Starting phenix.real_space_refine on Fri Mar 22 10:42:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v66_31736/03_2024/7v66_31736.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v66_31736/03_2024/7v66_31736.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v66_31736/03_2024/7v66_31736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v66_31736/03_2024/7v66_31736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v66_31736/03_2024/7v66_31736.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v66_31736/03_2024/7v66_31736.pdb" } resolution = 1.89 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 20904 2.51 5 N 5808 2.21 5 O 6336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "U ARG 5": "NH1" <-> "NH2" Residue "U GLU 163": "OE1" <-> "OE2" Residue "A ARG 5": "NH1" <-> "NH2" Residue "B GLU 90": "OE1" <-> "OE2" Residue "G ASP 167": "OD1" <-> "OD2" Residue "K ARG 5": "NH1" <-> "NH2" Residue "M ARG 5": "NH1" <-> "NH2" Residue "P ARG 5": "NH1" <-> "NH2" Residue "X GLU 163": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33216 Number of models: 1 Model: "" Number of chains: 24 Chain: "U" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "A" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "E" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "F" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "G" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "I" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "J" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "K" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "L" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "M" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "N" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "O" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "Q" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "R" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "S" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "T" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "V" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "W" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "X" Number of atoms: 1384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1384 Classifications: {'peptide': 172} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 3, 'TRANS': 168} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Time building chain proxies: 16.34, per 1000 atoms: 0.49 Number of scatterers: 33216 At special positions: 0 Unit cell: (130.295, 130.295, 130.295, 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 168 16.00 O 6336 8.00 N 5808 7.00 C 20904 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: 13.33 Conformation dependent library (CDL) restraints added in 5.7 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.10 Creating SS restraints... Processing helix chain 'U' and resid 9 through 38 Processing helix chain 'U' and resid 44 through 72 Processing helix chain 'U' and resid 91 through 120 Processing helix chain 'U' and resid 122 through 133 Processing helix chain 'U' and resid 133 through 154 Processing helix chain 'U' and resid 159 through 170 removed outlier: 3.809A pdb=" N GLU U 163 " --> pdb=" O SER U 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 38 Processing helix chain 'A' and resid 44 through 72 Processing helix chain 'A' and resid 91 through 120 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 133 through 154 Processing helix chain 'A' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 38 Processing helix chain 'B' and resid 44 through 72 Processing helix chain 'B' and resid 91 through 120 Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 133 through 154 Processing helix chain 'B' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU B 163 " --> pdb=" O SER B 159 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 37 Processing helix chain 'C' and resid 44 through 72 Processing helix chain 'C' and resid 91 through 120 Processing helix chain 'C' and resid 122 through 133 Processing helix chain 'C' and resid 133 through 154 Processing helix chain 'C' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU C 163 " --> pdb=" O SER C 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 9 through 37 Processing helix chain 'D' and resid 44 through 72 Processing helix chain 'D' and resid 91 through 120 Processing helix chain 