN cc_start: 0.8456 (mt0) cc_final: 0.8234 (mt0) REVERT: P 23 LEU cc_start: 0.9017 (mm) cc_final: 0.8373 (mm) REVERT: P 67 MET cc_start: 0.8186 (mtm) cc_final: 0.7764 (mtp) REVERT: P 98 MET cc_start: 0.5604 (mmt) cc_final: 0.5398 (mmt) REVERT: P 129 MET cc_start: 0.8358 (mtm) cc_final: 0.8106 (mtp) REVERT: P 150 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8582 (mp) REVERT: R 34 LYS cc_start: 0.8061 (mmpt) cc_final: 0.7859 (mptt) REVERT: R 67 MET cc_start: 0.8398 (mtm) cc_final: 0.7968 (mtp) REVERT: R 98 MET cc_start: 0.5488 (mmt) cc_final: 0.4660 (mmt) REVERT: S 32 ARG cc_start: 0.8669 (mmm-85) cc_final: 0.8075 (mmm-85) REVERT: T 129 MET cc_start: 0.8517 (mtm) cc_final: 0.8281 (mtp) REVERT: T 150 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8360 (mp) REVERT: T 153 ASN cc_start: 0.8019 (m-40) cc_final: 0.7649 (p0) REVERT: V 23 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8384 (mm) REVERT: V 63 SER cc_start: 0.8408 (m) cc_final: 0.8089 (m) REVERT: V 67 MET cc_start: 0.8312 (mtm) cc_final: 0.7692 (mtp) REVERT: V 76 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7486 (mp0) REVERT: V 98 MET cc_start: 0.5426 (mmt) cc_final: 0.4818 (mmt) REVERT: V 129 MET cc_start: 0.8414 (mtm) cc_final: 0.8199 (mtp) REVERT: V 150 LEU cc_start: 0.8522 (OUTLIER) cc_final: 0.8303 (mp) REVERT: V 266 LEU cc_start: 0.8716 (mt) cc_final: 0.8462 (mt) REVERT: X 67 MET cc_start: 0.8364 (mtm) cc_final: 0.8072 (mtp) REVERT: X 80 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8297 (mmtp) REVERT: X 98 MET cc_start: 0.5853 (mmt) cc_final: 0.4885 (mmt) REVERT: X 129 MET cc_start: 0.8623 (mtm) cc_final: 0.8129 (mtp) REVERT: X 191 MET cc_start: 0.8380 (mpp) cc_final: 0.8033 (mtm) outliers start: 106 outliers final: 73 residues processed: 810 average time/residue: 0.4893 time to fit residues: 641.8956 Evaluate side-chains 773 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 693 time to evaluate : 4.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 84 GLN Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 248 THR Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 84 GLN Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 246 ASN Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain K residue 84 GLN Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 246 ASN Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain N residue 76 GLU Chi-restraints excluded: chain N residue 227 GLU Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 84 GLN Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 54 ASP Chi-restraints excluded: chain Q residue 84 GLN Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 246 ASN Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain T residue 16 SER Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 23 LEU Chi-restraints excluded: chain V residue 76 GLU Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 248 THR Chi-restraints excluded: chain W residue 16 LEU Chi-restraints excluded: chain W residue 54 ASP Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain X residue 16 SER Chi-restraints excluded: chain X residue 196 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 399 optimal weight: 0.9980 chunk 421 optimal weight: 9.9990 chunk 384 optimal weight: 8.9990 chunk 409 optimal weight: 7.9990 chunk 420 optimal weight: 2.9990 chunk 246 optimal weight: 0.9980 chunk 178 optimal weight: 8.9990 chunk 321 optimal weight: 0.8980 chunk 125 optimal weight: 0.8980 chunk 370 optimal weight: 2.9990 chunk 387 optimal weight: 4.