Starting phenix.real_space_refine on Fri Feb 23 05:09:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfk_21185/02_2024/6vfk_21185.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfk_21185/02_2024/6vfk_21185.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfk_21185/02_2024/6vfk_21185.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfk_21185/02_2024/6vfk_21185.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfk_21185/02_2024/6vfk_21185.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vfk_21185/02_2024/6vfk_21185.pdb" } resolution = 4.25 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= 0.003 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 23580 2.51 5 N 6156 2.21 5 O 7176 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 12": "OE1" <-> "OE2" Residue "A TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 12": "OE1" <-> "OE2" Residue "D TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 12": "OE1" <-> "OE2" Residue "F TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 12": "OE1" <-> "OE2" Residue "H TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 12": "OE1" <-> "OE2" Residue "J TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 12": "OE1" <-> "OE2" Residue "L TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 12": "OE1" <-> "OE2" Residue "N TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 12": "OE1" <-> "OE2" Residue "P TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 12": "OE1" <-> "OE2" Residue "R TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 12": "OE1" <-> "OE2" Residue "T TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 12": "OE1" <-> "OE2" Residue "V TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 252": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 12": "OE1" <-> "OE2" Residue "X TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 95": "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: 37032 Number of models: 1 Model: "" Number of chains: 24 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: "A" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "C" 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: "D" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "E" 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: "F" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "G" 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: "H" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "I" 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: "J" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "K" 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: "L" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "M" 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: "N" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "O" 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: "P" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "Q" 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: "R" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "S" 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: "T" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "U" 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: "V" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "W" 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: "X" Number of atoms: 987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 987 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Time building chain proxies: 18.53, per 1000 atoms: 0.50 Number of scatterers: 37032 At special positions: 0 Unit cell: (175.95, 177.1, 173.65, 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 7176 8.00 N 6156 7.00 C 23580 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: 15.95 Conformation dependent library (CDL) restraints added in 6.4 seconds 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 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: 192 helices and 0 sheets defined 91.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.99 Creating SS restraints... Processing helix chain 'B' and resid 1 through 30 Processing helix chain 'B' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL B 36 " --> pdb=" O THR B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 93 Processing helix chain 'B' and resid 97 through 121 Processing helix chain 'B' and resid 125 through 153 Processing helix chain 'B' and resid 158 through 183 Processing helix chain 'B' and resid 187 through 215 Processing helix chain 'B' and resid 218 through 245 Processing helix chain 'B' and resid 249 through 277 Processing helix chain 'A' and resid 2 through 17 Processing helix chain 'A' and resid 19 through 34 Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 53 through 68 Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 87 through 102 Processing helix chain 'A' and resid 105 through 120 Processing helix chain 'C' and resid 1 through 30 Processing helix chain 'C' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 93 Processing helix chain 'C' and resid 97 through 121 Processing helix chain 'C' and resid 125 through 153 Processing helix chain 'C' and resid 158 through 183 Processing helix chain 'C' and resid 187 through 215 Processing helix chain 'C' and resid 218 through 245 Processing helix chain 'C' and resid 249 through 277 Processing helix chain 'D' and resid 2 through 17 Processing helix chain 'D' and resid 19 through 34 Processing helix chain 'D' and resid 37 through 50 Processing helix chain 'D' and resid 53 through 68 Processing helix chain 'D' and resid 71 through 85 Processing helix chain 'D' and resid 87 through 102 Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'E' and resid 1 through 30 Processing helix chain 'E' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL E 36 " --> pdb=" O THR E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 93 Processing helix chain 'E' and resid 97 through 121 Processing helix chain 'E' and resid 125 through 153 Processing helix chain 'E' and resid 158 through 183 Processing helix chain 'E' and resid 187 through 215 Processing helix chain 'E' and resid 218 through 245 Processing helix chain 'E' and resid 249 through 277 Processing helix chain 'F' and resid 2 through 17 Processing helix chain 'F' and resid 19 through 34 Processing helix chain 'F' and resid 37 through 50 Processing helix chain 'F' and resid 53 through 68 Processing helix chain 'F' and resid 71 through 85 Processing helix chain 'F' and resid 87 through 102 Processing helix chain 'F' and resid 105 through 120 Processing helix chain 'G' and resid 1 through 30 Processing helix chain 'G' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL G 36 " --> pdb=" O THR G 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 93 Processing helix chain 'G' and resid 97 through 121 Processing helix chain 'G' and resid 125 through 153 Processing helix chain 'G' and resid 158 through 183 Processing helix chain 'G' and resid 187 through 215 Processing helix chain 'G' and resid 218 through 245 Processing helix chain 'G' and resid 249 through 277 Processing helix chain 'H' and resid 2 through 17 Processing helix chain 'H' and resid 19 through 34 Processing helix chain 'H' and resid 37 through 50 Processing helix chain 'H' and resid 53 through 68 Processing helix chain 'H' and resid 71 through 85 Processing helix chain 'H' and resid 87 through 102 Processing helix chain 'H' and resid 105 through 120 Processing helix chain 'I' and resid 1 through 30 Processing helix chain 'I' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL I 36 " --> pdb=" O THR I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 93 Processing helix chain 'I' and resid 97 through 121 Processing helix chain 'I' and resid 125 through 153 Processing helix chain 'I' and resid 158 through 183 Processing helix chain 'I' and resid 187 through 215 Processing helix chain 'I' and resid 218 through 245 Processing helix chain 'I' and resid 249 through 277 Processing helix chain 'J' and resid 2 through 17 Processing helix chain 'J' and resid 19 through 34 Processing helix chain 'J' and resid 37 through 50 Processing helix chain 'J' and resid 53 through 68 Processing helix chain 'J' and resid 71 through 85 Processing helix chain 'J' and resid 87 through 102 Processing helix chain 'J' and resid 105 through 120 Processing helix chain 'K' and resid 1 through 30 Processing helix chain 'K' and resid 32 through 59 removed outlier: 3.502A pdb=" N VAL K 36 " --> pdb=" O THR K 32 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 93 Processing helix chain 'K' and resid 97 through 121 Processing helix chain 'K' and resid 125 through 153 Processing helix chain 'K' and resid 158 through 183 Processing helix chain 'K' and resid 187 through 215 Processing helix chain 'K' and resid 218 through 245 Processing helix chain 'K' and resid 249 through 277 Processing helix chain 'L' and resid 2 through 17 Processing helix chain 'L' and resid 19 through 34 Processing helix chain 'L' and resid 37 through 50 Processing helix chain 'L' and resid 53 through 68 Processing helix chain 'L' and resid 71 through 85 Processing helix chain 'L' and resid 87 through 102 Processing helix chain 'L' and resid 105 through 120 Processing helix chain 'M' and resid 1 through 30 Processing helix chain 'M' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL M 36 " --> pdb=" O THR M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 93 Processing helix chain 'M' and resid 97 through 121 Processing helix chain 'M' and resid 125 through 153 Processing helix chain 'M' and resid 158 through 183 Processing helix chain 'M' and resid 187 through 215 Processing helix chain 'M' and resid 218 through 245 Processing helix chain 'M' and resid 249 through 277 Processing helix chain 'N' and resid 2 through 17 Processing helix chain 'N' and resid 19 through 34 Processing helix chain 'N' and resid 37 through 50 Processing helix chain 'N' and resid 53 through 68 Processing helix chain 'N' and resid 71 through 85 Processing helix chain 'N' and resid 87 through 102 Processing helix chain 'N' and resid 105 through 120 Processing helix chain 'O' and resid 1 through 30 Processing helix chain 'O' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL O 36 " --> pdb=" O THR O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 93 Processing helix chain 'O' and resid 97 through 121 Processing helix chain 'O' and resid 125 through 153 Processing helix chain 'O' and resid 158 through 183 Processing helix chain 'O' and resid 187 through 215 Processing helix chain 'O' and resid 218 through 245 Processing helix chain 'O' and resid 249 through 277 Processing helix chain 'P' and resid 2 through 17 Processing helix chain 'P' and resid 19 through 34 Processing helix chain 'P' and resid 37 through 50 Processing helix chain 'P' and resid 53 through 68 Processing helix chain 'P' and resid 71 through 85 Processing helix chain 'P' and resid 87 through 102 Processing helix chain 'P' and resid 105 through 120 Processing helix chain 'Q' and resid 1 through 30 Processing helix chain 'Q' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL Q 36 " --> pdb=" O THR Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 93 Processing helix chain 'Q' and resid 97 through 121 Processing helix chain 'Q' and resid 125 through 153 Processing helix chain 'Q' and resid 158 through 183 Processing helix chain 'Q' and resid 187 through 215 Processing helix chain 'Q' and resid 218 through 245 Processing helix chain 'Q' and resid 249 through 277 Processing helix chain 'R' and resid 2 through 17 Processing helix chain 'R' and resid 19 through 34 Processing helix chain 'R' and resid 37 through 50 Processing helix chain 'R' and resid 53 through 68 Processing helix chain 'R' and resid 71 through 85 Processing helix chain 'R' and resid 87 through 102 Processing helix chain 'R' and resid 105 through 120 Processing helix chain 'S' and resid 1 through 30 Processing helix chain 'S' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL S 36 " --> pdb=" O THR S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 93 Processing helix chain 'S' and resid 97 through 121 Processing helix chain 'S' and resid 125 through 153 Processing helix chain 'S' and resid 158 through 183 Processing