'D' and resid 122 through 133 Processing helix chain 'D' and resid 133 through 154 Processing helix chain 'D' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU D 163 " --> pdb=" O SER D 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 38 Processing helix chain 'E' and resid 44 through 72 Processing helix chain 'E' and resid 91 through 120 Processing helix chain 'E' and resid 122 through 133 Processing helix chain 'E' and resid 133 through 154 Processing helix chain 'E' and resid 159 through 170 removed outlier: 3.809A pdb=" N GLU E 163 " --> pdb=" O SER E 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 9 through 38 Processing helix chain 'F' and resid 44 through 72 Processing helix chain 'F' and resid 91 through 120 Processing helix chain 'F' and resid 122 through 133 Processing helix chain 'F' and resid 133 through 154 Processing helix chain 'F' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU F 163 " --> pdb=" O SER F 159 " (cutoff:3.500A) Processing helix chain 'G' and resid 9 through 38 Processing helix chain 'G' and resid 44 through 72 Processing helix chain 'G' and resid 91 through 120 Processing helix chain 'G' and resid 122 through 133 Processing helix chain 'G' and resid 133 through 154 Processing helix chain 'G' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU G 163 " --> pdb=" O SER G 159 " (cutoff:3.500A) Processing helix chain 'H' and resid 9 through 38 Processing helix chain 'H' and resid 44 through 72 Processing helix chain 'H' and resid 91 through 120 Processing helix chain 'H' and resid 122 through 133 Processing helix chain 'H' and resid 133 through 154 Processing helix chain 'H' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU H 163 " --> pdb=" O SER H 159 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 38 Processing helix chain 'I' and resid 44 through 72 Processing helix chain 'I' and resid 91 through 120 Processing helix chain 'I' and resid 122 through 133 Processing helix chain 'I' and resid 133 through 154 Processing helix chain 'I' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU I 163 " --> pdb=" O SER I 159 " (cutoff:3.500A) Processing helix chain 'J' and resid 9 through 38 Processing helix chain 'J' and resid 44 through 72 Processing helix chain 'J' and resid 91 through 120 Processing helix chain 'J' and resid 122 through 133 Processing helix chain 'J' and resid 133 through 154 Processing helix chain 'J' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU J 163 " --> pdb=" O SER J 159 " (cutoff:3.500A) Processing helix chain 'K' and resid 9 through 38 Processing helix chain 'K' and resid 44 through 72 Processing helix chain 'K' and resid 91 through 120 Processing helix chain 'K' and resid 122 through 133 Processing helix chain 'K' and resid 133 through 154 Processing helix chain 'K' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU K 163 " --> pdb=" O SER K 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 38 Processing helix chain 'L' and resid 44 through 72 Processing helix chain 'L' and resid 91 through 120 Processing helix chain 'L' and resid 122 through 133 Processing helix chain 'L' and resid 133 through 154 Processing helix chain 'L' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU L 163 " --> pdb=" O SER L 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 9 through 38 Processing helix chain 'M' and resid 44 through 72 Processing helix chain 'M' and resid 91 through 120 Processing helix chain 'M' and resid 122 through 133 Processing helix chain 'M' and resid 133 through 154 Processing helix chain 'M' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU M 163 " --> pdb=" O SER M 159 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 37 Processing helix chain 'N' and resid 44 through 72 Processing helix chain 'N' and resid 91 through 120 Processing helix chain 'N' and resid 122 through 133 Processing helix chain 'N' and resid 133 through 154 Processing helix chain 'N' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU N 163 " --> pdb=" O SER N 159 " (cutoff:3.500A) Processing helix chain 'O' and resid 9 through 38 Processing helix chain 'O' and resid 44 through 72 Processing helix chain 'O' and resid 91 through 120 Processing helix chain 'O' and resid 122 through 133 Processing helix chain 'O' and resid 133 through 154 Processing helix chain 'O' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU O 163 " --> pdb=" O SER O 159 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 38 Processing helix chain 'P' and resid 44 through 72 Processing helix chain 'P' and resid 91 through 120 Processing helix chain 'P' and resid 122 through 133 Processing helix chain 'P' and resid 133 through 154 Processing helix chain 'P' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU P 163 " --> pdb=" O SER P 159 " (cutoff:3.500A) Processing helix chain 'Q' and resid 9 through 38 Processing helix chain 'Q' and resid 44 through 72 Processing helix chain 'Q' and resid 91 through 120 Processing helix chain 'Q' and resid 122 through 133 Processing helix chain 'Q' and resid 133 through 154 Processing helix chain 'Q' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU Q 163 " --> pdb=" O SER Q 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 9 through 38 Processing helix chain 'R' and resid 44 through 72 Processing helix chain 'R' and resid 91 through 120 Processing helix chain 'R' and resid 122 through 133 Processing helix chain 'R' and resid 133 through 154 Processing helix chain 'R' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU R 163 " --> pdb=" O SER R 159 " (cutoff:3.500A) Processing helix chain 'S' and resid 9 through 38 Processing helix chain 'S' and resid 44 through 72 Processing helix chain 'S' and resid 91 through 120 Processing helix chain 'S' and resid 122 through 133 Processing helix chain 'S' and resid 133 through 154 Processing helix chain 'S' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU S 163 " --> pdb=" O SER S 159 " (cutoff:3.500A) Processing helix chain 'T' and resid 9 through 38 Processing helix chain 'T' and resid 44 through 72 Processing helix chain 'T' and resid 91 through 120 Processing helix chain 'T' and resid 122 through 133 Processing helix chain 'T' and resid 133 through 154 Processing helix chain 'T' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU T 163 " --> pdb=" O SER T 159 " (cutoff:3.500A) Processing helix chain 'V' and resid 9 through 38 Processing helix chain 'V' and resid 44 through 72 Processing helix chain 'V' and resid 91 through 120 Processing helix chain 'V' and resid 122 through 133 Processing helix chain 'V' and resid 133 through 154 Processing helix chain 'V' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU V 163 " --> pdb=" O SER V 159 " (cutoff:3.500A) Processing helix chain 'W' and resid 9 through 38 Processing helix chain 'W' and resid 44 through 72 Processing helix chain 'W' and resid 91 through 120 Processing helix chain 'W' and resid 122 through 133 Processing helix chain 'W' and resid 133 through 154 Processing helix chain 'W' and resid 159 through 170 removed outlier: 3.804A pdb=" N GLU W 163 " --> pdb=" O SER W 159 " (cutoff:3.500A) Processing helix chain 'X' and resid 9 through 38 Processing helix chain 'X' and resid 44 through 72 Processing helix chain 'X' and resid 91 through 120 Processing helix chain 'X' and resid 122 through 133 Processing helix chain 'X' and resid 133 through 154 Processing helix chain 'X' and resid 159 through 170 removed outlier: 3.806A pdb=" N GLU X 163 " --> pdb=" O SER X 159 " (cutoff:3.500A) 2637 hydrogen bonds defined for protein. 7911 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: 9.99 Time building geometry restraints manager: 14.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10606 1.34 - 1.46: 4943 1.46 - 1.57: 18099 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 33912 Sorted by residual: bond pdb=" C ALA M 156 " pdb=" N PRO M 157 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.50e+00 bond pdb=" C ALA V 156 " pdb=" N PRO V 157 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.50e+00 bond pdb=" C ALA T 156 " pdb=" N PRO T 157 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.50e+00 bond pdb=" C ALA A 156 " pdb=" N PRO A 157 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.50e+00 bond pdb=" C ALA X 156 " pdb=" N PRO X 157 " ideal model delta sigma weight residual 1.336 1.358 -0.022 1.20e-02 6.94e+03 3.50e+00 ... (remaining 33907 not shown) Histogram of bond angle deviations from ideal: 99.45 - 106.33: 653 106.33 - 113.20: 17808 113.20 - 120.07: 12204 120.07 - 126.95: 14719 126.95 - 133.82: 408 Bond angle restraints: 45792 Sorted by residual: angle pdb=" C ALA W 156 " pdb=" N PRO W 157 " pdb=" CA PRO W 157 " ideal model delta sigma weight residual 119.84 129.45 -9.61 1.25e+00 6.40e-01 5.91e+01 angle pdb=" N GLU B 90 " pdb=" CA GLU B 90 " pdb=" C GLU B 90 " ideal model delta sigma weight residual 110.80 123.65 -12.85 2.13e+00 2.20e-01 3.64e+01 angle pdb=" N LYS S 45 " pdb=" CA LYS S 45 " pdb=" C LYS S 45 " ideal model delta sigma weight residual 111.28 117.33 -6.05 1.09e+00 8.42e-01 3.08e+01 angle pdb=" N THR U 131 " pdb=" CA THR U 131 " pdb=" C THR U 131 " ideal model delta sigma weight residual 111.82 117.22 -5.40 1.16e+00 7.43e-01 2.17e+01 angle pdb=" N THR B 131 " pdb=" CA THR B 131 " pdb=" C THR B 131 " ideal model delta sigma weight residual 111.82 117.22 -5.40 1.16e+00 7.43e-01 2.16e+01 ... (remaining 45787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.57: 19381 17.57 - 35.14: 609 35.14 - 52.71: 287 52.71 - 70.28: 50 70.28 - 87.84: 25 Dihedral angle restraints: 20352 sinusoidal: 8112 harmonic: 12240 Sorted by residual: dihedral pdb=" CA TRP H 89 " pdb=" C TRP H 89 " pdb=" N GLU H 90 " pdb=" CA GLU H 90 " ideal model delta harmonic sigma weight residual 180.00 160.80 19.20 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA TRP A 89 " pdb=" C TRP A 89 " pdb=" N GLU A 90 " pdb=" CA GLU A 90 " ideal model delta harmonic sigma weight residual 180.00 160.80 19.20 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA TRP T 89 " pdb=" C TRP T 89 " pdb=" N GLU T 90 " pdb=" CA GLU T 90 " ideal model delta harmonic sigma weight residual 180.00 160.80 19.20 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 20349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.118: 4699 0.118 - 0.236: 154 0.236 - 0.354: 19 0.354 - 0.472: 1 0.472 - 0.590: 23 Chirality restraints: 4896 Sorted by residual: chirality pdb=" CG LEU K 151 " pdb=" CB LEU K 151 " pdb=" CD1 LEU K 151 " pdb=" CD2 LEU K 151 " both_signs ideal model delta sigma weight residual False -2.59 -2.00 -0.59 2.00e-01 2.50e+01 8.69e+00 chirality pdb=" CG LEU I 151 " pdb=" CB LEU I 151 " pdb=" CD1 LEU I 151 " pdb=" CD2 LEU I 151 " both_signs ideal model delta sigma weight residual False -2.59 -2.00 -0.59 2.00e-01 2.50e+01 8.69e+00 chirality pdb=" CG LEU J 151 " pdb=" CB LEU J 151 " pdb=" CD1 LEU J 151 " pdb=" CD2 LEU J 151 " both_signs ideal model delta sigma weight residual False -2.59 -2.00 -0.59 2.00e-01 2.50e+01 8.69e+00 ... (remaining 4893 not shown) Planarity restraints: 6024 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR H 28 " -0.035 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" CG TYR H 28 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR H 28 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR H 28 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR H 28 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR H 28 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR H 28 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR H 28 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 28 " -0.035 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" CG TYR A 28 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR A 28 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 28 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 28 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR A 28 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR A 28 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR A 28 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 28 " -0.035 2.00e-02 2.50e+03 2.63e-02 1.38e+01 pdb=" CG TYR B 28 " 0.063 2.00e-02 2.50e+03 pdb=" CD1 TYR B 28 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 28 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 28 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 28 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 28 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 28 " -0.006 2.00e-02 2.50e+03 ... (remaining 6021 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 92 2.52 - 3.12: 24800 3.12 - 3.71: 56422 3.71 - 4.31: 80819 4.31 - 4.90: 131955 Nonbonded interactions: 294088 Sorted by model distance: nonbonded pdb=" O GLY D 155 " pdb=" OG SER D 159 " model vdw 1.929 2.440 nonbonded pdb=" O GLY W 155 " pdb=" OG SER W 159 " model vdw 2.206 2.440 nonbonded pdb=" OD2 ASP B 40 " pdb=" OG SER D 2 " model vdw 2.305 2.440 nonbonded pdb=" OG SER Q 2 " pdb=" OD2 ASP W 40 " model vdw 2.305 2.440 nonbonded