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 ASN ** H 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 ASN K 109 GLN ** N 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 185 HIS R 60 ASN ** T 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 246 ASN ** X 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.5872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 37428 Z= 0.210 Angle : 0.582 14.841 50568 Z= 0.306 Chirality : 0.040 0.376 5964 Planarity : 0.003 0.027 6432 Dihedral : 3.269 13.802 5160 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.82 % Allowed : 18.91 % Favored : 78.27 % 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: 3.93 (0.12), residues: 4704 helix: 2.87 (0.07), residues: 4260 sheet: None (None), residues: 0 loop : -0.45 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 40 HIS 0.004 0.001 HIS P 185 PHE 0.009 0.001 PHE H 190 TYR 0.015 0.001 TYR L 210 ARG 0.005 0.000 ARG N 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 821 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 719 time to evaluate : 4.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 80 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8305 (mmtm) REVERT: B 149 ARG cc_start: 0.7739 (mtp85) cc_final: 0.7469 (mtp180) REVERT: B 150 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8194 (mp) REVERT: D 8 MET cc_start: 0.8483 (mtp) cc_final: 0.8148 (mtm) REVERT: D 98 MET cc_start: 0.5707 (mmt) cc_final: 0.5084 (mmt) REVERT: D 207 GLU cc_start: 0.8248 (tt0) cc_final: 0.7872 (tt0) REVERT: F 67 MET cc_start: 0.8364 (mtm) cc_final: 0.7948 (mtp) REVERT: F 80 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8304 (mmtp) REVERT: F 98 MET cc_start: 0.5792 (mmt) cc_final: 0.5351 (mmt) REVERT: F 150 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8330 (mp) REVERT: F 196 MET cc_start: 0.7453 (tpp) cc_final: 0.7226 (tpp) REVERT: F 210 TYR cc_start: 0.8081 (t80) cc_final: 0.7773 (t80) REVERT: H 23 LEU cc_start: 0.9044 (mm) cc_final: 0.8635 (mm) REVERT: J 61 LEU cc_start: 0.8616 (mt) cc_final: 0.8372 (mt) REVERT: J 67 MET cc_start: 0.8213 (mtm) cc_final: 0.7758 (mtp) REVERT: J 149 ARG cc_start: 0.7794 (mmm-85) cc_final: 0.7393 (mtp180) REVERT: K 32 ARG cc_start: 0.8522 (mmm-85) cc_final: 0.7839 (mmm-85) REVERT: L 23 LEU cc_start: 0.8851 (mm) cc_final: 0.8448 (mm) REVERT: L 129 MET cc_start: 0.8480 (mtm) cc_final: 0.8214 (mtp) REVERT: N 67 MET cc_start: 0.8271 (mtm) cc_final: 0.7800 (mtp) REVERT: N 98 MET cc_start: 0.5925 (mmt) cc_final: 0.4869 (mmt) REVERT: O 48 TYR cc_start: 0.8497 (t80) cc_final: 0.8215 (t80) REVERT: P 23 LEU cc_start: 0.8887 (mm) cc_final: 0.8516 (mm) REVERT: P 67 MET cc_start: 0.8207 (mtm) cc_final: 0.7786 (mtp) REVERT: P 98 MET cc_start: 0.5689 (mmt) cc_final: 0.5475 (mmt) REVERT: P 129 MET cc_start: 0.8408 (mtm) cc_final: 0.8128 (mtp) REVERT: P 150 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8471 (mp) REVERT: R 67 MET cc_start: 0.8416 (mtm) cc_final: 0.7859 (mtp) REVERT: R 98 MET cc_start: 0.5569 (mmt) cc_final: 0.4840 (mmt) REVERT: T 129 MET cc_start: 0.8534 (mtm) cc_final: 0.8228 (mtp) REVERT: T 150 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.8397 (mp) REVERT: T 153 ASN cc_start: 0.8071 (m-40) cc_final: 0.7670 (p0) REVERT: V 63 SER cc_start: 0.8484 (m) cc_final: 0.8163 (m) REVERT: V 67 MET cc_start: 0.8337 (mtm) cc_final: 0.7754 (mtp) REVERT: V 76 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7562 (mp0) REVERT: V 98 MET cc_start: 0.5410 (mmt) cc_final: 0.4781 (mmt) REVERT: V 129 MET cc_start: 0.8434 (mtm) cc_final: 0.8175 (mtp) REVERT: V 150 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8368 (mp) REVERT: V 266 LEU cc_start: 0.8816 (mt) cc_final: 0.8544 (mt) REVERT: X 67 MET cc_start: 0.8386 (mtm) cc_final: 0.8095 (mtp) REVERT: X 80 LYS cc_start: 0.8747 (mmtt) cc_final: 0.8286 (mmtp) REVERT: X 98 MET cc_start: 0.5996 (mmt) cc_final: 0.5053 (mmt) REVERT: X 129 MET cc_start: 0.8661 (mtm) cc_final: 0.8182 (mtp) outliers start: 102 outliers final: 79 residues processed: 769 average time/residue: 0.5171 time to fit residues: 640.8734 Evaluate side-chains 764 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 679 time to evaluate : 4.