helix chain 'S' and resid 187 through 215 Processing helix chain 'S' and resid 218 through 245 Processing helix chain 'S' and resid 249 through 277 Processing helix chain 'T' and resid 2 through 17 Processing helix chain 'T' and resid 19 through 34 Processing helix chain 'T' and resid 37 through 50 Processing helix chain 'T' and resid 53 through 68 Processing helix chain 'T' and resid 71 through 85 Processing helix chain 'T' and resid 87 through 102 Processing helix chain 'T' and resid 105 through 120 Processing helix chain 'U' and resid 1 through 30 Processing helix chain 'U' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL U 36 " --> pdb=" O THR U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 63 through 93 Processing helix chain 'U' and resid 97 through 121 Processing helix chain 'U' and resid 125 through 153 Processing helix chain 'U' and resid 158 through 183 Processing helix chain 'U' and resid 187 through 215 Processing helix chain 'U' and resid 218 through 245 Processing helix chain 'U' and resid 249 through 277 Processing helix chain 'V' and resid 2 through 17 Processing helix chain 'V' and resid 19 through 34 Processing helix chain 'V' and resid 37 through 50 Processing helix chain 'V' and resid 53 through 68 Processing helix chain 'V' and resid 71 through 85 Processing helix chain 'V' and resid 87 through 102 Processing helix chain 'V' and resid 105 through 120 Processing helix chain 'W' and resid 1 through 30 Processing helix chain 'W' and resid 32 through 59 removed outlier: 3.503A pdb=" N VAL W 36 " --> pdb=" O THR W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 63 through 93 Processing helix chain 'W' and resid 97 through 121 Processing helix chain 'W' and resid 125 through 153 Processing helix chain 'W' and resid 158 through 183 Processing helix chain 'W' and resid 187 through 215 Processing helix chain 'W' and resid 218 through 245 Processing helix chain 'W' and resid 249 through 277 Processing helix chain 'X' and resid 2 through 17 Processing helix chain 'X' and resid 19 through 34 Processing helix chain 'X' and resid 37 through 50 Processing helix chain 'X' and resid 53 through 68 Processing helix chain 'X' and resid 71 through 85 Processing helix chain 'X' and resid 87 through 102 Processing helix chain 'X' and resid 105 through 120 3588 hydrogen bonds defined for protein. 10764 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: 16.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 7435 1.31 - 1.44: 10073 1.44 - 1.57: 19515 1.57 - 1.69: 213 1.69 - 1.82: 240 Bond restraints: 37476 Sorted by residual: bond pdb=" CB HIS M 123 " pdb=" CG HIS M 123 " ideal model delta sigma weight residual 1.497 1.370 0.127 1.40e-02 5.10e+03 8.27e+01 bond pdb=" CB HIS Q 123 " pdb=" CG HIS Q 123 " ideal model delta sigma weight residual 1.497 1.370 0.127 1.40e-02 5.10e+03 8.26e+01 bond pdb=" CB HIS E 123 " pdb=" CG HIS E 123 " ideal model delta sigma weight residual 1.497 1.370 0.127 1.40e-02 5.10e+03 8.25e+01 bond pdb=" CB HIS B 123 " pdb=" CG HIS B 123 " ideal model delta sigma weight residual 1.497 1.370 0.127 1.40e-02 5.10e+03 8.25e+01 bond pdb=" CB HIS S 123 " pdb=" CG HIS S 123 " ideal model delta sigma weight residual 1.497 1.370 0.127 1.40e-02 5.10e+03 8.25e+01 ... (remaining 37471 not shown) Histogram of bond angle deviations from ideal: 101.09 - 107.66: 1168 107.66 - 114.23: 20767 114.23 - 120.80: 19318 120.80 - 127.37: 9224 127.37 - 133.94: 151 Bond angle restraints: 50628 Sorted by residual: angle pdb=" C ASP N 34 " pdb=" N PRO N 35 " pdb=" CA PRO N 35 " ideal model delta sigma weight residual 119.82 127.79 -7.97 9.80e-01 1.04e+00 6.61e+01 angle pdb=" C ASP T 34 " pdb=" N PRO T 35 " pdb=" CA PRO T 35 " ideal model delta sigma weight residual 119.82 127.76 -7.94 9.80e-01 1.04e+00 6.56e+01 angle pdb=" C ASP H 34 " pdb=" N PRO H 35 " pdb=" CA PRO H 35 " ideal model delta sigma weight residual 119.82 127.76 -7.94 9.80e-01 1.04e+00 6.56e+01 angle pdb=" C ASP L 34 " pdb=" N PRO L 35 " pdb=" CA PRO L 35 " ideal model delta sigma weight residual 119.82 127.75 -7.93 9.80e-01 1.04e+00 6.55e+01 angle pdb=" C ASP V 34 " pdb=" N PRO V 35 " pdb=" CA PRO V 35 " ideal model delta sigma weight residual 119.82 127.75 -7.93 9.80e-01 1.04e+00 6.55e+01 ... (remaining 50623 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.11: 22253 15.11 - 30.22: 739 30.22 - 45.32: 192 45.32 - 60.43: 48 60.43 - 75.54: 48 Dihedral angle restraints: 23280 sinusoidal: 8952 harmonic: 14328 Sorted by residual: dihedral pdb=" CB GLU V 12 " pdb=" CG GLU V 12 " pdb=" CD GLU V 12 " pdb=" OE1 GLU V 12 " ideal model delta sinusoidal sigma weight residual 0.00 -75.54 75.54 1 3.00e+01 1.11e-03 8.00e+00 dihedral pdb=" CB GLU D 12 " pdb=" CG GLU D 12 " pdb=" CD GLU D 12 " pdb=" OE1 GLU D 12 " ideal model delta sinusoidal sigma weight residual 0.00 -75.52 75.52 1 3.00e+01 1.11e-03 8.00e+00 dihedral pdb=" CB GLU P 12 " pdb=" CG GLU P 12 " pdb=" CD GLU P 12 " pdb=" OE1 GLU P 12 " ideal model delta sinusoidal sigma weight residual 0.00 -75.51 75.51 1 3.00e+01 1.11e-03 8.00e+00 ... (remaining 23277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 3645 0.072 - 0.145: 1729 0.145 - 0.217: 511 0.217 - 0.289: 57 0.289 - 0.361: 22 Chirality restraints: 5964 Sorted by residual: chirality pdb=" CG LEU P 106 " pdb=" CB LEU P 106 " pdb=" CD1 LEU P 106 " pdb=" CD2 LEU P 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.95 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" CG LEU T 106 " pdb=" CB LEU T 106 " pdb=" CD1 LEU T 106 " pdb=" CD2 LEU T 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.95 0.36 2.00e-01 2.50e+01 3.25e+00 chirality pdb=" CG LEU R 106 " pdb=" CB LEU R 106 " pdb=" CD1 LEU R 106 " pdb=" CD2 LEU R 106 " both_signs ideal model delta sigma weight residual False -2.59 -2.95 0.36 2.00e-01 2.50e+01 3.25e+00 ... (remaining 5961 not shown) Planarity restraints: 6444 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR W 148 " 0.082 2.00e-02 2.50e+03 4.52e-02 4.08e+01 pdb=" CG TYR W 148 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR W 148 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR W 148 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR W 148 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR W 148 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR W 148 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR W 148 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 148 " 0.082 2.00e-02 2.50e+03 4.50e-02 4.06e+01 pdb=" CG TYR C 148 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR C 148 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR C 148 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR C 148 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR C 148 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR C 148 " -0.014 2.00e-02 2.50e+03 pdb=" OH TYR C 148 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 148 " 0.082 2.00e-02 2.50e+03 4.50e-02 4.06e+01 pdb=" CG TYR Q 148 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 148 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 148 " -0.038 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 148 " -0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 148 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR Q 148 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR Q 148 " 0.072 2.00e-02 2.50e+03 ... (remaining 6441 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 15949 2.89 - 3.39: 42847 3.39 - 3.90: 65743 3.90 - 4.40: 79769 4.40 - 4.90: 121318 Nonbonded interactions: 325626 Sorted by model distance: nonbonded pdb=" OG1 THR W 156 " pdb=" N ASP W 157 " model vdw 2.389 2.520 nonbonded pdb=" OG1 THR U 156 " pdb=" N ASP U 157 " model vdw 2.389 2.520 nonbonded pdb=" OG1 THR I 156 " pdb=" N ASP I 157 " model vdw 2.389 2.520 nonbonded pdb=" OG1 THR O 156 " pdb=" N ASP O 157 " model vdw 2.389 2.520 nonbonded pdb=" OG1 THR E 156 " pdb=" N ASP E 157 " model vdw 2.390 2.520 ... (remaining 325621 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 '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' } ncs_group { reference = chain 'B' 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' } 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: 3.770 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: 20.520 Check model and map are aligned: 0.640 Set scattering table: 0.370 Process input model: 98.080 Find NCS groups from input model: 2.690 Set up NCS constraints: 0.420 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: 0.020 Load rotamer database and sin/cos tables:3.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 129.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 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 : 0.021 0.127 37476 Z= 1.336 Angle : 1.410 7.966 50628 Z= 0.968 Chirality : 0.086 0.361 5964 Planarity : 0.009 0.045 6444 Dihedral : 10.301 75.538 13944 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.59 (0.10), residues: 4716 helix: 1.80 (0.06), residues: 4344 sheet: None (None), residues: 0 loop : 1.15 (0.35), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.009 TRP N 41 HIS 0.016 0.007 HIS M 216 PHE 0.033 0.009 PHE C 159 TYR 0.082 0.012 TYR S 148 ARG 0.008 0.001 ARG F 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1316 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1316 time to evaluate : 4.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 67 MET cc_start: 0.9138 (mtp) cc_final: 0.8650 (mtp) REVERT: B 85 ILE cc_start: 0.9698 (mt) cc_final: 0.9482 (tt) REVERT: B 160 MET cc_start: 0.7955 (ptm) cc_final: 0.7262 (ptm) REVERT: A 31 LEU cc_start: 0.9135 (mt) cc_final: 0.8886 (mt) REVERT: A 55 ASP cc_start: 0.8379 (m-30) cc_final: 0.8155 (t70) REVERT: A 102 ASP cc_start: 0.8713 (t0) cc_final: 0.8468 (t0) REVERT: A 118 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8449 (mppt) REVERT: C 67 MET cc_start: 0.9080 (mtp) cc_final: 0.8877 (mtp) REVERT: C 160 MET cc_start: 0.8129 (ptm) cc_final: 0.7541 (ptm) REVERT: D 42 TYR cc_start: 0.8591 (t80) cc_final: 0.8318 (t80) REVERT: D 55 ASP cc_start: 0.8106 (m-30) cc_final: 0.7789 (t70) REVERT: D 97 LYS cc_start: 0.9313 (tppt) cc_final: 0.8867 (ttmt) REVERT: D 102 ASP cc_start: 0.8719 (t0) cc_final: 0.7220 (t0) REVERT: D 118 LYS cc_start: 0.8534 (mmtt) cc_final: 0.8285 (mppt) REVERT: E 15 SER cc_start: 0.9446 (t) cc_final: 0.9228 (p) REVERT: E 160 MET cc_start: 0.8064 (ptm) cc_final: 0.7476 (ptm) REVERT: F 31 LEU cc_start: 0.9231 (mt) cc_final: 0.8989 (mt) REVERT: F 55 ASP cc_start: 0.8550 (m-30) cc_final: 0.8071 (t0) REVERT: F 97 LYS cc_start: 0.9324 (tppt) cc_final: 0.9010 (ttmt) REVERT: F 102 ASP cc_start: 0.8701 (t0) cc_final: 0.8264 (t0) REVERT: F 117 ASP cc_start: 0.8918 (t70) cc_final: 0.7210 (t0) REVERT: F 118 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8383 (mppt) REVERT: G 19 SER cc_start: 0.9295 (m) cc_final: 0.8957 (p) REVERT: G 67 MET cc_start: 0.8977 (mtp) cc_final: 0.8638 (mtp) REVERT: G 113 ILE cc_start: 0.9341 (mt) cc_final: 0.9137 (tt) REVERT: G 160 MET cc_start: 0.8034 (ptm) cc_final: 0.7671 (ptm) REVERT: G 266 LEU cc_start: 0.9430 (tt) cc_final: 0.9203 (tt) REVERT: H 31 LEU cc_start: 0.9261 (mt) cc_final: 0.9025 (mt) REVERT: H 55 ASP cc_start: 0.8382 (m-30) cc_final: 0.7983 (t70) REVERT: H 102 ASP cc_start: 0.8622 (t0) cc_final: 0.8103 (t0) REVERT: H 118 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8403 (mppt) REVERT: I 15 SER cc_start: 0.9524 (t) cc_final: 0.9320 (p) REVERT: I 19 SER cc_start: 0.9331 (m) cc_final: 0.9006 (p) REVERT: I 67 MET cc_start: 0.9122 (mtp) cc_final: 0.8697 (mtp) REVERT: I 160 MET cc_start: 0.8001 (ptm) cc_final: 0.7704 (ptm) REVERT: J 36 ASN cc_start: 0.8480 (m-40) cc_final: 0.8026 (t0) REVERT: J 55 ASP cc_start: 0.8240 (m-30) cc_final: 0.7982 (t0) REVERT: J 63 LYS cc_start: 0.8782 (mmtt) cc_final: 0.8375 (ttpt) REVERT: J 97 LYS cc_start: 0.9225 (tppt) cc_final: 0.8919 (mtmt) REVERT: J 102 ASP cc_start: 0.8522 (t0) cc_final: 0.8234 (t0) REVERT: K 5 VAL cc_start: 0.9376 (t) cc_final: 0.9152 (p) REVERT: K 15 SER cc_start: 0.9482 (t) cc_final: 0.9280 (p) REVERT: K 19 SER cc_start: 0.9286 (m) cc_final: 0.8996 (p) REVERT: K 67 MET cc_start: 0.9029 (mtp) cc_final: 0.8369 (mtp) REVERT: K 160 MET cc_start: 0.8068 (ptm) cc_final: 0.7486 (ptm) REVERT: K 221 TYR cc_start: 0.7022 (m-80) cc_final: 0.6686 (m-80) REVERT: K 266 LEU cc_start: 0.9432 (tt) cc_final: 0.9151 (tt) REVERT: L 31 LEU cc_start: 0.9177 (mt) cc_final: 0.8967 (mt) REVERT: L 97 LYS cc_start: 0.9308 (tppt) cc_final: 0.9036 (mttt) REVERT: L 102 ASP cc_start: 0.8786 (t0) cc_final: 0.8200 (t0) REVERT: L 118 LYS cc_start: 0.8591 (mmtt) cc_final: 0.8252 (mppt) REVERT: M 19 SER cc_start: 0.9302 (m) cc_final: 0.8996 (p) REVERT: M 67 MET cc_start: 0.9072 (mtp) cc_final: 0.8603 (mtp) REVERT: M 160 MET cc_start: 0.7985 (ptm) cc_final: 0.7567 (ptm) REVERT: M 221 TYR cc_start: 0.6987 (m-80) cc_final: 0.6602 (m-80) REVERT: M 268 LYS cc_start: 0.9240 (tptt) cc_final: 0.9039 (tptt) REVERT: N 102 ASP cc_start: 0.8641 (t0) cc_final: 0.8027 (t0) REVERT: N 118 LYS cc_start: 0.8680 (mmtt) cc_final: 0.8339 (mppt) REVERT: O 67 MET cc_start: 0.9206 (mtp) cc_final: 0.8700 (mtp) REVERT: O 77 LEU cc_start: 0.9463 (mt) cc_final: 0.9248 (tp) REVERT: O 160 MET cc_start: 0.8227 (ptm) cc_final: 0.7793 (ptm) REVERT: P 55 ASP cc_start: 0.8167 (m-30) cc_final: 0.7842 (t0) REVERT: P 102 ASP cc_start: 0.8601 (t0) cc_final: 0.7232 (t0) REVERT: P 118 LYS cc_start: 0.8628 (mmtt) cc_final: 0.8425 (mppt) REVERT: Q 5 VAL cc_start: 0.9384 (t) cc_final: 0.9174 (p) REVERT: Q 67 MET cc_start: 0.9223 (mtp) cc_final: 0.8813 (mtp) REVERT: Q 160 MET cc_start: 0.8119 (ptm) cc_final: 0.7763 (ptm) REVERT: Q 221 TYR cc_start: 0.6985 (m-80) cc_final: 0.6577 (m-80) REVERT: R 36 ASN cc_start: 0.8592 (m-40) cc_final: 0.8069 (t0) REVERT: R 55 ASP cc_start: 0.8006 (m-30) cc_final: 0.7700 (t0) REVERT: R 102 ASP cc_start: 0.8598 (t0) cc_final: 0.7105 (t0) REVERT: R 118 LYS cc_start: 0.8712 (mmtt) cc_final: 0.8385 (mppt) REVERT: S 67 MET cc_start: 0.8995 (mtp) cc_final: 0.8571 (mtp) REVERT: S 160 MET cc_start: 0.7920 (ptm) cc_final: 0.7466 (ptm) REVERT: S 221 TYR cc_start: 0.6823 (m-80) cc_final: 0.6620 (m-80) REVERT: T 55 ASP cc_start: 0.8423 (m-30) cc_final: 0.8175 (t0) REVERT: T 63 LYS cc_start: 0.8769 (mmtt) cc_final: 0.8311 (ttpt) REVERT: T 97 LYS cc_start: 0.9356 (tppt) cc_final: 0.8952 (ttmt) REVERT: T 102 ASP cc_start: 0.8507 (t0) cc_final: 0.8104 (t0) REVERT: T 118 LYS cc_start: 0.8788 (mmtt) cc_final: 0.8471 (mppt) REVERT: U 67 MET cc_start: 0.8896 (mtp) cc_final: 0.8644 (mtp) REVERT: U 136 ILE cc_start: 0.9345 (mt) cc_final: 0.8971 (mt) REVERT: V 36 ASN cc_start: 0.8487 (m-40) cc_final: 0.8002 (t0) REVERT: V 102 ASP cc_start: 0.8669 (t0) cc_final: 0.8090 (t0) REVERT: W 67 MET cc_start: 0.9113 (mtp) cc_final: 0.8768 (mtp) REVERT: W 77 LEU cc_start: 0.9553 (mt) cc_final: 0.9347 (tp) REVERT: W 160 MET cc_start: 0.7920 (ptm) cc_final: 0.7671 (ptm) REVERT: W 221 TYR cc_start: 0.6763 (m-80) cc_final: 0.6320 (m-80) REVERT: X 36 ASN cc_start: 0.8500 (m-40) cc_final: 0.7960 (t0) REVERT: X 55 ASP cc_start: 0.8455 (m-30) cc_final: 0.8199 (t0) REVERT: X 97 LYS cc_start: 0.9353 (tppt) cc_final: 0.9109 (mmmm) REVERT: X 102 ASP cc_start: 0.8534 (t0) cc_final: 0.8213 (t0) outliers start: 0 outliers final: 0 residues processed: 1316 average time/residue: 0.5647 time to fit residues: 1167.9883 Evaluate side-chains 544 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 544 time to evaluate : 4.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 395 optimal weight: 0.8980 chunk 354 optimal weight: 2.9990 chunk 196 optimal weight: 0.6980 chunk 121 optimal weight: 0.8980 chunk 239 optimal weight: 0.7980 chunk 189 optimal weight: 1.9990 chunk 366 optimal weight: 0.9990 chunk 141 optimal weight: 4.9990 chunk 223 optimal weight: 2.9990 chunk 273 optimal weight: 0.9990 chunk 424 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 HIS D 105 ASN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 277 ASN ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 277 ASN ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 277 ASN ** Q 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 105 ASN S 122 ASN ** U 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 185 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 277 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37476 Z= 0.219 Angle : 0.559 8.687 50628 Z= 0.305 Chirality : 0.039 0.252 5964 Planarity : 0.004 0.042 6444 Dihedral : 3.661 19.520 5172 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 0.03 % Allowed : 1.58 % Favored : 98.39 % 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: 4.31 (0.11), residues: 4716 helix: 3.01 (0.07), residues: 4380 sheet: None (None), residues: 0 loop : -0.01 (0.35), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP T 75 HIS 0.015 0.003 HIS U 123 PHE 0.018 0.003 PHE W 97 TYR 0.020 0.002 TYR O 221 ARG 0.008 0.001 ARG K 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 845 time to evaluate : 3.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 MET cc_start: 0.7726 (ptm) cc_final: 0.7303 (ptm) REVERT: B 212 LEU cc_start: 0.8890 (mt) cc_final: 0.8591 (mt) REVERT: B 221 TYR cc_start: 0.7902 (m-10) cc_final: 0.7341 (m-80) REVERT: A 62 GLN cc_start: 0.9251 (mt0) cc_final: 0.8917 (mt0) REVERT: A 102 ASP cc_start: 0.8618 (t0) cc_final: 0.8391 (t0) REVERT: C 160 MET cc_start: 0.7833 (ptm) cc_final: 0.6609 (ptm) REVERT: C 191 MET cc_start: 0.8867 (mtt) cc_final: 0.8650 (tpp) REVERT: C 221 TYR cc_start: 0.7854 (m-10) cc_final: 0.7449 (m-80) REVERT: D 34 ASP cc_start: 0.9187 (t0) cc_final: 0.8828 (t0) REVERT: D 36 ASN cc_start: 0.8603 (m-40) cc_final: 0.7948 (t0) REVERT: D 55 ASP cc_start: 0.8159 (m-30) cc_final: 0.7847 (t0) REVERT: D 97 LYS cc_start: 0.9374 (tppt) cc_final: 0.8786 (ttmt) REVERT: D 102 ASP cc_start: 0.8738 (t0) cc_final: 0.8491 (t0) REVERT: E 160 MET cc_start: 0.7642 (ptm) cc_final: 0.7409 (ptm) REVERT: E 221 TYR cc_start: 0.7765 (m-10) cc_final: 0.7070 (m-80) REVERT: E 268 LYS cc_start: 0.9227 (tptt) cc_final: 0.8761 (tptp) REVERT: F 31 LEU cc_start: 0.9166 (mt) cc_final: 0.8952 (mt) REVERT: F 36 ASN cc_start: 0.8621 (m-40) cc_final: 0.8150 (t0) REVERT: F 55 ASP cc_start: 0.8325 (m-30) cc_final: 0.8038 (t0) REVERT: F 62 GLN cc_start: 0.9183 (mt0) cc_final: 0.8964 (mt0) REVERT: F 63 LYS cc_start: 0.9079 (mmtt) cc_final: 0.8815 (mttm) REVERT: F 97 LYS cc_start: 0.9398 (tppt) cc_final: 0.9029 (ttmt) REVERT: F 102 ASP cc_start: 0.8667 (t0) cc_final: 0.8396 (t0) REVERT: F 105 ASN cc_start: 0.8241 (m-40) cc_final: 0.7590 (p0) REVERT: G 19 SER cc_start: 0.9435 (m) cc_final: 0.9157 (p) REVERT: G 160 MET cc_start: 0.7710 (ptm) cc_final: 0.6891 (ptm) REVERT: G 221 TYR cc_start: 0.7744 (m-10) cc_final: 0.7259 (m-80) REVERT: H 55 ASP cc_start: 0.8234 (m-30) cc_final: 0.7970 (t0) REVERT: H 62 GLN cc_start: 0.9152 (mt0) cc_final: 0.8841 (mt0) REVERT: H 97 LYS cc_start: 0.9390 (mmmm) cc_final: 0.8775 (mttp) REVERT: H 102 ASP cc_start: 0.8834 (t0) cc_final: 0.8513 (t0) REVERT: I 19 SER cc_start: 0.9486 (m) cc_final: 0.9171 (p) REVERT: I 67 MET cc_start: 0.9053 (mtp) cc_final: 0.8514 (mtp) REVERT: I 160 MET cc_start: 0.7629 (ptm) cc_final: 0.7111 (ptm) REVERT: I 221 TYR cc_start: 0.8080 (m-10) cc_final: 0.7431 (m-80) REVERT: I 268 LYS cc_start: 0.9155 (tptt) cc_final: 0.8864 (tptp) REVERT: J 36 ASN cc_start: 0.8487 (m-40) cc_final: 0.8074 (t0) REVERT: J 62 GLN cc_start: 0.9216 (mt0) cc_final: 0.8937 (mt0) REVERT: J 63 LYS cc_start: 0.9087 (mmtt) cc_final: 0.8884 (mttm) REVERT: J 70 ASN cc_start: 0.8178 (m110) cc_final: 0.7611 (t0) REVERT: J 97 LYS cc_start: 0.9340 (tppt) cc_final: 0.9046 (mmmm) REVERT: J 102 ASP cc_start: 0.8545 (t0) cc_final: 0.7684 (t0) REVERT: K 19 SER cc_start: 0.9435 (m) cc_final: 0.9219 (p) REVERT: K 67 MET cc_start: 0.9044 (mtp) cc_final: 0.8700 (mtp) REVERT: K 160 MET cc_start: 0.7816 (ptm) cc_final: 0.7238 (ptm) REVERT: K 212 LEU cc_start: 0.9042 (mt) cc_final: 0.8585 (mt) REVERT: L 62 GLN cc_start: 0.9186 (mt0) cc_final: 0.8841 (mt0) REVERT: L 97 LYS cc_start: 0.9362 (tppt) cc_final: 0.8975 (mttt) REVERT: L 102 ASP cc_start: 0.8918 (t0) cc_final: 0.8308 (t0) REVERT: M 19 SER cc_start: 0.9435 (m) cc_final: 0.9132 (p) REVERT: M 160 MET cc_start: 0.7872 (ptm) cc_final: 0.7577 (ptm) REVERT: M 212 LEU cc_start: 0.8937 (mt) cc_final: 0.8571 (mt) REVERT: M 221 TYR cc_start: 0.6562 (m-80) cc_final: 0.6200 (m-80) REVERT: M 226 ILE cc_start: 0.9412 (mt) cc_final: 0.9031 (mm) REVERT: N 62 GLN cc_start: 0.9201 (mt0) cc_final: 0.8868 (mt0) REVERT: N 63 LYS cc_start: 0.9058 (mmtt) cc_final: 0.8784 (mttm) REVERT: N 102 ASP cc_start: 0.8622 (t0) cc_final: 0.8209 (t0) REVERT: O 160 MET cc_start: 0.7929 (ptm) cc_final: 0.7193 (ptm) REVERT: O 221 TYR cc_start: 0.8038 (m-10) cc_final: 0.7525 (m-80) REVERT: P 33 ARG cc_start: 0.8135 (tpt170) cc_final: 0.7934 (tpt90) REVERT: P 36 ASN cc_start: 0.8527 (m-40) cc_final: 0.8167 (t0) REVERT: P 62 GLN cc_start: 0.9146 (mt0) cc_final: 0.8841 (mt0) REVERT: P 63 LYS cc_start: 0.9090 (mmtt) cc_final: 0.8871 (mttm) REVERT: P 102 ASP cc_start: 0.8705 (t0) cc_final: 0.8271 (t0) REVERT: Q 67 MET cc_start: 0.8999 (mtp) cc_final: 0.8738 (mtp) REVERT: Q 160 MET cc_start: 0.7803 (ptm) cc_final: 0.7497 (ptm) REVERT: R 36 ASN cc_start: 0.8671 (m-40) cc_final: 0.8284 (t0) REVERT: R 55 ASP cc_start: 0.8161 (m-30) cc_final: 0.7784 (t0) REVERT: R 62 GLN cc_start: 0.9115 (mt0) cc_final: 0.8783 (mt0) REVERT: R 102 ASP cc_start: 0.8669 (t0) cc_final: 0.8308 (t0) REVERT: S 67 MET cc_start: 0.8945 (mtp) cc_final: 0.8503 (mtp) REVERT: S 221 TYR cc_start: 0.6633 (m-80) cc_final: 0.6428 (m-80) REVERT: S 226 ILE cc_start: 0.9470 (mt) cc_final: 0.9052 (mm) REVERT: T 36 ASN cc_start: 0.8677 (m-40) cc_final: 0.8305 (t0) REVERT: T 62 GLN cc_start: 0.9139 (mt0) cc_final: 0.8764 (mt0) REVERT: T 63 LYS cc_start: 0.9043 (mmtt) cc_final: 0.8461 (ttpt) REVERT: T 97 LYS cc_start: 0.9379 (tppt) cc_final: 0.9140 (mmtp) REVERT: U 160 MET cc_start: 0.7493 (ptm) cc_final: 0.6949 (ptm) REVERT: U 221 TYR cc_start: 0.7931 (m-10) cc_final: 0.7347 (m-80) REVERT: U 252 TYR cc_start: 0.8737 (m-80) cc_final: 0.8457 (m-80) REVERT: U 268 LYS cc_start: 0.9201 (tptt) cc_final: 0.8703 (tptp) REVERT: V 36 ASN cc_start: 0.8691 (m-40) cc_final: 0.8340 (t0) REVERT: V 63 LYS cc_start: 0.9106 (mmtt) cc_final: 0.8771 (mttm) REVERT: V 102 ASP cc_start: 0.8727 (t0) cc_final: 0.8377 (t0) REVERT: V 105 ASN cc_start: 0.8237 (m-40) cc_final: 0.7704 (p0) REVERT: W 221 TYR cc_start: 0.6590 (m-80) cc_final: 0.6373 (m-80) REVERT: X 55 ASP cc_start: 0.8262 (m-30) cc_final: 0.8053 (t0) REVERT: X 63 LYS cc_start: 0.9042 (mmtt) cc_final: 0.8758 (mmmm) REVERT: X 70 ASN cc_start: 0.7907 (m110) cc_final: 0.7466 (t0) REVERT: X 97 LYS cc_start: 0.9333 (tppt) cc_final: 0.9034 (mmmm) REVERT: X 102 ASP cc_start: 0.8598 (t0) cc_final: 0.8106 (t0) outliers start: 1 outliers final: 0 residues processed: 846 average time/residue: 0.5017 time to fit residues: 694.5237 Evaluate side-chains 467 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 467 time to evaluate : 4.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 236 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 353 optimal weight: 0.6980 chunk 289 optimal weight: 0.9980 chunk 117 optimal weight: 5.9990 chunk 425 optimal weight: 0.8980 chunk 459 optimal weight: 4.9990 chunk 379 optimal weight: 4.9990 chunk 422 optimal weight: 0.7980 chunk 145 optimal weight: 1.9990 chunk 341 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN B 122 ASN ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN C 277 ASN E 52 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN G 122 ASN G 277 ASN I 92 HIS ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 185 HIS K 52 GLN K 122 ASN M 122 ASN M 185 HIS O 52 GLN O 92 HIS ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 277 ASN U 52 GLN ** U 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 37476 Z= 0.195 Angle : 0.513 11.188 50628 Z= 0.277 Chirality : 0.037 0.332 5964 Planarity : 0.003 0.037 6444 Dihedral : 3.518 15.626 5172 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.17 % Allowed : 1.83 % Favored : 98.01 % 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: 4.29 (0.11), residues: 4716 helix: 3.05 (0.07), residues: 4380 sheet: None (None), residues: 0 loop : -0.90 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 41 HIS 0.019 0.003 HIS I 123 PHE 0.015 0.002 PHE U 97 TYR 0.009 0.001 TYR D 42 ARG 0.006 0.001 ARG Q 211 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 665 time to evaluate : 4.