pdb=" OD2 ASP O 40 " pdb=" OG SER R 2 " model vdw 2.305 2.440 ... (remaining 294083 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.420 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: 0.020 Extract box with map and model: 16.030 Check model and map are aligned: 0.480 Set scattering table: 0.270 Process input model: 81.810 Find NCS groups from input model: 2.420 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0489 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 : 0.006 0.059 33912 Z= 0.372 Angle : 1.018 12.850 45792 Z= 0.581 Chirality : 0.067 0.590 4896 Planarity : 0.006 0.026 6024 Dihedral : 12.145 87.844 12432 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 1.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.91 % Favored : 98.04 % Rotamer: Outliers : 2.07 % Allowed : 2.73 % Favored : 95.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.13), residues: 4080 helix: 1.80 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : -0.65 (0.24), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP H 89 HIS 0.026 0.005 HIS M 147 PHE 0.016 0.004 PHE N 37 TYR 0.063 0.006 TYR A 28 ARG 0.009 0.003 ARG O 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 288 time to evaluate : 3.364 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: U 19 GLN cc_start: 0.2173 (tp40) cc_final: 0.1938 (mm-40) REVERT: A 19 GLN cc_start: 0.2205 (tp40) cc_final: 0.1933 (mm-40) REVERT: B 19 GLN cc_start: 0.2189 (tp40) cc_final: 0.1947 (mm-40) REVERT: C 19 GLN cc_start: 0.2198 (tp40) cc_final: 0.1934 (mm-40) REVERT: D 19 GLN cc_start: 0.2214 (tp40) cc_final: 0.1948 (mm-40) REVERT: E 19 GLN cc_start: 0.2198 (tp40) cc_final: 0.1926 (mm-40) REVERT: F 19 GLN cc_start: 0.2203 (tp40) cc_final: 0.1962 (mm-40) REVERT: G 19 GLN cc_start: 0.2191 (tp40) cc_final: 0.1926 (mm-40) REVERT: H 19 GLN cc_start: 0.2191 (tp40) cc_final: 0.1927 (mm-40) REVERT: I 19 GLN cc_start: 0.2188 (tp40) cc_final: 0.1919 (mm-40) REVERT: J 19 GLN cc_start: 0.2202 (tp40) cc_final: 0.1932 (mm-40) REVERT: K 19 GLN cc_start: 0.2201 (tp40) cc_final: 0.1936 (mm-40) REVERT: L 19 GLN cc_start: 0.2201 (tp40) cc_final: 0.1934 (mm-40) REVERT: M 19 GLN cc_start: 0.2166 (tp40) cc_final: 0.1933 (mm-40) REVERT: N 19 GLN cc_start: 0.2164 (tp40) cc_final: 0.1930 (mm-40) REVERT: O 19 GLN cc_start: 0.2194 (tp40) cc_final: 0.1928 (mm-40) REVERT: P 19 GLN cc_start: 0.2196 (tp40) cc_final: 0.1923 (mm-40) REVERT: Q 19 GLN cc_start: 0.2196 (tp40) cc_final: 0.1937 (mm-40) REVERT: R 19 GLN cc_start: 0.2202 (tp40) cc_final: 0.1939 (mm-40) REVERT: S 19 GLN cc_start: 0.2198 (tp40) cc_final: 0.1933 (mm-40) REVERT: T 19 GLN cc_start: 0.2204 (tp40) cc_final: 0.1939 (mm-40) REVERT: V 19 GLN cc_start: 0.2195 (tp40) cc_final: 0.1935 (mm-40) REVERT: W 19 GLN cc_start: 0.2197 (tp40) cc_final: 0.1928 (mm-40) REVERT: X 19 GLN cc_start: 0.2199 (tp40) cc_final: 0.1936 (mm-40) outliers start: 72 outliers final: 0 residues processed: 360 average time/residue: 1.1280 time to fit residues: 507.9859 Evaluate side-chains 264 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 3.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 3.9990 chunk 309 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 chunk 105 optimal weight: 0.9980 chunk 208 optimal weight: 0.8980 chunk 165 optimal weight: 8.9990 chunk 319 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 370 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 94 ASN U 135 ASN A 7 ASN A 94 ASN A 135 ASN A 150 ASN B 7 ASN B 10 GLN B 94 ASN B 135 ASN B 150 ASN C 7 ASN C 94 ASN C 150 ASN D 7 ASN D 94 ASN D 150 ASN E 7 ASN E 94 ASN E 150 ASN F 7 ASN F 94 ASN F 150 ASN G 7 ASN G 94 ASN G 132 HIS G 150 ASN H 7 ASN H 94 ASN H 150 ASN I 7 ASN I 94 ASN I 132 HIS I 135 ASN I 150 ASN J 7 ASN J 79 GLN J 94 ASN J 150 ASN K 7 ASN K 94 ASN K 150 ASN L 7 ASN L 94 ASN L 150 ASN M 7 ASN M 94 ASN M 150 ASN N 7 ASN N 94 ASN N 150 ASN O 7 ASN O 94 ASN O 150 ASN P 7 ASN P 94 ASN P 150 ASN Q 7 ASN Q 94 ASN Q 132 HIS Q 150 ASN R 7 ASN R 94 ASN R 132 HIS R 135 ASN R 150 ASN S 7 ASN S 94 ASN S 132 HIS S 150 ASN T 7 ASN T 94 ASN T 150 ASN V 7 ASN V 94 ASN V 150 ASN W 7 ASN W 94 ASN W 150 ASN X 7 ASN X 94 ASN X 150 ASN Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0912 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33912 Z= 0.198 Angle : 0.626 9.909 45792 Z= 0.330 Chirality : 0.041 0.184 4896 Planarity : 0.004 