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 84 GLN Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 23 LEU Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 248 THR Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 84 GLN Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 246 ASN Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain K residue 84 GLN Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 246 ASN Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 115 MET Chi-restraints excluded: chain N residue 76 GLU Chi-restraints excluded: chain N residue 227 GLU Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 84 GLN Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 152 ASP Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 246 ASN Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 54 ASP Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 84 GLN Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 246 ASN Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain T residue 16 SER Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 76 GLU Chi-restraints excluded: chain V residue 150 LEU Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 248 THR Chi-restraints excluded: chain W residue 16 LEU Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain X residue 16 SER Chi-restraints excluded: chain X residue 196 MET Chi-restraints excluded: chain X residue 248 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 408 optimal weight: 0.6980 chunk 268 optimal weight: 1.9990 chunk 433 optimal weight: 1.9990 chunk 264 optimal weight: 0.9990 chunk 205 optimal weight: 1.9990 chunk 301 optimal weight: 5.9990 chunk 454 optimal weight: 3.9990 chunk 418 optimal weight: 5.9990 chunk 361 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 279 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 ASN ** N 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 61 GLN ** T 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.5975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 37428 Z= 0.212 Angle : 0.588 14.320 50568 Z= 0.311 Chirality : 0.041 0.400 5964 Planarity : 0.003 0.028 6432 Dihedral : 3.302 13.669 5160 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.57 % Allowed : 19.63 % Favored : 77.80 % 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: 3.86 (0.12), residues: 4704 helix: 2.82 (0.07), residues: 4272 sheet: None (None), residues: 0 loop : -0.55 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 40 HIS 0.004 0.001 HIS V 185 PHE 0.007 0.001 PHE H 97 TYR 0.015 0.001 TYR P 86 ARG 0.005 0.000 ARG N 25 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9408 Ramachandran restraints generated. 4704 Oldfield, 0 Emsley, 4704 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 814 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 721 time to evaluate : 4.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8419 (mmm-85) cc_final: 0.7878 (mmm-85) REVERT: B 149 ARG cc_start: 0.7732 (mtp85) cc_final: 0.7446 (mtp180) REVERT: B 150 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8087 (mp) REVERT: D 8 MET cc_start: 0.8474 (mtp) cc_final: 0.8167 (mtm) REVERT: D 98 MET cc_start: 0.5747 (mmt) cc_final: 0.5192 (mmt) REVERT: D 152 ASP cc_start: 0.8179 (t0) cc_final: 0.7931 (t70) REVERT: D 207 GLU cc_start: 0.8227 (tt0) cc_final: 0.7863 (tt0) REVERT: F 67 MET cc_start: 0.8321 (mtm) cc_final: 0.7972 (mtp) REVERT: F 80 LYS cc_start: 0.8832 (mmtt) cc_final: 0.8264 (mmtp) REVERT: F 150 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8247 (mp) REVERT: F 210 TYR cc_start: 0.8035 (t80) cc_final: 0.7751 (t80) REVERT: F 227 GLU cc_start: 0.7894 (tp30) cc_final: 