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 MET cc_start: 0.7863 (ptm) cc_final: 0.7175 (ptm) REVERT: B 212 LEU cc_start: 0.8903 (mt) cc_final: 0.8627 (tp) REVERT: B 257 LYS cc_start: 0.9161 (mtmt) cc_final: 0.8855 (ptpp) REVERT: A 36 ASN cc_start: 0.8518 (m-40) cc_final: 0.8170 (t0) REVERT: A 62 GLN cc_start: 0.9269 (mt0) cc_final: 0.8961 (mt0) REVERT: A 63 LYS cc_start: 0.9098 (mmtt) cc_final: 0.8853 (mmmm) REVERT: A 102 ASP cc_start: 0.8761 (t0) cc_final: 0.8502 (t0) REVERT: C 8 MET cc_start: 0.8681 (mtt) cc_final: 0.8370 (mtp) REVERT: C 160 MET cc_start: 0.7896 (ptm) cc_final: 0.6845 (ptm) REVERT: C 226 ILE cc_start: 0.9576 (mt) cc_final: 0.9104 (mm) REVERT: C 257 LYS cc_start: 0.9163 (mtmt) cc_final: 0.8924 (ptpp) REVERT: D 36 ASN cc_start: 0.8613 (m-40) cc_final: 0.8213 (t0) REVERT: D 55 ASP cc_start: 0.8304 (m-30) cc_final: 0.7856 (t0) REVERT: D 97 LYS cc_start: 0.9419 (tppt) cc_final: 0.8959 (ttmt) REVERT: D 102 ASP cc_start: 0.8734 (t0) cc_final: 0.8435 (t0) REVERT: E 160 MET cc_start: 0.7795 (ptm) cc_final: 0.6626 (ptm) REVERT: E 209 ILE cc_start: 0.9444 (mt) cc_final: 0.9192 (mm) REVERT: E 257 LYS cc_start: 0.9141 (mtmt) cc_final: 0.8912 (ptpp) REVERT: F 36 ASN cc_start: 0.8635 (m-40) cc_final: 0.8232 (t0) REVERT: F 55 ASP cc_start: 0.8478 (m-30) cc_final: 0.7983 (t0) REVERT: F 62 GLN cc_start: 0.9226 (mt0) cc_final: 0.8987 (mt0) REVERT: F 63 LYS cc_start: 0.9205 (mmtt) cc_final: 0.8983 (mttm) REVERT: F 97 LYS cc_start: 0.9466 (tppt) cc_final: 0.9074 (ttmt) REVERT: F 102 ASP cc_start: 0.8632 (t0) cc_final: 0.8402 (t0) REVERT: F 105 ASN cc_start: 0.8193 (m-40) cc_final: 0.7673 (p0) REVERT: F 117 ASP cc_start: 0.8583 (t70) cc_final: 0.8082 (t0) REVERT: G 160 MET cc_start: 0.7777 (ptm) cc_final: 0.7425 (ptm) REVERT: G 209 ILE cc_start: 0.9545 (mt) cc_final: 0.9316 (mm) REVERT: G 257 LYS cc_start: 0.9260 (mtmt) cc_final: 0.8783 (ptpp) REVERT: H 55 ASP cc_start: 0.8421 (m-30) cc_final: 0.7986 (t0) REVERT: H 62 GLN cc_start: 0.9190 (mt0) cc_final: 0.8891 (mt0) REVERT: H 63 LYS cc_start: 0.9190 (mmtt) cc_final: 0.8881 (mmmm) REVERT: H 97 LYS cc_start: 0.9345 (mmmm) cc_final: 0.8813 (mttp) REVERT: H 102 ASP cc_start: 0.8943 (t0) cc_final: 0.8643 (t0) REVERT: I 19 SER cc_start: 0.9539 (m) cc_final: 0.9258 (p) REVERT: I 160 MET cc_start: 0.7521 (ptm) cc_final: 0.7281 (ptm) REVERT: I 209 ILE cc_start: 0.9387 (mt) cc_final: 0.9162 (mm) REVERT: I 221 TYR cc_start: 0.7990 (m-10) cc_final: 0.7716 (m-80) REVERT: J 31 LEU cc_start: 0.9246 (mt) cc_final: 0.9036 (mt) REVERT: J 62 GLN cc_start: 0.9249 (mt0) cc_final: 0.8932 (mt0) REVERT: J 70 ASN cc_start: 0.8444 (m110) cc_final: 0.7689 (t0) REVERT: J 97 LYS cc_start: 0.9340 (tppt) cc_final: 0.9001 (mmmm) REVERT: J 102 ASP cc_start: 0.8820 (t0) cc_final: 0.8489 (t0) REVERT: K 8 MET cc_start: 0.8931 (mtp) cc_final: 0.8430 (mtp) REVERT: K 19 SER cc_start: 0.9589 (m) cc_final: 0.9375 (p) REVERT: K 67 MET cc_start: 0.9012 (mtp) cc_final: 0.8769 (mtp) REVERT: K 160 MET cc_start: 0.7950 (ptm) cc_final: 0.7152 (ptm) REVERT: K 209 ILE cc_start: 0.9557 (mt) cc_final: 0.9337 (mm) REVERT: K 212 LEU cc_start: 0.9083 (mt) cc_final: 0.8691 (mt) REVERT: K 257 LYS cc_start: 0.9267 (mtmt) cc_final: 0.8999 (ptpp) REVERT: L 62 GLN cc_start: 0.9219 (mt0) cc_final: 0.8853 (mt0) REVERT: L 63 LYS cc_start: 0.9330 (mmtt) cc_final: 0.9023 (mttm) REVERT: L 97 LYS cc_start: 0.9370 (tppt) cc_final: 0.8998 (mttt) REVERT: L 102 ASP cc_start: 0.8959 (t0) cc_final: 0.8559 (t0) REVERT: L 105 ASN cc_start: 0.8176 (m-40) cc_final: 0.7790 (p0) REVERT: M 8 MET cc_start: 0.8499 (mtp) cc_final: 0.8156 (mtp) REVERT: M 19 SER cc_start: 0.9452 (m) cc_final: 0.9180 (p) REVERT: M 209 ILE cc_start: 0.9405 (mt) cc_final: 0.9158 (mm) REVERT: M 212 LEU cc_start: 0.8829 (mt) cc_final: 0.8444 (mt) REVERT: M 257 LYS cc_start: 0.9283 (mtmt) cc_final: 0.9060 (ptpp) REVERT: N 62 GLN cc_start: 0.9293 (mt0) cc_final: 0.8908 (mt0) REVERT: N 63 LYS cc_start: 0.9262 (mmtt) cc_final: 0.9001 (mmmm) REVERT: N 102 ASP cc_start: 0.8739 (t0) cc_final: 0.7753 (t0) REVERT: N 105 ASN cc_start: 0.8088 (m-40) cc_final: 0.7812 (m110) REVERT: O 160 MET cc_start: 0.7985 (ptm) cc_final: 0.7281 (ptm) REVERT: O 191 MET cc_start: 0.8536 (tpp) cc_final: 0.8060 (tpp) REVERT: O 221 TYR cc_start: 0.7918 (m-10) cc_final: 0.7651 (m-80) REVERT: P 36 ASN cc_start: 0.8559 (m-40) cc_final: 0.8254 (t0) REVERT: P 62 GLN cc_start: 0.9176 (mt0) cc_final: 0.8902 (mt0) REVERT: P 63 LYS cc_start: 0.9196 (mmtt) cc_final: 0.8962 (mttp) REVERT: P 102 ASP cc_start: 0.8732 (t0) cc_final: 0.8450 (t0) REVERT: Q 67 MET cc_start: 0.8989 (mtp) cc_final: 0.8643 (mtp) REVERT: Q 160 MET cc_start: 0.7933 (ptm) cc_final: 0.7467 (ptm) REVERT: R 36 ASN cc_start: 0.8870 (m-40) cc_final: 0.8399 (t0) REVERT: R 55 ASP cc_start: 0.8418 (m-30) cc_final: 0.7957 (t0) REVERT: R 102 ASP cc_start: 0.8648 (t0) cc_final: 0.8256 (t0) REVERT: S 160 MET cc_start: 0.7855 (ptm) cc_final: 0.7449 (ttp) REVERT: S 226 ILE cc_start: 0.9539 (mt) cc_final: 0.9036 (mm) REVERT: S 257 LYS cc_start: 0.9209 (mtmt) cc_final: 0.8930 (ptpp) REVERT: T 62 GLN cc_start: 0.9243 (mt0) cc_final: 0.8859 (mt0) REVERT: T 63 LYS cc_start: 0.9156 (mmtt) cc_final: 0.8788 (mmmm) REVERT: T 87 ASP cc_start: 0.6781 (t0) cc_final: 0.5211 (t0) REVERT: T 97 LYS cc_start: 0.9387 (tppt) cc_final: 0.8995 (ttmt) REVERT: T 117 ASP cc_start: 0.8907 (t70) cc_final: 0.8683 (t0) REVERT: U 67 MET cc_start: 0.8748 (mtp) cc_final: 0.8258 (mmt) REVERT: U 160 MET cc_start: 0.7799 (ptm) cc_final: 0.7359 (ptm) REVERT: U 191 MET cc_start: 0.8453 (tpp) cc_final: 0.8108 (tpp) REVERT: U 221 TYR cc_start: 0.7941 (m-10) cc_final: 0.7713 (m-80) REVERT: U 226 ILE cc_start: 0.9380 (mt) cc_final: 0.8785 (mm) REVERT: U 252 TYR cc_start: 0.8785 (m-80) cc_final: 0.8580 (m-80) REVERT: U 257 LYS cc_start: 0.9196 (mtmt) cc_final: 0.8936 (ptpp) REVERT: V 33 ARG cc_start: 0.8829 (mmm160) cc_final: 0.8455 (mmm-85) REVERT: V 36 ASN cc_start: 0.8671 (m-40) cc_final: 0.8301 (t0) REVERT: V 105 ASN cc_start: 0.8084 (m-40) cc_final: 0.7722 (p0) REVERT: X 55 ASP cc_start: 0.8509 (m-30) cc_final: 0.8168 (t0) REVERT: X 62 GLN cc_start: 0.9280 (mt0) cc_final: 0.9057 (mt0) REVERT: X 63 LYS cc_start: 0.9231 (mmtt) cc_final: 0.8946 (mmmm) REVERT: X 70 ASN cc_start: 0.8156 (m110) cc_final: 0.7627 (t0) REVERT: X 97 LYS cc_start: 0.9314 (tppt) cc_final: 0.8994 (mmmm) REVERT: X 102 ASP cc_start: 0.8677 (t0) cc_final: 0.8311 (t0) outliers start: 6 outliers final: 3 residues processed: 671 average time/residue: 0.4737 time to fit residues: 532.2822 Evaluate side-chains 434 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 431 time to evaluate : 4.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 420 optimal weight: 7.9990 chunk 320 optimal weight: 3.9990 chunk 220 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 285 optimal weight: 0.7980 chunk 427 optimal weight: 6.9990 chunk 452 optimal weight: 0.7980 chunk 223 optimal weight: 5.9990 chunk 404 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN E 52 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 GLN G 52 GLN ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 185 HIS ** Q 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 ASN S 277 ASN U 52 GLN ** U 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 277 ASN ** X 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 37476 Z= 0.237 Angle : 0.533 10.836 50628 Z= 0.291 Chirality : 0.037 0.205 5964 Planarity : 0.003 0.035 6444 Dihedral : 3.634 17.225 5172 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.00 % Favored : 98.79 % Rotamer: Outliers : 0.06 % Allowed : 2.16 % Favored : 97.79 % 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: 3.97 (0.11), residues: 4716 helix: 2.90 (0.07), residues: 4380 sheet: None (None), residues: 0 loop : -1.75 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP L 41 HIS 0.017 0.002 HIS B 123 PHE 0.024 0.002 PHE E 66 TYR 0.017 0.001 TYR Q 221 ARG 0.009 0.000 ARG R 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 587 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 585 time to evaluate : 4.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 MET cc_start: 0.8577 (mtp) cc_final: 0.8089 (mtp) REVERT: B 160 MET cc_start: 0.8090 (ptm) cc_final: 0.7842 (ptm) REVERT: B 212 LEU cc_start: 0.8895 (mt) cc_final: 0.8491 (mt) REVERT: B 257 LYS cc_start: 0.9215 (mtmt) cc_final: 0.8767 (mttt) REVERT: A 36 ASN cc_start: 0.8547 (m-40) cc_final: 0.8251 (t0) REVERT: A 62 GLN cc_start: 0.9358 (mt0) cc_final: 0.9052 (mt0) REVERT: A 63 LYS cc_start: 0.9304 (mmtt) cc_final: 0.8946 (mmmm) REVERT: A 102 ASP cc_start: 0.8884 (t0) cc_final: 0.8617 (t0) REVERT: A 117 ASP cc_start: 0.8435 (t0) cc_final: 0.8190 (t0) REVERT: C 8 MET cc_start: 0.8710 (mtt) cc_final: 0.8453 (mtp) REVERT: C 160 MET cc_start: 0.8047 (ptm) cc_final: 0.6983 (ptm) REVERT: C 191 MET cc_start: 0.8511 (tpp) cc_final: 0.7957 (tpp) REVERT: C 243 LEU cc_start: 0.9281 (mp) cc_final: 0.8800 (mm) REVERT: C 257 LYS cc_start: 0.9234 (mtmt) cc_final: 0.8950 (ptpp) REVERT: D 33 ARG cc_start: 0.8831 (mmm160) cc_final: 0.8494 (mmt180) REVERT: D 36 ASN cc_start: 0.8622 (m-40) cc_final: 0.8320 (t0) REVERT: D 55 ASP cc_start: 0.8473 (m-30) cc_final: 0.8109 (t70) REVERT: D 62 GLN cc_start: 0.9310 (mt0) cc_final: 0.9061 (mt0) REVERT: D 63 LYS cc_start: 0.9349 (mmtt) cc_final: 0.9046 (mmmm) REVERT: D 97 LYS cc_start: 0.9421 (tppt) cc_final: 0.8969 (ttmt) REVERT: D 102 ASP cc_start: 0.8815 (t0) cc_final: 0.8365 (t0) REVERT: E 160 MET cc_start: 0.7989 (ptm) cc_final: 0.6789 (ptm) REVERT: E 257 LYS cc_start: 0.9161 (mtmt) cc_final: 0.8854 (ptpp) REVERT: F 33 ARG cc_start: 0.8832 (mmm160) cc_final: 0.8401 (mmt180) REVERT: F 36 ASN cc_start: 0.8626 (m-40) cc_final: 0.8333 (t0) REVERT: F 55 ASP cc_start: 0.8661 (m-30) cc_final: 0.8189 (t0) REVERT: F 62 GLN cc_start: 0.9326 (mt0) cc_final: 0.9074 (mt0) REVERT: F 97 LYS cc_start: 0.9485 (tppt) cc_final: 0.9080 (ttmt) REVERT: F 102 ASP cc_start: 0.8655 (t0) cc_final: 0.8334 (t0) REVERT: F 105 ASN cc_start: 0.8184 (m-40) cc_final: 0.7686 (p0) REVERT: F 117 ASP cc_start: 0.8642 (t70) cc_final: 0.7788 (t0) REVERT: G 160 MET cc_start: 0.7949 (ptm) cc_final: 0.7665 (ptm) REVERT: G 257 LYS cc_start: 0.9315 (mtmt) cc_final: 0.8991 (ptpp) REVERT: H 33 ARG cc_start: 0.8828 (mmm160) cc_final: 0.8322 (tpt170) REVERT: H 36 ASN cc_start: 0.8662 (m-40) cc_final: 0.8410 (t0) REVERT: H 55 ASP cc_start: 0.8605 (m-30) cc_final: 0.8194 (t0) REVERT: H 62 GLN cc_start: 0.9325 (mt0) cc_final: 0.9012 (mt0) REVERT: H 63 LYS cc_start: 0.9239 (mmtt) cc_final: 0.8984 (mmmm) REVERT: H 97 LYS cc_start: 0.9396 (mmmm) cc_final: 0.8931 (mttp) REVERT: H 102 ASP cc_start: 0.9018 (t0) cc_final: 0.8702 (t0) REVERT: I 67 MET cc_start: 0.8858 (mtp) cc_final: 0.8593 (mtp) REVERT: I 160 MET cc_start: 0.7914 (ptm) cc_final: 0.7600 (ptm) REVERT: J 62 GLN cc_start: 0.9274 (mt0) cc_final: 0.8986 (mt0) REVERT: J 63 LYS cc_start: 0.9211 (mttm) cc_final: 0.8739 (ttmt) REVERT: J 70 ASN cc_start: 0.8592 (m110) cc_final: 0.8020 (t0) REVERT: J 97 LYS cc_start: 0.9371 (tppt) cc_final: 0.9078 (mmmm) REVERT: J 102 ASP cc_start: 0.8774 (t0) cc_final: 0.8478 (t0) REVERT: K 67 MET cc_start: 0.9039 (mtp) cc_final: 0.8692 (mtp) REVERT: K 160 MET cc_start: 0.8199 (ptm) cc_final: 0.7313 (ptm) REVERT: K 212 LEU cc_start: 0.9036 (mt) cc_final: 0.8669 (mt) REVERT: K 257 LYS cc_start: 0.9308 (mtmt) cc_final: 0.9003 (ptpp) REVERT: L 33 ARG cc_start: 0.8786 (mmm160) cc_final: 0.8120 (tpt170) REVERT: L 62 GLN cc_start: 0.9307 (mt0) cc_final: 0.8979 (mt0) REVERT: L 63 LYS cc_start: 0.9369 (mmtt) cc_final: 0.8891 (mmmm) REVERT: L 97 LYS cc_start: 0.9389 (tppt) cc_final: 0.9014 (mttt) REVERT: L 102 ASP cc_start: 0.8875 (t0) cc_final: 0.8575 (t0) REVERT: M 8 MET cc_start: 0.8475 (mtp) cc_final: 0.8096 (mtp) REVERT: M 63 SER cc_start: 0.8463 (t) cc_final: 0.8218 (t) REVERT: M 160 MET cc_start: 0.8222 (ptm) cc_final: 0.7919 (ptm) REVERT: M 212 LEU cc_start: 0.8915 (mt) cc_final: 0.8532 (mt) REVERT: M 257 LYS cc_start: 0.9292 (mtmt) cc_final: 0.9040 (ptpp) REVERT: N 33 ARG cc_start: 0.8812 (mmm160) cc_final: 0.7833 (mmt180) REVERT: N 62 GLN cc_start: 0.9354 (mt0) cc_final: 0.8989 (mt0) REVERT: N 63 LYS cc_start: 0.9393 (mmtt) cc_final: 0.8973 (mmmm) REVERT: N 102 ASP cc_start: 0.8798 (t0) cc_final: 0.7907 (t0) REVERT: N 105 ASN cc_start: 0.7963 (m-40) cc_final: 0.7710 (m110) REVERT: O 160 MET cc_start: 0.8080 (ptm) cc_final: 0.7538 (ptm) REVERT: O 212 LEU cc_start: 0.8826 (mt) cc_final: 0.8543 (mt) REVERT: P 36 ASN cc_start: 0.8703 (m-40) cc_final: 0.8346 (t0) REVERT: P 62 GLN cc_start: 0.9296 (mt0) cc_final: 0.9011 (mt0) REVERT: P 102 ASP cc_start: 0.8830 (t0) cc_final: 0.8346 (t0) REVERT: Q 67 MET cc_start: 0.8994 (mtp) cc_final: 0.8789 (mtp) REVERT: Q 160 MET cc_start: 0.8092 (ptm) cc_final: 0.7582 (ptm) REVERT: Q 191 MET cc_start: 0.8500 (tpp) cc_final: 0.8004 (tpp) REVERT: Q 243 LEU cc_start: 0.9344 (mp) cc_final: 0.8813 (mm) REVERT: R 33 ARG cc_start: 0.8713 (mmm160) cc_final: 0.7580 (tpt170) REVERT: R 36 ASN cc_start: 0.8891 (m-40) cc_final: 0.8436 (t0) REVERT: R 55 ASP cc_start: 0.8532 (m-30) cc_final: 0.8018 (t0) REVERT: R 102 ASP cc_start: 0.8787 (t0) cc_final: 0.8399 (t0) REVERT: S 148 TYR cc_start: 0.8026 (t80) cc_final: 0.7789 (t80) REVERT: S 160 MET cc_start: 0.7997 (ptm) cc_final: 0.7410 (ptm) REVERT: S 257 LYS cc_start: 0.9256 (mtmt) cc_final: 0.8932 (mttt) REVERT: T 62 GLN cc_start: 0.9359 (mt0) cc_final: 0.9010 (mt0) REVERT: T 63 LYS cc_start: 0.9356 (mmtt) cc_final: 0.8869 (mmmm) REVERT: T 97 LYS cc_start: 0.9482 (tppt) cc_final: 0.8991 (ttmt) REVERT: T 102 ASP cc_start: 0.8913 (t70) cc_final: 0.8709 (t0) REVERT: T 117 ASP cc_start: 0.8876 (t70) cc_final: 0.7488 (t0) REVERT: T 118 LYS cc_start: 0.9120 (mmmm) cc_final: 0.8713 (mppt) REVERT: U 67 MET cc_start: 0.8767 (mtp) cc_final: 0.8265 (mmt) REVERT: U 136 ILE cc_start: 0.9108 (mt) cc_final: 0.8857 (tt) REVERT: U 160 MET cc_start: 0.7981 (ptm) cc_final: 0.7246 (ptm) REVERT: U 242 MET cc_start: 0.9027 (ttm) cc_final: 0.8721 (ttt) REVERT: U 257 LYS cc_start: 0.9226 (mtmt) cc_final: 0.8916 (ptpp) REVERT: U 271 ILE cc_start: 0.9023 (pt) cc_final: 0.8590 (tt) REVERT: V 33 ARG cc_start: 0.8683 (mmm160) cc_final: 0.8419 (mmt180) REVERT: V 36 ASN cc_start: 0.8677 (m-40) cc_final: 0.8383 (t0) REVERT: V 62 GLN cc_start: 0.9273 (mt0) cc_final: 0.9068 (mt0) REVERT: V 63 LYS cc_start: 0.9229 (mttm) cc_final: 0.9009 (ttmm) REVERT: V 105 ASN cc_start: 0.7968 (m-40) cc_final: 0.7745 (p0) REVERT: W 136 ILE cc_start: 0.9199 (mt) cc_final: 0.8864 (tt) REVERT: W 160 MET cc_start: 0.7940 (ptm) cc_final: 0.7724 (ptm) REVERT: W 191 MET cc_start: 0.8706 (tpp) cc_final: 0.8365 (tpp) REVERT: X 55 ASP cc_start: 0.8436 (m-30) cc_final: 0.8108 (t0) REVERT: X 62 GLN cc_start: 0.9298 (mt0) cc_final: 0.9031 (mt0) REVERT: X 63 LYS cc_start: 0.9265 (mmtt) cc_final: 0.8974 (mmmm) REVERT: X 70 ASN cc_start: 0.8539 (m110) cc_final: 0.7941 (t0) REVERT: X 97 LYS cc_start: 0.9395 (tppt) cc_final: 0.9093 (mmmm) REVERT: X 102 ASP cc_start: 0.8676 (t0) cc_final: 0.8390 (t0) outliers start: 2 outliers final: 1 residues processed: 587 average time/residue: 0.4866 time to fit residues: 462.7040 Evaluate side-chains 407 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 406 time to evaluate : 4.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 376 optimal weight: 0.7980 chunk 256 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 336 optimal weight: 0.9980 chunk 186 optimal weight: 0.6980 chunk 386 optimal weight: 4.9990 chunk 312 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 230 optimal weight: 4.9990 chunk 406 optimal weight: 0.9990 chunk 114 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 185 HIS ** A 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 ASN K 122 ASN L 71 ASN ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 185 HIS U 52 GLN ** X 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 37476 Z= 0.176 Angle : 0.479 9.098 50628 Z= 0.263 Chirality : 0.035 0.121 5964 Planarity : 0.003 0.038 6444 Dihedral : 3.549 17.056 5172 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.25 % Allowed : 0.85 % Favored : 98.90 % Rotamer: Outliers : 0.11 % Allowed : 1.36 % Favored : 98.53 % 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: 4.14 (0.11), residues: 4716 helix: 3.04 (0.07), residues: 4380 sheet: None (None), residues: 0 loop : -2.22 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP T 41 HIS 0.017 0.002 HIS Q 123 PHE 0.022 0.002 PHE I 128 TYR 0.017 0.001 TYR S 210 ARG 0.004 0.000 ARG H 21 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 588 time to evaluate : 5.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 MET cc_start: 0.8597 (mtp) cc_final: 0.8028 (mtp) REVERT: B 160 MET cc_start: 0.8249 (ptm) cc_final: 0.7099 (ptm) REVERT: B 196 MET cc_start: 0.8207 (tmm) cc_final: 0.7994 (tmm) REVERT: B 257 LYS cc_start: 0.9191 (mtmt) cc_final: 0.8716 (mttt) REVERT: A 36 ASN cc_start: 0.8561 (m-40) cc_final: 0.8305 (t0) REVERT: A 55 ASP cc_start: 0.8448 (t0) cc_final: 0.8226 (t0) REVERT: A 62 GLN cc_start: 0.9343 (mt0) cc_final: 0.8990 (mt0) REVERT: A 63 LYS cc_start: 0.9352 (mmtt) cc_final: 0.8904 (mmmm) REVERT: A 90 GLU cc_start: 0.8985 (mp0) cc_final: 0.8702 (mp0) REVERT: A 102 ASP cc_start: 0.8955 (t0) cc_final: 0.8594 (t0) REVERT: C 129 MET cc_start: 0.8706 (mtt) cc_final: 0.8493 (mmt) REVERT: C 160 MET cc_start: 0.8110 (ptm) cc_final: 0.6999 (ptm) REVERT: C 191 MET cc_start: 0.8631 (tpp) cc_final: 0.8312 (tpp) REVERT: C 226 ILE cc_start: 0.9351 (mt) cc_final: 0.9116 (mm) REVERT: C 257 LYS cc_start: 0.9214 (mtmt) cc_final: 0.8916 (ptpp) REVERT: D 6 LEU cc_start: 0.9217 (mt) cc_final: 0.8911 (tt) REVERT: D 33 ARG cc_start: 0.8767 (mmm160) cc_final: 0.8192 (tpp-160) REVERT: D 36 ASN cc_start: 0.8597 (m-40) cc_final: 0.8263 (t0) REVERT: D 55 ASP cc_start: 0.8497 (m-30) cc_final: 0.8052 (t0) REVERT: D 62 GLN cc_start: 0.9268 (mt0) cc_final: 0.9024 (mt0) REVERT: D 63 LYS cc_start: 0.9301 (mmtt) cc_final: 0.8916 (mmmm) REVERT: D 97 LYS cc_start: 0.9456 (tppt) cc_final: 0.9004 (ttmt) REVERT: D 102 ASP cc_start: 0.8829 (t0) cc_final: 0.8363 (t0) REVERT: E 160 MET cc_start: 0.8155 (ptm) cc_final: 0.7291 (ptm) REVERT: E 257 LYS cc_start: 0.9141 (mtmt) cc_final: 0.8802 (ptpp) REVERT: E 271 ILE cc_start: 0.8930 (pt) cc_final: 0.8577 (tt) REVERT: F 3 GLU cc_start: 0.8396 (tt0) cc_final: 0.8190 (tt0) REVERT: F 36 ASN cc_start: 0.8683 (m-40) cc_final: 0.8339 (t0) REVERT: F 55 ASP cc_start: 0.8624 (m-30) cc_final: 0.8132 (t0) REVERT: F 63 LYS cc_start: 0.9209 (mttm) cc_final: 0.8955 (ttmm) REVERT: F 97 LYS cc_start: 0.9465 (tppt) cc_final: 0.9037 (ttmt) REVERT: F 102 ASP cc_start: 0.8672 (t0) cc_final: 0.7970 (t0) REVERT: F 117 ASP cc_start: 0.8460 (t70) cc_final: 0.8239 (t0) REVERT: G 160 MET cc_start: 0.7959 (ptm) cc_final: 0.7664 (ptm) REVERT: G 242 MET cc_start: 0.8988 (ttm) cc_final: 0.8781 (ttt) REVERT: G 257 LYS cc_start: 0.9284 (mtmt) cc_final: 0.8904 (ptpp) REVERT: H 55 ASP cc_start: 0.8605 (m-30) cc_final: 0.8134 (t0) REVERT: H 63 LYS cc_start: 0.9193 (mmtt) cc_final: 0.8855 (mmmm) REVERT: H 97 LYS cc_start: 0.9373 (mmmm) cc_final: 0.8912 (mttp) REVERT: H 102 ASP cc_start: 0.9021 (t0) cc_final: 0.8767 (t0) REVERT: I 67 MET cc_start: 0.8931 (mtp) cc_final: 0.8359 (mtp) REVERT: I 160 MET cc_start: 0.7956 (ptm) cc_final: 0.7617 (ptm) REVERT: J 62 GLN cc_start: 0.9216 (mt0) cc_final: 0.8910 (mt0) REVERT: J 63 LYS cc_start: 0.9250 (mttm) cc_final: 0.8650 (ttmt) REVERT: J 70 ASN cc_start: 0.8656 (m110) cc_final: 0.8026 (t0) REVERT: J 97 LYS cc_start: 0.9352 (tppt) cc_final: 0.8995 (mmmm) REVERT: J 102 ASP cc_start: 0.8764 (t0) cc_final: 0.8502 (t0) REVERT: K 67 MET cc_start: 0.8988 (mtp) cc_final: 0.8514 (mtp) REVERT: K 160 MET cc_start: 0.7972 (ptm) cc_final: 0.7276 (ptm) REVERT: K 212 LEU cc_start: 0.8986 (mt) cc_final: 0.8595 (mt) REVERT: K 257 LYS cc_start: 0.9295 (mtmt) cc_final: 0.8926 (mttt) REVERT: L 62 GLN cc_start: 0.9182 (mt0) cc_final: 0.8917 (mt0) REVERT: L 63 LYS cc_start: 0.9364 (mmtt) cc_final: 0.9052 (mmmm) REVERT: L 87 ASP cc_start: 0.7140 (t0) cc_final: 0.6918 (t0) REVERT: L 97 LYS cc_start: 0.9353 (tppt) cc_final: 0.8956 (mttt) REVERT: L 102 ASP cc_start: 0.8997 (t0) cc_final: 0.8765 (t0) REVERT: M 8 MET cc_start: 0.8322 (mtp) cc_final: 0.7940 (mtp) REVERT: M 63 SER cc_start: 0.8111 (t) cc_final: 0.7852 (t) REVERT: M 160 MET cc_start: 0.8254 (ptm) cc_final: 0.7387 (ptm) REVERT: M 212 LEU cc_start: 0.9006 (mt) cc_final: 0.8614 (mt) REVERT: M 257 LYS cc_start: 0.9270 (mtmt) cc_final: 0.9010 (ptpp) REVERT: N 62 GLN cc_start: 0.9280 (mt0) cc_final: 0.8911 (mt0) REVERT: N 63 LYS cc_start: 0.9352 (mmtt) cc_final: 0.9018 (mmmm) REVERT: N 90 GLU cc_start: 0.9070 (mp0) cc_final: 0.8862 (mp0) REVERT: N 102 ASP cc_start: 0.8830 (t0) cc_final: 0.7930 (t0) REVERT: N 105 ASN cc_start: 0.7859 (m-40) cc_final: 0.7624 (m110) REVERT: O 160 MET cc_start: 0.8075 (ptm) cc_final: 0.7520 (ptm) REVERT: O 212 LEU cc_start: 0.8865 (mt) cc_final: 0.8552 (mt) REVERT: P 36 ASN cc_start: 0.8663 (m-40) cc_final: 0.8370 (t0) REVERT: P 63 LYS cc_start: 0.9337 (mttm) cc_final: 0.8953 (ttmm) REVERT: P 102 ASP cc_start: 0.8841 (t0) cc_final: 0.8305 (t0) REVERT: Q 67 MET cc_start: 0.8892 (mtp) cc_final: 0.8675 (mtp) REVERT: Q 160 MET cc_start: 0.8088 (ptm) cc_final: 0.7605 (ptm) REVERT: R 36 ASN cc_start: 0.8831 (m-40) cc_final: 0.8422 (t0) REVERT: R 55 ASP cc_start: 0.8621 (m-30) cc_final: 0.8136 (t0) REVERT: R 102 ASP cc_start: 0.8802 (t0) cc_final: 0.8407 (t0) REVERT: S 148 TYR cc_start: 0.8072 (t80) cc_final: 0.7832 (t80) REVERT: S 160 MET cc_start: 0.8066 (ptm) cc_final: 0.7596 (ptp) REVERT: S 196 MET cc_start: 0.8443 (tmm) cc_final: 0.7955 (tmm) REVERT: S 257 LYS cc_start: 0.9237 (mtmt) cc_final: 0.8907 (mttt) REVERT: S 268 LYS cc_start: 0.9066 (tptt) cc_final: 0.8604 (tptp) REVERT: T 62 GLN cc_start: 0.9343 (mt0) cc_final: 0.9005 (mt0) REVERT: T 63 LYS cc_start: 0.9305 (mmtt) cc_final: 0.8824 (mmmm) REVERT: T 97 LYS cc_start: 0.9472 (tppt) cc_final: 0.9023 (ttmt) REVERT: T 102 ASP cc_start: 0.8921 (t70) cc_final: 0.8709 (t0) REVERT: T 117 ASP cc_start: 0.8397 (t70) cc_final: 0.7781 (t0) REVERT: T 118 LYS cc_start: 0.9025 (mmmm) cc_final: 0.8604 (mppt) REVERT: U 160 MET cc_start: 0.7982 (ptm) cc_final: 0.7260 (ptm) REVERT: U 242 MET cc_start: 0.8973 (ttm) cc_final: 0.8727 (ttt) REVERT: U 257 LYS cc_start: 0.9233 (mtmt) cc_final: 0.8894 (ptpp) REVERT: V 36 ASN cc_start: 0.8653 (m-40) cc_final: 0.8339 (t0) REVERT: V 63 LYS cc_start: 0.9300 (mttm) cc_final: 0.8846 (ttmm) REVERT: V 105 ASN cc_start: 0.7994 (m-40) cc_final: 0.7772 (p0) REVERT: W 63 SER cc_start: 0.8381 (t) cc_final: 0.8031 (t) REVERT: W 242 MET cc_start: 0.8905 (ttm) cc_final: 0.8610 (ttt) REVERT: X 55 ASP cc_start: 0.8440 (m-30) cc_final: 0.7965 (t0) REVERT: X 62 GLN cc_start: 0.9257 (mt0) cc_final: 0.9015 (mt0) REVERT: X 70 ASN cc_start: 0.8586 (m110) cc_final: 0.8012 (t0) REVERT: X 97 LYS cc_start: 0.9378 (tppt) cc_final: 0.8928 (ttmt) REVERT: X 102 ASP cc_start: 0.8726 (t0) cc_final: 0.8458 (t0) outliers start: 4 outliers final: 2 residues processed: 592 average time/residue: 0.4851 time to fit residues: 471.8247 Evaluate side-chains 410 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 408 time to evaluate : 4.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 152 optimal weight: 3.9990 chunk 407 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 265 optimal weight: 0.9990 chunk 111 optimal weight: 0.0060 chunk 452 optimal weight: 3.9990 chunk 375 optimal weight: 3.9990 chunk 209 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 149 optimal weight: 0.9980 chunk 237 optimal weight: 5.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN H 36 ASN I 277 ASN M 52 GLN ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.6121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 37476 Z= 0.169 Angle : 0.476 16.725 50628 Z= 0.262 Chirality : 0.035 0.217 5964 Planarity : 0.003 0.041 6444 Dihedral : 3.514 16.539 5172 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.02 % Favored : 98.75 % Rotamer: Outliers : 0.06 % Allowed : 1.22 % Favored : 98.73 % 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: 4.21 (0.11), residues: 4716 helix: 3.09 (0.07), residues: 4380 sheet: None (None), residues: 0 loop : -2.39 (0.31), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 41 HIS 0.011 0.002 HIS K 123 PHE 0.017 0.002 PHE G 128 TYR 0.020 0.001 TYR K 148 ARG 0.011 0.000 ARG N 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 567 time to evaluate : 4.