0.028 6024 Dihedral : 4.623 21.297 4464 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.07 % Allowed : 5.14 % Favored : 91.78 % 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: 3.53 (0.13), residues: 4080 helix: 3.00 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : -0.63 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP U 89 HIS 0.006 0.002 HIS X 114 PHE 0.006 0.001 PHE S 47 TYR 0.023 0.003 TYR Q 164 ARG 0.005 0.001 ARG B 5 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 215 time to evaluate : 3.347 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: A 22 LEU cc_start: 0.2580 (OUTLIER) cc_final: 0.2271 (mt) REVERT: B 44 LEU cc_start: -0.0292 (OUTLIER) cc_final: -0.1209 (mm) REVERT: C 22 LEU cc_start: 0.2797 (OUTLIER) cc_final: 0.2428 (mt) REVERT: C 44 LEU cc_start: -0.0264 (OUTLIER) cc_final: -0.1188 (mm) REVERT: C 134 LEU cc_start: -0.0273 (OUTLIER) cc_final: -0.0521 (mt) REVERT: D 22 LEU cc_start: 0.2576 (OUTLIER) cc_final: 0.2257 (mt) REVERT: D 44 LEU cc_start: -0.0271 (OUTLIER) cc_final: -0.1147 (mm) REVERT: D 134 LEU cc_start: -0.0274 (OUTLIER) cc_final: -0.0532 (mt) REVERT: E 22 LEU cc_start: 0.2780 (OUTLIER) cc_final: 0.2418 (mt) REVERT: E 134 LEU cc_start: -0.0254 (OUTLIER) cc_final: -0.0464 (mt) REVERT: F 44 LEU cc_start: -0.0296 (OUTLIER) cc_final: -0.1216 (mm) REVERT: F 134 LEU cc_start: -0.0295 (OUTLIER) cc_final: -0.0532 (mt) REVERT: G 22 LEU cc_start: 0.2773 (OUTLIER) cc_final: 0.2407 (mt) REVERT: G 44 LEU cc_start: -0.0298 (OUTLIER) cc_final: -0.1212 (mm) REVERT: G 134 LEU cc_start: -0.0297 (OUTLIER) cc_final: -0.0550 (mt) REVERT: H 22 LEU cc_start: 0.2782 (OUTLIER) cc_final: 0.2419 (mt) REVERT: H 44 LEU cc_start: -0.0320 (OUTLIER) cc_final: -0.1239 (mm) REVERT: H 134 LEU cc_start: -0.0292 (OUTLIER) cc_final: -0.0542 (mt) REVERT: I 22 LEU cc_start: 0.2784 (OUTLIER) cc_final: 0.2418 (mt) REVERT: I 44 LEU cc_start: -0.0317 (OUTLIER) cc_final: -0.1217 (mm) REVERT: I 134 LEU cc_start: -0.0274 (OUTLIER) cc_final: -0.0510 (mt) REVERT: J 22 LEU cc_start: 0.2766 (OUTLIER) cc_final: 0.2392 (mt) REVERT: J 44 LEU cc_start: -0.0354 (OUTLIER) cc_final: -0.1238 (mm) REVERT: J 134 LEU cc_start: -0.0267 (OUTLIER) cc_final: -0.0522 (mt) REVERT: K 22 LEU cc_start: 0.2769 (OUTLIER) cc_final: 0.2405 (mt) REVERT: L 22 LEU cc_start: 0.2769 (OUTLIER) cc_final: 0.2408 (mt) REVERT: L 44 LEU cc_start: -0.0298 (OUTLIER) cc_final: -0.1219 (mm) REVERT: L 134 LEU cc_start: -0.0272 (OUTLIER) cc_final: -0.0522 (mt) REVERT: M 22 LEU cc_start: 0.2742 (OUTLIER) cc_final: 0.2508 (mt) REVERT: M 44 LEU cc_start: -0.0293 (OUTLIER) cc_final: -0.1213 (mm) REVERT: M 134 LEU cc_start: -0.0278 (OUTLIER) cc_final: -0.0525 (mt) REVERT: N 22 LEU cc_start: 0.2744 (OUTLIER) cc_final: 0.2487 (mt) REVERT: N 44 LEU cc_start: -0.0273 (OUTLIER) cc_final: -0.1188 (mm) REVERT: O 22 LEU cc_start: 0.2780 (OUTLIER) cc_final: 0.2413 (mt) REVERT: O 44 LEU cc_start: -0.0321 (OUTLIER) cc_final: -0.1237 (mm) REVERT: O 134 LEU cc_start: -0.0285 (OUTLIER) cc_final: -0.0535 (mt) REVERT: P 22 LEU cc_start: 0.2771 (OUTLIER) cc_final: 0.2411 (mt) REVERT: P 44 LEU cc_start: -0.0305 (OUTLIER) cc_final: -0.1224 (mm) REVERT: P 134 LEU cc_start: -0.0298 (OUTLIER) cc_final: -0.0552 (mt) REVERT: Q 22 LEU cc_start: 0.2774 (OUTLIER) cc_final: 0.2408 (mt) REVERT: Q 44 LEU cc_start: -0.0299 (OUTLIER) cc_final: -0.1234 (mm) REVERT: Q 134 LEU cc_start: -0.0289 (OUTLIER) cc_final: -0.0539 (mt) REVERT: R 22 LEU cc_start: 0.2760 (OUTLIER) cc_final: 0.2396 (mt) REVERT: R 44 LEU cc_start: -0.0297 (OUTLIER) cc_final: -0.1223 (mm) REVERT: R 134 LEU cc_start: -0.0254 (OUTLIER) cc_final: -0.0480 (mt) REVERT: S 22 LEU cc_start: 0.2760 (OUTLIER) cc_final: 0.2403 (mt) REVERT: S 44 LEU cc_start: -0.0384 (OUTLIER) cc_final: -0.1268 (mm) REVERT: S 134 LEU cc_start: -0.0260 (OUTLIER) cc_final: -0.0473 (mt) REVERT: T 22 LEU cc_start: 0.2770 (OUTLIER) cc_final: 0.2385 (mt) REVERT: T 44 LEU cc_start: -0.0292 (OUTLIER) cc_final: -0.1213 (mm) REVERT: V 22 LEU cc_start: 0.2768 (OUTLIER) cc_final: 0.2405 (mt) REVERT: V 44 LEU cc_start: -0.0302 (OUTLIER) cc_final: -0.1184 (mm) REVERT: V 134 LEU cc_start: -0.0266 (OUTLIER) cc_final: -0.0510 (mt) REVERT: W 22 LEU cc_start: 0.2771 (OUTLIER) cc_final: 0.2411 (mt) REVERT: W 44 LEU cc_start: -0.0305 (OUTLIER) cc_final: -0.1223 (mm) REVERT: W 134 LEU cc_start: -0.0253 (OUTLIER) cc_final: -0.0480 (mt) REVERT: X 22 LEU cc_start: 0.2770 (OUTLIER) cc_final: 0.2404 (mt) REVERT: X 134 LEU cc_start: -0.0272 (OUTLIER) cc_final: -0.0503 (mt) outliers start: 107 outliers final: 26 residues processed: 280 average time/residue: 1.0201 time to fit residues: 366.0044 Evaluate side-chains 298 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 214 time to evaluate : 3.