0.7595 (tp30) REVERT: H 23 LEU cc_start: 0.9040 (mm) cc_final: 0.8615 (mm) REVERT: J 67 MET cc_start: 0.8259 (mtm) cc_final: 0.7654 (mtp) REVERT: J 129 MET cc_start: 0.8411 (mtp) cc_final: 0.8169 (ttt) REVERT: K 32 ARG cc_start: 0.8451 (mmm-85) cc_final: 0.7800 (mmm-85) REVERT: L 23 LEU cc_start: 0.8832 (mm) cc_final: 0.8433 (mm) REVERT: L 129 MET cc_start: 0.8465 (mtm) cc_final: 0.8231 (mtp) REVERT: N 67 MET cc_start: 0.8273 (mtm) cc_final: 0.7801 (mtp) REVERT: N 98 MET cc_start: 0.5945 (mmt) cc_final: 0.4900 (mmt) REVERT: N 125 THR cc_start: 0.7559 (m) cc_final: 0.7085 (m) REVERT: N 152 ASP cc_start: 0.8262 (t70) cc_final: 0.7897 (t70) REVERT: O 48 TYR cc_start: 0.8501 (t80) cc_final: 0.8218 (t80) REVERT: P 23 LEU cc_start: 0.8865 (mm) cc_final: 0.8460 (mm) REVERT: P 67 MET cc_start: 0.8225 (mtm) cc_final: 0.7819 (mtp) REVERT: P 129 MET cc_start: 0.8414 (mtm) cc_final: 0.8135 (mtp) REVERT: R 67 MET cc_start: 0.8451 (mtm) cc_final: 0.7903 (mtp) REVERT: R 98 MET cc_start: 0.5679 (mmt) cc_final: 0.4885 (mmt) REVERT: S 32 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.8012 (mmm-85) REVERT: T 129 MET cc_start: 0.8561 (mtm) cc_final: 0.8231 (mtp) REVERT: T 150 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8324 (mp) REVERT: T 153 ASN cc_start: 0.8043 (m-40) cc_final: 0.7697 (p0) REVERT: V 63 SER cc_start: 0.8517 (m) cc_final: 0.8206 (m) REVERT: V 67 MET cc_start: 0.8367 (mtm) cc_final: 0.7780 (mtp) REVERT: V 76 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: V 98 MET cc_start: 0.5300 (mmt) cc_final: 0.4795 (mmt) REVERT: V 129 MET cc_start: 0.8465 (mtm) cc_final: 0.8185 (mtp) REVERT: X 67 MET cc_start: 0.8378 (mtm) cc_final: 0.8014 (mtp) REVERT: X 80 LYS cc_start: 0.8777 (mmtt) cc_final: 0.8267 (mmtp) REVERT: X 98 MET cc_start: 0.5963 (mmt) cc_final: 0.5060 (mmt) REVERT: X 129 MET cc_start: 0.8655 (mtm) cc_final: 0.8193 (mtp) REVERT: X 152 ASP cc_start: 0.8375 (t70) cc_final: 0.8101 (t70) outliers start: 93 outliers final: 82 residues processed: 766 average time/residue: 0.5056 time to fit residues: 622.3870 Evaluate side-chains 771 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 685 time to evaluate : 4.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain B residue 16 SER Chi-restraints excluded: chain B residue 23 LEU Chi-restraints excluded: chain B residue 150 LEU Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 266 LEU Chi-restraints excluded: chain C residue 16 LEU Chi-restraints excluded: chain C residue 88 ASP Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 248 THR Chi-restraints excluded: chain D residue 266 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 84 GLN Chi-restraints excluded: chain E residue 88 ASP Chi-restraints excluded: chain F residue 16 SER Chi-restraints excluded: chain F residue 108 LEU Chi-restraints excluded: chain F residue 114 LEU Chi-restraints excluded: chain F residue 119 LEU Chi-restraints excluded: chain F residue 150 LEU Chi-restraints excluded: chain F residue 240 ILE Chi-restraints excluded: chain F residue 243 LEU Chi-restraints excluded: chain G residue 16 LEU Chi-restraints excluded: chain G residue 54 ASP Chi-restraints excluded: chain G residue 88 ASP Chi-restraints excluded: chain H residue 16 SER Chi-restraints excluded: chain H residue 248 THR Chi-restraints excluded: chain H residue 266 LEU Chi-restraints excluded: chain I residue 54 ASP Chi-restraints excluded: chain I residue 84 GLN Chi-restraints excluded: chain I residue 88 ASP Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain J residue 152 ASP Chi-restraints excluded: chain J residue 173 LEU Chi-restraints excluded: chain J residue 246 ASN Chi-restraints excluded: chain J residue 248 THR Chi-restraints excluded: chain J residue 266 LEU Chi-restraints excluded: chain