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 MET cc_start: 0.8104 (ptm) cc_final: 0.7049 (ptm) REVERT: A 36 ASN cc_start: 0.8600 (m-40) cc_final: 0.8257 (t0) REVERT: A 55 ASP cc_start: 0.8409 (t0) cc_final: 0.8175 (t0) REVERT: A 58 ILE cc_start: 0.9536 (pt) cc_final: 0.9327 (pt) REVERT: A 62 GLN cc_start: 0.9334 (mt0) cc_final: 0.8995 (mt0) REVERT: A 102 ASP cc_start: 0.9005 (t0) cc_final: 0.8744 (t0) REVERT: C 129 MET cc_start: 0.8578 (mtt) cc_final: 0.8368 (mmt) REVERT: C 160 MET cc_start: 0.8197 (ptm) cc_final: 0.7103 (ptm) REVERT: C 191 MET cc_start: 0.8651 (tpp) cc_final: 0.8301 (tpp) REVERT: C 257 LYS cc_start: 0.9191 (mtmt) cc_final: 0.8889 (ptpp) REVERT: D 36 ASN cc_start: 0.8632 (m-40) cc_final: 0.8229 (t0) REVERT: D 55 ASP cc_start: 0.8420 (m-30) cc_final: 0.7962 (t0) REVERT: D 62 GLN cc_start: 0.9190 (mt0) cc_final: 0.8989 (mt0) REVERT: D 63 LYS cc_start: 0.9368 (mmtt) cc_final: 0.8999 (mmmm) REVERT: D 97 LYS cc_start: 0.9463 (tppt) cc_final: 0.9023 (ttmt) REVERT: D 102 ASP cc_start: 0.8732 (t0) cc_final: 0.8474 (t0) REVERT: E 160 MET cc_start: 0.8103 (ptm) cc_final: 0.7297 (ptm) REVERT: E 257 LYS cc_start: 0.9167 (mtmt) cc_final: 0.8791 (ptpp) REVERT: F 36 ASN cc_start: 0.8683 (m-40) cc_final: 0.8278 (t0) REVERT: F 55 ASP cc_start: 0.8544 (m-30) cc_final: 0.8054 (t0) REVERT: F 63 LYS cc_start: 0.9296 (mttm) cc_final: 0.8767 (ttmm) REVERT: F 97 LYS cc_start: 0.9464 (tppt) cc_final: 0.9049 (ttmt) REVERT: F 102 ASP cc_start: 0.8673 (t0) cc_final: 0.8180 (t0) REVERT: F 117 ASP cc_start: 0.8766 (t70) cc_final: 0.7956 (t0) REVERT: G 147 ILE cc_start: 0.9495 (mt) cc_final: 0.9256 (tp) REVERT: G 160 MET cc_start: 0.8206 (ptm) cc_final: 0.7427 (ptm) REVERT: G 257 LYS cc_start: 0.9278 (mtmt) cc_final: 0.8877 (ptpp) REVERT: H 55 ASP cc_start: 0.8500 (m-30) cc_final: 0.8039 (t0) REVERT: H 97 LYS cc_start: 0.9381 (mmmm) cc_final: 0.8934 (mttp) REVERT: H 102 ASP cc_start: 0.8938 (t0) cc_final: 0.8637 (t0) REVERT: I 67 MET cc_start: 0.8767 (mtp) cc_final: 0.8495 (mtp) REVERT: I 160 MET cc_start: 0.8049 (ptm) cc_final: 0.7673 (ptm) REVERT: I 193 ARG cc_start: 0.9145 (ttm110) cc_final: 0.8938 (ttp-110) REVERT: J 63 LYS cc_start: 0.9270 (mttm) cc_final: 0.8911 (ttmm) REVERT: J 70 ASN cc_start: 0.8693 (m110) cc_final: 0.8134 (t0) REVERT: J 97 LYS cc_start: 0.9347 (tppt) cc_final: 0.8892 (mtmt) REVERT: J 102 ASP cc_start: 0.8788 (t0) cc_final: 0.8547 (t0) REVERT: J 116 MET cc_start: 0.8398 (tpp) cc_final: 0.8157 (tpp) REVERT: K 67 MET cc_start: 0.8994 (mtp) cc_final: 0.8478 (mtp) REVERT: K 160 MET cc_start: 0.7971 (ptm) cc_final: 0.7267 (ptm) REVERT: K 212 LEU cc_start: 0.9045 (mt) cc_final: 0.8655 (mt) REVERT: K 257 LYS cc_start: 0.9302 (mtmt) cc_final: 0.8930 (mttt) REVERT: L 58 ILE cc_start: 0.9545 (pt) cc_final: 0.9314 (pt) REVERT: L 62 GLN cc_start: 0.9179 (mt0) cc_final: 0.8908 (mt0) REVERT: L 63 LYS cc_start: 0.9374 (mmtt) cc_final: 0.9103 (mmmm) REVERT: L 70 ASN cc_start: 0.8753 (m-40) cc_final: 0.8149 (t0) REVERT: L 97 LYS cc_start: 0.9365 (tppt) cc_final: 0.8966 (mttt) REVERT: L 102 ASP cc_start: 0.8980 (t0) cc_final: 0.8760 (t0) REVERT: M 8 MET cc_start: 0.8225 (mtp) cc_final: 0.7995 (mtp) REVERT: M 160 MET cc_start: 0.8254 (ptm) cc_final: 0.7356 (ptm) REVERT: M 212 LEU cc_start: 0.8986 (mt) cc_final: 0.8610 (mt) REVERT: M 257 LYS cc_start: 0.9279 (mtmt) cc_final: 0.8961 (ptpp) REVERT: N 62 GLN cc_start: 0.9132 (mt0) cc_final: 0.8901 (mt0) REVERT: N 63 LYS cc_start: 0.9372 (mmtt) cc_final: 0.9097 (mmmm) REVERT: N 90 GLU cc_start: 0.9025 (mp0) cc_final: 0.8812 (mp0) REVERT: N 102 ASP cc_start: 0.8835 (t0) cc_final: 0.8057 (t0) REVERT: N 105 ASN cc_start: 0.7780 (m-40) cc_final: 0.7547 (m-40) REVERT: O 160 MET cc_start: 0.8019 (ptm) cc_final: 0.7548 (ptm) REVERT: P 36 ASN cc_start: 0.8733 (m-40) cc_final: 0.8336 (t0) REVERT: P 102 ASP cc_start: 0.8845 (t0) cc_final: 0.8318 (t0) REVERT: Q 67 MET cc_start: 0.8935 (mtp) cc_final: 0.8694 (mtp) REVERT: Q 160 MET cc_start: 0.8132 (ptm) cc_final: 0.7574 (ptm) REVERT: Q 191 MET cc_start: 0.8517 (tpp) cc_final: 0.8195 (tpp) REVERT: R 36 ASN cc_start: 0.8936 (m-40) cc_final: 0.8452 (t0) REVERT: R 55 ASP cc_start: 0.8623 (m-30) cc_final: 0.8102 (t0) REVERT: R 87 ASP cc_start: 0.7085 (t0) cc_final: 0.6685 (t70) REVERT: R 102 ASP cc_start: 0.8828 (t0) cc_final: 0.8412 (t0) REVERT: S 160 MET cc_start: 0.8038 (ptm) cc_final: 0.7188 (ptm) REVERT: S 196 MET cc_start: 0.8688 (tmm) cc_final: 0.8281 (tmm) REVERT: S 257 LYS cc_start: 0.9271 (mtmt) cc_final: 0.8935 (mttt) REVERT: T 62 GLN cc_start: 0.9253 (mt0) cc_final: 0.8925 (mt0) REVERT: T 63 LYS cc_start: 0.9359 (mmtt) cc_final: 0.9076 (mtmm) REVERT: T 97 LYS cc_start: 0.9484 (tppt) cc_final: 0.9033 (ttmt) REVERT: T 102 ASP cc_start: 0.8875 (t70) cc_final: 0.8659 (t0) REVERT: T 116 MET cc_start: 0.8732 (tpp) cc_final: 0.8454 (tpp) REVERT: T 117 ASP cc_start: 0.8503 (t70) cc_final: 0.7963 (t0) REVERT: U 63 SER cc_start: 0.8682 (t) cc_final: 0.8278 (t) REVERT: U 147 ILE cc_start: 0.9517 (mt) cc_final: 0.9245 (tp) REVERT: U 160 MET cc_start: 0.8076 (ptm) cc_final: 0.7316 (ptm) REVERT: U 257 LYS cc_start: 0.9230 (mtmt) cc_final: 0.8786 (mttt) REVERT: V 36 ASN cc_start: 0.8644 (m-40) cc_final: 0.8389 (t0) REVERT: V 63 LYS cc_start: 0.9302 (mttm) cc_final: 0.9003 (ttmm) REVERT: W 63 SER cc_start: 0.8430 (t) cc_final: 0.8009 (t) REVERT: W 242 MET cc_start: 0.8923 (ttm) cc_final: 0.8606 (ttt) REVERT: X 55 ASP cc_start: 0.8480 (m-30) cc_final: 0.7905 (t0) REVERT: X 58 ILE cc_start: 0.9613 (pt) cc_final: 0.9379 (pt) REVERT: X 62 GLN cc_start: 0.9218 (mt0) cc_final: 0.8985 (mt0) REVERT: X 70 ASN cc_start: 0.8612 (m110) cc_final: 0.8121 (t0) REVERT: X 102 ASP cc_start: 0.8844 (t0) cc_final: 0.8620 (t0) outliers start: 2 outliers final: 0 residues processed: 569 average time/residue: 0.5124 time to fit residues: 471.8745 Evaluate side-chains 387 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 387 time to evaluate : 4.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 436 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 330 optimal weight: 6.9990 chunk 256 optimal weight: 1.9990 chunk 381 optimal weight: 8.9990 chunk 252 optimal weight: 0.9980 chunk 451 optimal weight: 0.9980 chunk 282 optimal weight: 7.9990 chunk 275 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 277 ASN C 52 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN I 92 HIS ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.6358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37476 Z= 0.215 Angle : 0.517 8.957 50628 Z= 0.282 Chirality : 0.036 0.185 5964 Planarity : 0.003 0.051 6444 Dihedral : 3.618 24.513 5172 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.08 % Favored : 98.71 % Rotamer: Outliers : 0.03 % Allowed : 1.11 % Favored : 98.86 % 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: 4.04 (0.11), residues: 4716 helix: 3.02 (0.07), residues: 4368 sheet: None (None), residues: 0 loop : -2.74 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP X 41 HIS 0.024 0.003 HIS M 123 PHE 0.019 0.002 PHE G 128 TYR 0.013 0.001 TYR M 148 ARG 0.013 0.000 ARG H 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 526 time to evaluate : 4.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 MET cc_start: 0.8645 (mtp) cc_final: 0.8093 (mtp) REVERT: B 160 MET cc_start: 0.7906 (ptm) cc_final: 0.7137 (ptm) REVERT: B 252 TYR cc_start: 0.8950 (m-80) cc_final: 0.8671 (m-80) REVERT: A 36 ASN cc_start: 0.8656 (m-40) cc_final: 0.8345 (t0) REVERT: A 55 ASP cc_start: 0.8400 (t0) cc_final: 0.8193 (t0) REVERT: A 62 GLN cc_start: 0.9300 (mt0) cc_final: 0.8935 (mt0) REVERT: A 87 ASP cc_start: 0.6781 (t70) cc_final: 0.6277 (t70) REVERT: A 102 ASP cc_start: 0.8963 (t0) cc_final: 0.8695 (t0) REVERT: C 129 MET cc_start: 0.8767 (mtt) cc_final: 0.8397 (mmt) REVERT: C 147 ILE cc_start: 0.9473 (mt) cc_final: 0.9237 (tp) REVERT: C 160 MET cc_start: 0.8377 (ptm) cc_final: 0.7311 (ptm) REVERT: C 191 MET cc_start: 0.8666 (tpp) cc_final: 0.8322 (tpp) REVERT: D 36 ASN cc_start: 0.8672 (m-40) cc_final: 0.8304 (t0) REVERT: D 55 ASP cc_start: 0.8409 (m-30) cc_final: 0.7912 (t0) REVERT: D 62 GLN cc_start: 0.9260 (mt0) cc_final: 0.9030 (mt0) REVERT: D 63 LYS cc_start: 0.9373 (mmtt) cc_final: 0.9038 (mmmm) REVERT: D 70 ASN cc_start: 0.8794 (m-40) cc_final: 0.8368 (t0) REVERT: D 97 LYS cc_start: 0.9490 (tppt) cc_final: 0.9198 (mtmt) REVERT: D 102 ASP cc_start: 0.8794 (t0) cc_final: 0.8493 (t0) REVERT: E 147 ILE cc_start: 0.9513 (mt) cc_final: 0.9308 (tp) REVERT: E 160 MET cc_start: 0.8160 (ptm) cc_final: 0.7560 (ptm) REVERT: E 196 MET cc_start: 0.8723 (tmm) cc_final: 0.7955 (tmm) REVERT: E 200 ILE cc_start: 0.9207 (mm) cc_final: 0.8903 (mm) REVERT: F 36 ASN cc_start: 0.8583 (m-40) cc_final: 0.8254 (t0) REVERT: F 55 ASP cc_start: 0.8597 (m-30) cc_final: 0.8009 (t0) REVERT: F 63 LYS cc_start: 0.9298 (mttm) cc_final: 0.8880 (ttmm) REVERT: F 97 LYS cc_start: 0.9407 (tppt) cc_final: 0.8968 (ttmt) REVERT: F 102 ASP cc_start: 0.8604 (t0) cc_final: 0.8073 (t0) REVERT: F 117 ASP cc_start: 0.8387 (t70) cc_final: 0.7708 (t0) REVERT: G 67 MET cc_start: 0.8638 (mtp) cc_final: 0.8435 (mtt) REVERT: G 147 ILE cc_start: 0.9482 (mt) cc_final: 0.9258 (tp) REVERT: G 160 MET cc_start: 0.8278 (ptm) cc_final: 0.7462 (ptm) REVERT: H 55 ASP cc_start: 0.8537 (m-30) cc_final: 0.7967 (t0) REVERT: H 63 LYS cc_start: 0.9356 (mttm) cc_final: 0.8907 (ttmm) REVERT: H 97 LYS cc_start: 0.9362 (mmmm) cc_final: 0.8944 (mttp) REVERT: H 102 ASP cc_start: 0.8916 (t0) cc_final: 0.8608 (t0) REVERT: I 147 ILE cc_start: 0.9503 (mt) cc_final: 0.9249 (tp) REVERT: I 160 MET cc_start: 0.8238 (ptm) cc_final: 0.7785 (ptm) REVERT: J 70 ASN cc_start: 0.8762 (m110) cc_final: 0.8259 (t0) REVERT: J 97 LYS cc_start: 0.9358 (tppt) cc_final: 0.8899 (ttmt) REVERT: J 102 ASP cc_start: 0.8851 (t0) cc_final: 0.8597 (t0) REVERT: K 67 MET cc_start: 0.9012 (mtp) cc_final: 0.8513 (mtp) REVERT: K 160 MET cc_start: 0.8065 (ptm) cc_final: 0.7358 (ptm) REVERT: K 212 LEU cc_start: 0.9004 (mt) cc_final: 0.8658 (mt) REVERT: K 257 LYS cc_start: 0.9313 (mtmt) cc_final: 0.8911 (mttt) REVERT: L 58 ILE cc_start: 0.9551 (pt) cc_final: 0.9346 (pt) REVERT: L 62 GLN cc_start: 0.9238 (mt0) cc_final: 0.8956 (mt0) REVERT: L 63 LYS cc_start: 0.9365 (mmtt) cc_final: 0.9116 (mmmm) REVERT: L 70 ASN cc_start: 0.8839 (m-40) cc_final: 0.8229 (t0) REVERT: L 97 LYS cc_start: 0.9420 (tppt) cc_final: 0.8980 (mttt) REVERT: L 102 ASP cc_start: 0.9028 (t0) cc_final: 0.8803 (t0) REVERT: M 8 MET cc_start: 0.8340 (mtp) cc_final: 0.7980 (mtp) REVERT: M 63 SER cc_start: 0.8336 (t) cc_final: 0.7896 (t) REVERT: M 160 MET cc_start: 0.8354 (ptm) cc_final: 0.7413 (ptm) REVERT: M 212 LEU cc_start: 0.9010 (mt) cc_final: 0.8636 (mt) REVERT: M 257 LYS cc_start: 0.9301 (mtmt) cc_final: 0.8951 (ptpp) REVERT: N 62 GLN cc_start: 0.9202 (mt0) cc_final: 0.8858 (mt0) REVERT: N 63 LYS cc_start: 0.9444 (mmtt) cc_final: 0.9091 (mmmm) REVERT: N 102 ASP cc_start: 0.8900 (t0) cc_final: 0.8118 (t0) REVERT: N 105 ASN cc_start: 0.7819 (m-40) cc_final: 0.7554 (m-40) REVERT: O 160 MET cc_start: 0.8137 (ptm) cc_final: 0.7593 (ptm) REVERT: O 212 LEU cc_start: 0.8867 (mt) cc_final: 0.8541 (mt) REVERT: P 36 ASN cc_start: 0.8742 (m-40) cc_final: 0.8351 (t0) REVERT: P 70 ASN cc_start: 0.8657 (m-40) cc_final: 0.8045 (t0) REVERT: P 102 ASP cc_start: 0.8937 (t0) cc_final: 0.8442 (t0) REVERT: Q 147 ILE cc_start: 0.9528 (mt) cc_final: 0.9255 (tp) REVERT: Q 160 MET cc_start: 0.8244 (ptm) cc_final: 0.7665 (ptm) REVERT: R 36 ASN cc_start: 0.8908 (m-40) cc_final: 0.8386 (t0) REVERT: R 55 ASP cc_start: 0.8681 (m-30) cc_final: 0.8151 (t0) REVERT: R 102 ASP cc_start: 0.8834 (t0) cc_final: 0.8416 (t0) REVERT: S 160 MET cc_start: 0.8253 (ptm) cc_final: 0.7440 (ptm) REVERT: S 196 MET cc_start: 0.8678 (tmm) cc_final: 0.8311 (tmm) REVERT: T 62 GLN cc_start: 0.9317 (mt0) cc_final: 0.8983 (mt0) REVERT: T 87 ASP cc_start: 0.6363 (t70) cc_final: 0.5103 (t70) REVERT: T 90 GLU cc_start: 0.9099 (mp0) cc_final: 0.8806 (mp0) REVERT: T 97 LYS cc_start: 0.9511 (tppt) cc_final: 0.9040 (ttmt) REVERT: T 102 ASP cc_start: 0.8872 (t70) cc_final: 0.8661 (t0) REVERT: T 116 MET cc_start: 0.8741 (tpp) cc_final: 0.8481 (tpp) REVERT: T 117 ASP cc_start: 0.8547 (t70) cc_final: 0.8084 (t0) REVERT: U 147 ILE cc_start: 0.9560 (mt) cc_final: 0.9206 (tp) REVERT: U 160 MET cc_start: 0.8114 (ptm) cc_final: 0.7425 (ptm) REVERT: V 63 LYS cc_start: 0.9380 (mttm) cc_final: 0.8954 (ttmm) REVERT: W 147 ILE cc_start: 0.9522 (mt) cc_final: 0.9269 (tp) REVERT: W 160 MET cc_start: 0.8259 (ptm) cc_final: 0.7875 (ptm) REVERT: W 191 MET cc_start: 0.8570 (tpp) cc_final: 0.8337 (tpp) REVERT: W 242 MET cc_start: 0.8984 (ttm) cc_final: 0.8665 (ttt) REVERT: X 55 ASP cc_start: 0.8659 (m-30) cc_final: 0.8063 (t0) REVERT: X 70 ASN cc_start: 0.8804 (m110) cc_final: 0.8270 (t0) REVERT: X 97 LYS cc_start: 0.9527 (mmmt) cc_final: 0.8814 (ttmt) REVERT: X 102 ASP cc_start: 0.8812 (t0) cc_final: 0.8611 (t0) outliers start: 1 outliers final: 0 residues processed: 527 average time/residue: 0.4825 time to fit residues: 419.3215 Evaluate side-chains 389 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 389 time to evaluate : 4.