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ASN Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain D residue 7 ASN Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain G residue 7 ASN Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain I residue 7 ASN Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 7 ASN Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain K residue 7 ASN Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 134 LEU Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain M residue 7 ASN Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain N residue 7 ASN Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 134 LEU Chi-restraints excluded: chain O residue 7 ASN Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain P residue 7 ASN Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain Q residue 7 ASN Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 134 LEU Chi-restraints excluded: chain R residue 7 ASN Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain S residue 7 ASN Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain T residue 7 ASN Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain V residue 7 ASN Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 134 LEU Chi-restraints excluded: chain W residue 7 ASN Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain X residue 7 ASN Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 134 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 7.9990 chunk 114 optimal weight: 2.9990 chunk 308 optimal weight: 9.9990 chunk 252 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 0.7980 chunk 400 optimal weight: 4.9990 chunk 330 optimal weight: 6.9990 chunk 368 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 297 optimal weight: 3.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 54 GLN U 108 GLN U 132 HIS ** U 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 137 GLN ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN A 54 GLN A 108 GLN ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN B 54 GLN B 108 GLN B 132 HIS ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 137 GLN ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN C 54 GLN C 108 GLN C 132 HIS C 137 GLN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN D 54 GLN D 108 GLN D 132 HIS D 137 GLN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN E 54 GLN E 108 GLN E 132 HIS ** E 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 GLN ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN F 54 GLN F 108 GLN F 132 HIS F 137 GLN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN G 54 GLN G 108 GLN G 137 GLN ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN H 54 GLN H 108 GLN H 132 HIS H 137 GLN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN I 54 GLN I 108 GLN ** I 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 137 GLN ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN J 54 GLN J 108 GLN J 132 HIS J 137 GLN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 19 GLN K 54 GLN K 108 GLN K 132 HIS K 137 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN L 54 GLN L 108 GLN L 132 HIS L 137 GLN ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN M 54 GLN M 108 GLN M 132 HIS M 137 GLN ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 19 GLN N 54 GLN N 108 GLN N 132 HIS N 137 GLN ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN O 54 GLN O 108 GLN O 132 HIS O 137 GLN ** P 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN P 54 GLN P 108 GLN P 132 HIS P 137 GLN ** Q 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN Q 54 GLN Q 108 GLN Q 137 GLN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 GLN R 54 GLN R 108 GLN ** R 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 137 GLN ** S 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 19 GLN S 54 GLN S 108 GLN ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 137 GLN ** T 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 