K residue 47 TYR Chi-restraints excluded: chain K residue 84 GLN Chi-restraints excluded: chain K residue 88 ASP Chi-restraints excluded: chain L residue 16 SER Chi-restraints excluded: chain L residue 246 ASN Chi-restraints excluded: chain L residue 266 LEU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 54 ASP Chi-restraints excluded: chain M residue 64 LEU Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 115 MET Chi-restraints excluded: chain N residue 76 GLU Chi-restraints excluded: chain N residue 227 GLU Chi-restraints excluded: chain N residue 266 LEU Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 54 ASP Chi-restraints excluded: chain O residue 84 GLN Chi-restraints excluded: chain O residue 88 ASP Chi-restraints excluded: chain P residue 169 LEU Chi-restraints excluded: chain P residue 246 ASN Chi-restraints excluded: chain Q residue 38 GLU Chi-restraints excluded: chain Q residue 54 ASP Chi-restraints excluded: chain Q residue 64 LEU Chi-restraints excluded: chain Q residue 88 ASP Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 16 SER Chi-restraints excluded: chain R residue 169 LEU Chi-restraints excluded: chain R residue 246 ASN Chi-restraints excluded: chain S residue 16 LEU Chi-restraints excluded: chain S residue 88 ASP Chi-restraints excluded: chain T residue 16 SER Chi-restraints excluded: chain T residue 23 LEU Chi-restraints excluded: chain T residue 108 LEU Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 152 ASP Chi-restraints excluded: chain T residue 165 GLU Chi-restraints excluded: chain U residue 88 ASP Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain V residue 16 SER Chi-restraints excluded: chain V residue 76 GLU Chi-restraints excluded: chain V residue 165 GLU Chi-restraints excluded: chain V residue 248 THR Chi-restraints excluded: chain W residue 16 LEU Chi-restraints excluded: chain W residue 54 ASP Chi-restraints excluded: chain W residue 88 ASP Chi-restraints excluded: chain W residue 112 LEU Chi-restraints excluded: chain X residue 16 SER Chi-restraints excluded: chain X residue 196 MET Chi-restraints excluded: chain X residue 248 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 456 random chunks: chunk 221 optimal weight: 0.9990 chunk 287 optimal weight: 0.9990 chunk 385 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 333 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 362 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 372 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 184 ASN ** F 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 184 ASN ** H 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 184 ASN ** N 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.140305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.120797 restraints weight = 76589.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.122066 restraints weight = 63274.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.122971 restraints weight = 55633.017| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.6072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 37428 Z= 0.201 Angle : 0.599 15.047 50568 Z= 0.314 Chirality : 0.041 0.402 5964 Planarity : 0.003 0.029 6432 Dihedral : 3.301 14.513 5160 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.71 % Allowed : 19.77 % Favored : 77.52 % 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: 3.81 (0.12), residues: 4704 helix: 2.79 (0.07), residues: 4272 sheet: None (None), residues: 0 loop : -0.66 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP I 40 HIS 0.003 0.001 HIS D 185 PHE 0.007 0.001 PHE X 97 TYR 0.012 0.001 TYR P 210 ARG 0.005 0.000 ARG N 25 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10784.23 seconds wall clock time: 194 minutes 23.88 seconds (11663.88 seconds total)