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 279 optimal weight: 0.6980 chunk 180 optimal weight: 0.5980 chunk 269 optimal weight: 2.9990 chunk 135 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 87 optimal weight: 7.9990 chunk 286 optimal weight: 0.7980 chunk 307 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 354 optimal weight: 10.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN E 52 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN G 92 HIS ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 122 ASN ** K 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN O 92 HIS ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN U 92 HIS V 36 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.6537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37476 Z= 0.192 Angle : 0.509 9.095 50628 Z= 0.279 Chirality : 0.036 0.179 5964 Planarity : 0.003 0.052 6444 Dihedral : 3.626 25.751 5172 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.31 % Favored : 98.47 % Rotamer: Outliers : 0.11 % Allowed : 1.16 % Favored : 98.73 % 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: 4.05 (0.11), residues: 4716 helix: 3.04 (0.07), residues: 4368 sheet: None (None), residues: 0 loop : -3.03 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 41 HIS 0.016 0.003 HIS O 123 PHE 0.013 0.002 PHE B 128 TYR 0.021 0.001 TYR Q 210 ARG 0.013 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 526 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 522 time to evaluate : 4.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 MET cc_start: 0.7967 (ptm) cc_final: 0.7105 (ptm) REVERT: B 252 TYR cc_start: 0.8969 (m-80) cc_final: 0.8751 (m-80) REVERT: A 36 ASN cc_start: 0.8702 (m-40) cc_final: 0.8385 (t0) REVERT: A 58 ILE cc_start: 0.9531 (pt) cc_final: 0.9316 (pt) REVERT: A 62 GLN cc_start: 0.9276 (mt0) cc_final: 0.8929 (mt0) REVERT: A 87 ASP cc_start: 0.6862 (t70) cc_final: 0.6322 (t70) REVERT: A 102 ASP cc_start: 0.8989 (t0) cc_final: 0.8739 (t0) REVERT: A 118 LYS cc_start: 0.9086 (mmmm) cc_final: 0.8555 (mppt) REVERT: C 67 MET cc_start: 0.8667 (mtp) cc_final: 0.8436 (mtp) REVERT: C 147 ILE cc_start: 0.9474 (mt) cc_final: 0.9224 (tp) REVERT: C 160 MET cc_start: 0.8363 (ptm) cc_final: 0.7315 (ptm) REVERT: C 191 MET cc_start: 0.8648 (tpp) cc_final: 0.8288 (tpp) REVERT: D 36 ASN cc_start: 0.8615 (m-40) cc_final: 0.8308 (t0) REVERT: D 55 ASP cc_start: 0.8408 (m-30) cc_final: 0.7931 (t0) REVERT: D 62 GLN cc_start: 0.9224 (mt0) cc_final: 0.9006 (mt0) REVERT: D 63 LYS cc_start: 0.9347 (mmtt) cc_final: 0.9048 (mttm) REVERT: D 70 ASN cc_start: 0.8792 (m-40) cc_final: 0.8372 (t0) REVERT: D 97 LYS cc_start: 0.9551 (tppt) cc_final: 0.9225 (mtmt) REVERT: D 102 ASP cc_start: 0.8826 (t0) cc_final: 0.8543 (t0) REVERT: E 147 ILE cc_start: 0.9516 (mt) cc_final: 0.9303 (tp) REVERT: E 160 MET cc_start: 0.8191 (ptm) cc_final: 0.7593 (ptm) REVERT: E 200 ILE cc_start: 0.9191 (mm) cc_final: 0.8930 (mm) REVERT: F 36 ASN cc_start: 0.8641 (m-40) cc_final: 0.8349 (t0) REVERT: F 55 ASP cc_start: 0.8572 (m-30) cc_final: 0.7993 (t0) REVERT: F 63 LYS cc_start: 0.9314 (mttm) cc_final: 0.8757 (ttmm) REVERT: F 70 ASN cc_start: 0.8748 (m-40) cc_final: 0.8264 (t0) REVERT: F 97 LYS cc_start: 0.9435 (tppt) cc_final: 0.9014 (ttmt) REVERT: F 102 ASP cc_start: 0.8635 (t0) cc_final: 0.8090 (t0) REVERT: F 117 ASP cc_start: 0.8339 (t70) cc_final: 0.7688 (t0) REVERT: G 147 ILE cc_start: 0.9483 (mt) cc_final: 0.9260 (tp) REVERT: G 160 MET cc_start: 0.8312 (ptm) cc_final: 0.7504 (ptm) REVERT: H 55 ASP cc_start: 0.8367 (m-30) cc_final: 0.7775 (t0) REVERT: H 63 LYS cc_start: 0.9359 (mttm) cc_final: 0.9029 (ttmm) REVERT: H 97 LYS cc_start: 0.9354 (mmmm) cc_final: 0.8954 (mttp) REVERT: H 102 ASP cc_start: 0.8888 (t0) cc_final: 0.8589 (t0) REVERT: I 63 SER cc_start: 0.8534 (t) cc_final: 0.8281 (t) REVERT: I 147 ILE cc_start: 0.9491 (mt) cc_final: 0.9242 (tp) REVERT: I 160 MET cc_start: 0.8177 (ptm) cc_final: 0.7529 (ptm) REVERT: I 191 MET cc_start: 0.8619 (tpp) cc_final: 0.8402 (tpp) REVERT: J 70 ASN cc_start: 0.8812 (m110) cc_final: 0.8304 (t0) REVERT: J 97 LYS cc_start: 0.9352 (tppt) cc_final: 0.8904 (ttmt) REVERT: J 102 ASP cc_start: 0.8831 (t0) cc_final: 0.8586 (t0) REVERT: K 67 MET cc_start: 0.9056 (mtp) cc_final: 0.8445 (mtp) REVERT: K 160 MET cc_start: 0.8089 (ptm) cc_final: 0.7351 (ptm) REVERT: K 212 LEU cc_start: 0.9083 (mt) cc_final: 0.8695 (mt) REVERT: K 257 LYS cc_start: 0.9309 (mtmt) cc_final: 0.8910 (mttt) REVERT: L 58 ILE cc_start: 0.9549 (pt) cc_final: 0.9321 (pt) REVERT: L 62 GLN cc_start: 0.9198 (mt0) cc_final: 0.8952 (mt0) REVERT: L 63 LYS cc_start: 0.9357 (mmtt) cc_final: 0.9107 (mmmm) REVERT: L 97 LYS cc_start: 0.9399 (tppt) cc_final: 0.8943 (mttt) REVERT: L 102 ASP cc_start: 0.9056 (t0) cc_final: 0.8831 (t0) REVERT: L 116 MET cc_start: 0.8434 (ttm) cc_final: 0.8197 (tpp) REVERT: M 8 MET cc_start: 0.8312 (mtp) cc_final: 0.8072 (mtp) REVERT: M 160 MET cc_start: 0.8293 (ptm) cc_final: 0.7477 (ptm) REVERT: M 257 LYS cc_start: 0.9287 (mtmt) cc_final: 0.8947 (ptpp) REVERT: N 62 GLN cc_start: 0.9114 (mt0) cc_final: 0.8757 (mt0) REVERT: N 63 LYS cc_start: 0.9470 (mmtt) cc_final: 0.9144 (mmmm) REVERT: N 102 ASP cc_start: 0.8864 (t0) cc_final: 0.8127 (t0) REVERT: N 105 ASN cc_start: 0.7776 (m-40) cc_final: 0.7531 (m-40) REVERT: O 160 MET cc_start: 0.8282 (ptm) cc_final: 0.7690 (ptm) REVERT: O 212 LEU cc_start: 0.8906 (mt) cc_final: 0.8600 (mt) REVERT: P 36 ASN cc_start: 0.8689 (m-40) cc_final: 0.8246 (t0) REVERT: P 70 ASN cc_start: 0.8663 (m-40) cc_final: 0.8112 (t0) REVERT: P 102 ASP cc_start: 0.8971 (t0) cc_final: 0.8500 (t0) REVERT: Q 147 ILE cc_start: 0.9512 (mt) cc_final: 0.9249 (tp) REVERT: Q 160 MET cc_start: 0.8280 (ptm) cc_final: 0.7698 (ptm) REVERT: R 36 ASN cc_start: 0.8873 (m-40) cc_final: 0.8341 (t0) REVERT: R 55 ASP cc_start: 0.8564 (m-30) cc_final: 0.8022 (t0) REVERT: R 90 GLU cc_start: 0.9015 (mp0) cc_final: 0.8616 (mp0) REVERT: R 102 ASP cc_start: 0.8879 (t0) cc_final: 0.8452 (t0) REVERT: S 160 MET cc_start: 0.8268 (ptm) cc_final: 0.7483 (ptm) REVERT: S 196 MET cc_start: 0.8756 (tmm) cc_final: 0.8473 (tmm) REVERT: T 62 GLN cc_start: 0.9291 (mt0) cc_final: 0.9011 (mt0) REVERT: T 87 ASP cc_start: 0.6390 (t70) cc_final: 0.5033 (t70) REVERT: T 90 GLU cc_start: 0.9080 (mp0) cc_final: 0.8790 (mp0) REVERT: T 97 LYS cc_start: 0.9506 (tppt) cc_final: 0.9055 (ttmt) REVERT: T 102 ASP cc_start: 0.8880 (t70) cc_final: 0.8664 (t0) REVERT: T 116 MET cc_start: 0.8663 (tpp) cc_final: 0.8382 (tpp) REVERT: T 117 ASP cc_start: 0.8504 (t70) cc_final: 0.7838 (t0) REVERT: T 118 LYS cc_start: 0.8854 (mmmt) cc_final: 0.8287 (mppt) REVERT: U 147 ILE cc_start: 0.9537 (mt) cc_final: 0.9185 (tp) REVERT: U 160 MET cc_start: 0.8040 (ptm) cc_final: 0.7187 (ptm) REVERT: V 63 LYS cc_start: 0.9375 (mttm) cc_final: 0.9070 (ttmm) REVERT: W 147 ILE cc_start: 0.9507 (mt) cc_final: 0.9260 (tp) REVERT: W 242 MET cc_start: 0.8997 (ttm) cc_final: 0.8664 (ttt) REVERT: X 55 ASP cc_start: 0.8652 (m-30) cc_final: 0.8019 (t0) REVERT: X 70 ASN cc_start: 0.8802 (m110) cc_final: 0.8343 (t0) REVERT: X 97 LYS cc_start: 0.9541 (mmmt) cc_final: 0.8900 (ttmt) outliers start: 4 outliers final: 3 residues processed: 526 average time/residue: 0.4927 time to fit residues: 431.2169 Evaluate side-chains 384 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 381 time to evaluate : 4.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 410 optimal weight: 0.4980 chunk 432 optimal weight: 0.2980 chunk 394 optimal weight: 2.9990 chunk 420 optimal weight: 4.9990 chunk 253 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 330 optimal weight: 4.9990 chunk 128 optimal weight: 0.7980 chunk 379 optimal weight: 1.9990 chunk 397 optimal weight: 0.9980 chunk 418 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN G 92 HIS ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 185 HIS ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 122 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.6704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37476 Z= 0.168 Angle : 0.499 10.640 50628 Z= 0.272 Chirality : 0.035 0.157 5964 Planarity : 0.003 0.054 6444 Dihedral : 3.597 26.030 5172 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.34 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.09 (0.12), residues: 4716 helix: 3.08 (0.07), residues: 4368 sheet: None (None), residues: 0 loop : -3.14 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 41 HIS 0.020 0.002 HIS Q 123 PHE 0.016 0.002 PHE G 128 TYR 0.020 0.001 TYR D 48 ARG 0.012 0.000 ARG R 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 535 time to evaluate : 4.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 160 MET cc_start: 0.7855 (ptm) cc_final: 0.7094 (ptm) REVERT: B 252 TYR cc_start: 0.8895 (m-80) cc_final: 0.8691 (m-80) REVERT: A 36 ASN cc_start: 0.8694 (m-40) cc_final: 0.8371 (t0) REVERT: A 62 GLN cc_start: 0.9229 (mt0) cc_final: 0.8909 (mt0) REVERT: A 63 LYS cc_start: 0.9261 (mmtp) cc_final: 0.8864 (mtmm) REVERT: A 87 ASP cc_start: 0.6754 (t70) cc_final: 0.5070 (t70) REVERT: A 102 ASP cc_start: 0.9014 (t0) cc_final: 0.8710 (t0) REVERT: C 8 MET cc_start: 0.8534 (mtt) cc_final: 0.8330 (mtt) REVERT: C 67 MET cc_start: 0.8688 (mtp) cc_final: 0.8482 (mtp) REVERT: C 147 ILE cc_start: 0.9459 (mt) cc_final: 0.9213 (tp) REVERT: C 160 MET cc_start: 0.8329 (ptm) cc_final: 0.7382 (ptm) REVERT: C 191 MET cc_start: 0.8623 (tpp) cc_final: 0.8250 (tpp) REVERT: D 36 ASN cc_start: 0.8705 (m-40) cc_final: 0.8355 (t0) REVERT: D 55 ASP cc_start: 0.8366 (m-30) cc_final: 0.7877 (t0) REVERT: D 63 LYS cc_start: 0.9382 (mmtt) cc_final: 0.9111 (mttm) REVERT: D 70 ASN cc_start: 0.8799 (m-40) cc_final: 0.8411 (t0) REVERT: D 97 LYS cc_start: 0.9555 (tppt) cc_final: 0.9213 (mtmt) REVERT: D 102 ASP cc_start: 0.8860 (t0) cc_final: 0.8564 (t0) REVERT: E 30 LYS cc_start: 0.7948 (mtmt) cc_final: 0.7232 (mmtt) REVERT: E 160 MET cc_start: 0.8211 (ptm) cc_final: 0.7531 (ptm) REVERT: E 196 MET cc_start: 0.8532 (tmm) cc_final: 0.7752 (tmm) REVERT: E 200 ILE cc_start: 0.9188 (mm) cc_final: 0.8806 (mm) REVERT: F 36 ASN cc_start: 0.8659 (m-40) cc_final: 0.8332 (t0) REVERT: F 55 ASP cc_start: 0.8555 (m-30) cc_final: 0.7985 (t0) REVERT: F 63 LYS cc_start: 0.9301 (mttm) cc_final: 0.8731 (ttmm) REVERT: F 70 ASN cc_start: 0.8705 (m-40) cc_final: 0.8246 (t0) REVERT: F 97 LYS cc_start: 0.9428 (tppt) cc_final: 0.8998 (ttmt) REVERT: F 102 ASP cc_start: 0.8691 (t0) cc_final: 0.8134 (t0) REVERT: F 117 ASP cc_start: 0.8265 (t70) cc_final: 0.7512 (t0) REVERT: G 147 ILE cc_start: 0.9449 (mt) cc_final: 0.9233 (tp) REVERT: G 160 MET cc_start: 0.8246 (ptm) cc_final: 0.7587 (ptm) REVERT: H 55 ASP cc_start: 0.8379 (m-30) cc_final: 0.7844 (t0) REVERT: H 63 LYS cc_start: 0.9356 (mttm) cc_final: 0.9022 (ttmm) REVERT: H 97 LYS cc_start: 0.9369 (mmmm) cc_final: 0.8995 (mttp) REVERT: H 102 ASP cc_start: 0.8895 (t0) cc_final: 0.8600 (t0) REVERT: I 147 ILE cc_start: 0.9483 (mt) cc_final: 0.9234 (tp) REVERT: I 160 MET cc_start: 0.8245 (ptm) cc_final: 0.7535 (ptm) REVERT: J 70 ASN cc_start: 0.8782 (m110) cc_final: 0.8367 (t0) REVERT: J 97 LYS cc_start: 0.9353 (tppt) cc_final: 0.8899 (ttmt) REVERT: J 102 ASP cc_start: 0.8863 (t0) cc_final: 0.8628 (t0) REVERT: K 67 MET cc_start: 0.9044 (mtp) cc_final: 0.8598 (mtp) REVERT: K 160 MET cc_start: 0.8100 (ptm) cc_final: 0.7446 (ptm) REVERT: K 212 LEU cc_start: 0.8967 (mt) cc_final: 0.8616 (mt) REVERT: L 58 ILE cc_start: 0.9540 (pt) cc_final: 0.9286 (pt) REVERT: L 63 LYS cc_start: 0.9363 (mmtt) cc_final: 0.9131 (mmmm) REVERT: L 97 LYS cc_start: 0.9418 (tppt) cc_final: 0.8941 (mttt) REVERT: L 102 ASP cc_start: 0.9068 (t0) cc_final: 0.8852 (t0) REVERT: M 8 MET cc_start: 0.8124 (mtp) cc_final: 0.7907 (mtp) REVERT: M 147 ILE cc_start: 0.9483 (mt) cc_final: 0.9240 (tp) REVERT: M 160 MET cc_start: 0.8303 (ptm) cc_final: 0.7494 (ptm) REVERT: M 212 LEU cc_start: 0.8975 (mt) cc_final: 0.8627 (mt) REVERT: N 62 GLN cc_start: 0.9082 (mt0) cc_final: 0.8771 (mt0) REVERT: N 102 ASP cc_start: 0.8828 (t0) cc_final: 0.8081 (t0) REVERT: N 105 ASN cc_start: 0.7758 (m-40) cc_final: 0.7499 (m-40) REVERT: O 160 MET cc_start: 0.8235 (ptm) cc_final: 0.7667 (ptm) REVERT: P 36 ASN cc_start: 0.8680 (m-40) cc_final: 0.8235 (t0) REVERT: P 70 ASN cc_start: 0.8671 (m-40) cc_final: 0.8156 (t0) REVERT: P 102 ASP cc_start: 0.8953 (t0) cc_final: 0.8466 (t0) REVERT: Q 147 ILE cc_start: 0.9512 (mt) cc_final: 0.9246 (tp) REVERT: Q 160 MET cc_start: 0.8233 (ptm) cc_final: 0.7548 (ptm) REVERT: R 22 ILE cc_start: 0.9292 (mp) cc_final: 0.9028 (mt) REVERT: R 36 ASN cc_start: 0.8815 (m-40) cc_final: 0.8348 (t0) REVERT: R 55 ASP cc_start: 0.8481 (m-30) cc_final: 0.7979 (t0) REVERT: R 90 GLU cc_start: 0.8953 (mp0) cc_final: 0.8561 (mp0) REVERT: R 102 ASP cc_start: 0.8900 (t0) cc_final: 0.8480 (t0) REVERT: S 98 MET cc_start: 0.8263 (mmm) cc_final: 0.7984 (mmp) REVERT: S 147 ILE cc_start: 0.9491 (mt) cc_final: 0.9210 (tp) REVERT: S 160 MET cc_start: 0.8275 (ptm) cc_final: 0.7549 (ptm) REVERT: S 196 MET cc_start: 0.8467 (tmm) cc_final: 0.8237 (tmm) REVERT: T 33 ARG cc_start: 0.8466 (mmm160) cc_final: 0.8059 (tpt170) REVERT: T 62 GLN cc_start: 0.9210 (mt0) cc_final: 0.8943 (mt0) REVERT: T 70 ASN cc_start: 0.8643 (m-40) cc_final: 0.8295 (t0) REVERT: T 87 ASP cc_start: 0.6371 (t70) cc_final: 0.4527 (t70) REVERT: T 90 GLU cc_start: 0.9017 (mp0) cc_final: 0.8696 (mp0) REVERT: T 97 LYS cc_start: 0.9517 (tppt) cc_final: 0.9102 (ttmt) REVERT: T 102 ASP cc_start: 0.8880 (t70) cc_final: 0.8645 (t0) REVERT: T 116 MET cc_start: 0.8645 (tpp) cc_final: 0.8384 (tpp) REVERT: T 117 ASP cc_start: 0.8404 (t70) cc_final: 0.7945 (t0) REVERT: U 147 ILE cc_start: 0.9527 (mt) cc_final: 0.9182 (tp) REVERT: U 160 MET cc_start: 0.8118 (ptm) cc_final: 0.7241 (ptm) REVERT: U 191 MET cc_start: 0.8475 (tpp) cc_final: 0.8024 (tpp) REVERT: V 63 LYS cc_start: 0.9360 (mttm) cc_final: 0.8991 (ttmm) REVERT: W 147 ILE cc_start: 0.9499 (mt) cc_final: 0.9248 (tp) REVERT: W 242 MET cc_start: 0.9000 (ttm) cc_final: 0.8667 (ttt) REVERT: X 55 ASP cc_start: 0.8628 (m-30) cc_final: 0.7999 (t0) REVERT: X 70 ASN cc_start: 0.8792 (m110) cc_final: 0.8377 (t0) REVERT: X 97 LYS cc_start: 0.9528 (mmmt) cc_final: 0.8889 (ttmt) outliers start: 0 outliers final: 0 residues processed: 535 average time/residue: 0.4854 time to fit residues: 429.3588 Evaluate side-chains 391 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 391 time to evaluate : 4.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 276 optimal weight: 0.8980 chunk 444 optimal weight: 2.9990 chunk 271 optimal weight: 0.8980 chunk 210 optimal weight: 0.0980 chunk 308 optimal weight: 3.9990 chunk 466 optimal weight: 0.3980 chunk 429 optimal weight: 0.9990 chunk 371 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 286 optimal weight: 0.9990 chunk 227 optimal weight: 3.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 GLN C 52 GLN ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN M 277 ASN ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 92 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.6870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37476 Z= 0.171 Angle : 0.517 11.378 50628 Z= 0.282 Chirality : 0.036 0.163 5964 Planarity : 0.003 0.062 6444 Dihedral : 3.680 24.118 5172 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.40 % Favored : 98.39 % Rotamer: Outliers : 0.03 % Allowed : 0.25 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.06 (0.12), residues: 4716 helix: 3.06 (0.07), residues: 4368 sheet: None (None), residues: 0 loop : -3.21 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 41 HIS 0.016 0.002 HIS M 123 PHE 0.018 0.002 PHE K 128 TYR 0.021 0.001 TYR M 148 ARG 0.014 0.000 ARG X 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9432 Ramachandran restraints generated. 4716 Oldfield, 0 Emsley, 4716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 520 time to evaluate : 4.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 8 MET cc_start: 0.8553 (mtp) cc_final: 0.8039 (mtp) REVERT: B 123 HIS cc_start: 0.6795 (p90) cc_final: 0.6333 (p90) REVERT: B 147 ILE cc_start: 0.9516 (mt) cc_final: 0.9272 (tp) REVERT: B 160 MET cc_start: 0.7884 (ptm) cc_final: 0.7179 (ptm) REVERT: B 252 TYR cc_start: 0.8892 (m-80) cc_final: 0.8669 (m-80) REVERT: A 36 ASN cc_start: 0.8710 (m-40) cc_final: 0.8355 (t0) REVERT: A 62 GLN cc_start: 0.9204 (mt0) cc_final: 0.8904 (mt0) REVERT: A 63 LYS cc_start: 0.9258 (mmtp) cc_final: 0.8924 (mttm) REVERT: A 102 ASP cc_start: 0.9048 (t0) cc_final: 0.8764 (t0) REVERT: A 117 ASP cc_start: 0.8080 (t0) cc_final: 0.7464 (t0) REVERT: C 67 MET cc_start: 0.8694 (mtp) cc_final: 0.8480 (mtp) REVERT: C 129 MET cc_start: 0.8748 (mtt) cc_final: 0.8410 (mmt) REVERT: C 147 ILE cc_start: 0.9419 (mt) cc_final: 0.9165 (tp) REVERT: C 160 MET cc_start: 0.8284 (ptm) cc_final: 0.7381 (ptm) REVERT: C 191 MET cc_start: 0.8621 (tpp) cc_final: 0.8241 (tpp) REVERT: D 36 ASN cc_start: 0.8692 (m-40) cc_final: 0.8311 (t0) REVERT: D 55 ASP cc_start: 0.8270 (m-30) cc_final: 0.7879 (t0) REVERT: D 63 LYS cc_start: 0.9406 (mmtt) cc_final: 0.9131 (mttm) REVERT: D 70 ASN cc_start: 0.8805 (m-40) cc_final: 0.8426 (t0) REVERT: D 97 LYS cc_start: 0.9558 (tppt) cc_final: 0.9199 (mtmt) REVERT: D 102 ASP cc_start: 0.8880 (t0) cc_final: 0.8548 (t0) REVERT: E 30 LYS cc_start: 0.7837 (mtmt) cc_final: 0.7169 (mmtt) REVERT: E 160 MET cc_start: 0.8205 (ptm) cc_final: 0.7620 (ptm) REVERT: E 196 MET cc_start: 0.8529 (tmm) cc_final: 0.8281 (tmm) REVERT: F 36 ASN cc_start: 0.8659 (m-40) cc_final: 0.8311 (t0) REVERT: F 55 ASP cc_start: 0.8429 (m-30) cc_final: 0.7779 (t0) REVERT: F 63 LYS cc_start: 0.9324 (mttm) cc_final: 0.8848 (ttmm) REVERT: F 70 ASN cc_start: 0.8702 (m-40) cc_final: 0.8267 (t0) REVERT: F 97 LYS cc_start: 0.9422 (tppt) cc_final: 0.8986 (ttmt) REVERT: F 102 ASP cc_start: 0.8791 (t0) cc_final: 0.8266 (t0) REVERT: G 8 MET cc_start: 0.8620 (mtt) cc_final: 0.8283 (mtp) REVERT: G 147 ILE cc_start: 0.9435 (mt) cc_final: 0.9185 (tp) REVERT: G 160 MET cc_start: 0.8286 (ptm) cc_final: 0.7567 (ptm) REVERT: H 55 ASP cc_start: 0.8298 (m-30) cc_final: 0.7761 (t0) REVERT: H 63 LYS cc_start: 0.9357 (mttm) cc_final: 0.9053 (ttmm) REVERT: H 97 LYS cc_start: 0.9362 (mmmm) cc_final: 0.9025 (mttp) REVERT: H 102 ASP cc_start: 0.8973 (t0) cc_final: 0.8679 (t0) REVERT: H 118 LYS cc_start: 0.8983 (mmmm) cc_final: 0.8399 (mppt) REVERT: I 98 MET cc_start: 0.8285 (mmm) cc_final: 0.8020 (mmp) REVERT: I 147 ILE cc_start: 0.9455 (mt) cc_final: 0.9202 (tp) REVERT: I 160 MET cc_start: 0.8200 (ptm) cc_final: 0.7513 (ptm) REVERT: J 70 ASN cc_start: 0.8801 (m110) cc_final: 0.8410 (t0) REVERT: J 97 LYS cc_start: 0.9366 (tppt) cc_final: 0.8938 (ttmt) REVERT: K 67 MET cc_start: 0.8977 (mtp) cc_final: 0.8325 (mtp) REVERT: K 160 MET cc_start: 0.8060 (ptm) cc_final: 0.7434 (ptm) REVERT: K 212 LEU cc_start: 0.8975 (mt) cc_final: 0.8620 (mt) REVERT: L 63 LYS cc_start: 0.9377 (mmtt) cc_final: 0.9141 (mmmm) REVERT: L 97 LYS cc_start: 0.9419 (tppt) cc_final: 0.9007 (mttt) REVERT: L 102 ASP cc_start: 0.9080 (t0) cc_final: 0.8879 (t0) REVERT: M 8 MET cc_start: 0.8115 (mtp) cc_final: 0.7895 (mtp) REVERT: M 160 MET cc_start: 0.8302 (ptm) cc_final: 0.7602 (ptm) REVERT: M 181 LEU cc_start: 0.9132 (mt) cc_final: 0.8876 (mt) REVERT: M 212 LEU cc_start: 0.8990 (mt) cc_final: 0.8637 (mt) REVERT: N 102 ASP cc_start: 0.8801 (t0) cc_final: 0.8065 (t0) REVERT: N 105 ASN cc_start: 0.7739 (m-40) cc_final: 0.7488 (m-40) REVERT: O 160 MET cc_start: 0.8233 (ptm) cc_final: 0.7662 (ptm) REVERT: O 181 LEU cc_start: 0.9162 (mp) cc_final: 0.8822 (mp) REVERT: P 36 ASN cc_start: 0.8686 (m-40) cc_final: 0.8248 (t0) REVERT: P 70 ASN cc_start: 0.8684 (m-40) cc_final: 0.8206 (t0) REVERT: P 102 ASP cc_start: 0.8968 (t0) cc_final: 0.8492 (t0) REVERT: Q 147 ILE cc_start: 0.9433 (mt) cc_final: 0.9177 (tp) REVERT: Q 160 MET cc_start: 0.8243 (ptm) cc_final: 0.7588 (ptm) REVERT: R 22 ILE cc_start: 0.9266 (mp) cc_final: 0.9027 (mt) REVERT: R 36 ASN cc_start: 0.8783 (m-40) cc_final: 0.8373 (t0) REVERT: R 55 ASP cc_start: 0.8343 (m-30) cc_final: 0.7923 (t0) REVERT: R 87 ASP cc_start: 0.6932 (t70) cc_final: 0.4920 (t70) REVERT: R 90 GLU cc_start: 0.8932 (mp0) cc_final: 0.8678 (mp0) REVERT: R 102 ASP cc_start: 0.8908 (t0) cc_final: 0.8475 (t0) REVERT: S 147 ILE cc_start: 0.9492 (mt) cc_final: 0.9226 (tp) REVERT: S 160 MET cc_start: 0.8046 (ptm) cc_final: 0.7536 (ptm) REVERT: S 196 MET cc_start: 0.8486 (tmm) cc_final: 0.8204 (tmm) REVERT: T 62 GLN cc_start: 0.9185 (mt0) cc_final: 0.8939 (mt0) REVERT: T 70 ASN cc_start: 0.8628 (m-40) cc_final: 0.8276 (t0) REVERT: T 87 ASP cc_start: 0.6401 (t70) cc_final: 0.4567 (t70) REVERT: T 90 GLU cc_start: 0.9016 (mp0) cc_final: 0.8702 (mp0) REVERT: T 97 LYS cc_start: 0.9510 (tppt) cc_final: 0.9083 (ttmt) REVERT: T 102 ASP cc_start: 0.8887 (t70) cc_final: 0.8657 (t0) REVERT: T 116 MET cc_start: 0.8672 (tpp) cc_final: 0.8419 (tpp) REVERT: T 117 ASP cc_start: 0.8409 (t70) cc_final: 0.7905 (t0) REVERT: U 8 MET cc_start: 0.8556 (mtp) cc_final: 0.8083 (mtp) REVERT: U 147 ILE cc_start: 0.9529 (mt) cc_final: 0.9198 (tp) REVERT: U 160 MET cc_start: 0.8405 (ptm) cc_final: 0.7637 (ptm) REVERT: U 191 MET cc_start: 0.8478 (tpp) cc_final: 0.8016 (tpp) REVERT: V 58 ILE cc_start: 0.9581 (pt) cc_final: 0.9344 (pt) REVERT: V 63 LYS cc_start: 0.9420 (mttm) cc_final: 0.9060 (ttmm) REVERT: W 147 ILE cc_start: 0.9507 (mt) cc_final: 0.9261 (tp) REVERT: W 242 MET cc_start: 0.8992 (ttm) cc_final: 0.8686 (ttt) REVERT: X 55 ASP cc_start: 0.8513 (m-30) cc_final: 0.7873 (t0) REVERT: X 70 ASN cc_start: 0.8715 (m110) cc_final: 0.8362 (t0) REVERT: X 97 LYS cc_start: 0.9541 (mmmt) cc_final: 0.8952 (mtmt) outliers start: 1 outliers final: 1 residues processed: 521 average time/residue: 0.4696 time to fit residues: 408.4910 Evaluate side-chains 391 residues out of total 3612 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 390 time to evaluate : 4.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 468 random chunks: chunk 294 optimal weight: 0.9980 chunk 395 optimal weight: 0.0570 chunk 113 optimal weight: 4.9990 chunk 342 optimal weight: 0.0870 chunk 54 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 371 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 381 optimal weight: 10.0000 chunk 47 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 0.5876 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 GLN ** C 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 52 GLN ** I 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 GLN ** O 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.066731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.052769 restraints weight = 165646.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.053924 restraints weight = 122807.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.054678 restraints weight = 100271.985| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.7019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37476 Z= 0.167 Angle : 0.513 16.627 50628 Z= 0.279 Chirality : 0.035 0.159 5964 Planarity : 0.003 0.044 6444 Dihedral : 3.669 23.822 5172 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.23 % Allowed : 1.40 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 4.06 (0.12), residues: 4716 helix: 3.07 (0.07), residues: 4368 sheet: None (None), residues: 0 loop : -3.26 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 41 HIS 0.012 0.002 HIS O 123 PHE 0.017 0.002 PHE G 128 TYR 0.019 0.001 TYR Q 210 ARG 0.007 0.000 ARG X 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9150.29 seconds wall clock time: 166 minutes 35.59 seconds (9995.59 seconds total)