GLN T 54 GLN T 108 GLN T 132 HIS ** T 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 137 GLN ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN V 54 GLN V 108 GLN V 132 HIS V 137 GLN ** W 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 19 GLN W 54 GLN W 108 GLN W 132 HIS ** W 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 137 GLN ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 GLN X 54 GLN X 108 GLN X 132 HIS X 137 GLN Total number of N/Q/H flips: 113 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1374 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 33912 Z= 0.356 Angle : 0.860 10.598 45792 Z= 0.460 Chirality : 0.048 0.202 4896 Planarity : 0.006 0.044 6024 Dihedral : 5.542 19.575 4464 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 4.34 % Allowed : 5.75 % Favored : 89.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.13), residues: 4080 helix: 1.25 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : -1.38 (0.23), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 89 HIS 0.013 0.002 HIS T 132 PHE 0.012 0.003 PHE G 128 TYR 0.038 0.004 TYR G 164 ARG 0.004 0.001 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 240 time to evaluate : 3.373 Fit side-chains REVERT: U 61 HIS cc_start: 0.2650 (m170) cc_final: 0.2133 (m170) REVERT: U 83 LYS cc_start: 0.1884 (OUTLIER) cc_final: 0.1430 (ptmm) REVERT: A 22 LEU cc_start: 0.3569 (OUTLIER) cc_final: 0.2948 (mp) REVERT: A 61 HIS cc_start: 0.2623 (m170) cc_final: 0.2124 (m170) REVERT: A 96 MET cc_start: 0.1034 (mmp) cc_final: -0.1219 (mmp) REVERT: A 134 LEU cc_start: -0.0323 (OUTLIER) cc_final: -0.0774 (mt) REVERT: B 44 LEU cc_start: -0.0119 (OUTLIER) cc_final: -0.1112 (mm) REVERT: B 61 HIS cc_start: 0.2671 (m170) cc_final: 0.2186 (m170) REVERT: B 96 MET cc_start: 0.1044 (mmp) cc_final: -0.1183 (mmp) REVERT: C 22 LEU cc_start: 0.3576 (OUTLIER) cc_final: 0.2962 (mp) REVERT: C 44 LEU cc_start: -0.0101 (OUTLIER) cc_final: -0.1089 (mm) REVERT: C 61 HIS cc_start: 0.2682 (m170) cc_final: 0.2177 (m170) REVERT: C 96 MET cc_start: 0.0985 (mmp) cc_final: -0.1021 (mmp) REVERT: C 134 LEU cc_start: -0.0273 (OUTLIER) cc_final: -0.0727 (mt) REVERT: D 22 LEU cc_start: 0.3613 (OUTLIER) cc_final: 0.3030 (mp) REVERT: D 44 LEU cc_start: -0.0118 (OUTLIER) cc_final: -0.1088 (mm) REVERT: D 61 HIS cc_start: 0.2687 (m170) cc_final: 0.2187 (m170) REVERT: D 96 MET cc_start: 0.1001 (mmp) cc_final: -0.1024 (mmp) REVERT: D 134 LEU cc_start: -0.0287 (OUTLIER) cc_final: -0.0744 (mt) REVERT: E 22 LEU cc_start: 0.3573 (OUTLIER) cc_final: 0.2924 (mp) REVERT: E 61 HIS cc_start: 0.2669 (m170) cc_final: 0.2151 (m170) REVERT: E 96 MET cc_start: 0.1007 (mmp) cc_final: -0.1279 (mmp) REVERT: E 134 LEU cc_start: -0.0317 (OUTLIER) cc_final: -0.0750 (mt) REVERT: F 44 LEU cc_start: -0.0106 (OUTLIER) cc_final: -0.1103 (mm) REVERT: F 61 HIS cc_start: 0.2681 (m170) cc_final: 0.2180 (m170) REVERT: F 96 MET cc_start: 0.0983 (mmp) cc_final: -0.1270 (mmp) REVERT: F 134 LEU cc_start: -0.0296 (OUTLIER) cc_final: -0.0760 (mt) REVERT: G 22 LEU cc_start: 0.3565 (OUTLIER) cc_final: 0.2808 (mp) REVERT: G 44 LEU cc_start: -0.0003 (OUTLIER) cc_final: -0.1071 (mm) REVERT: G 61 HIS cc_start: 0.2695 (m170) cc_final: 0.2178 (m170) REVERT: G 134 LEU cc_start: -0.0343 (OUTLIER) cc_final: -0.0789 (mt) REVERT: H 22 LEU cc_start: 0.3573 (OUTLIER) cc_final: 0.2813 (mp) REVERT: H 44 LEU cc_start: -0.0076 (OUTLIER) cc_final: -0.1126 (mm) REVERT: H 61 HIS cc_start: 0.2687 (m170) cc_final: 0.2171 (m170) REVERT: H 134 LEU cc_start: -0.0294 (OUTLIER) cc_final: -0.0739 (mt) REVERT: I 22 LEU cc_start: 0.3575 (OUTLIER) cc_final: 0.2819 (mp) REVERT: I 44 LEU cc_start: -0.0049 (OUTLIER) cc_final: -0.1153 (mm) REVERT: I 61 HIS cc_start: 0.2695 (m170) cc_final: 0.2178 (m170) REVERT: I 96 MET cc_start: 0.1008 (mmp) cc_final: -0.1224 (mmp) REVERT: I 134 LEU cc_start: -0.0330 (OUTLIER) cc_final: -0.0783 (mt) REVERT: I 154 MET cc_start: 0.1760 (OUTLIER) cc_final: 0.1458 (mpt) REVERT: J 22 LEU cc_start: 0.3570 (OUTLIER) cc_final: 0.2911 (mp) REVERT: J 44 LEU cc_start: -0.0061 (OUTLIER) cc_final: -0.1124 (mm) REVERT: J 61 HIS cc_start: 0.2693 (m170) cc_final: 0.2181 (m170) REVERT: J 96 MET cc_start: 0.0987 (mmp) cc_final: -0.1254 (mmp) REVERT: J 134 LEU cc_start: -0.0274 (OUTLIER) cc_final: -0.0741 (mt) REVERT: J 154 MET cc_start: 0.1819 (OUTLIER) cc_final: 0.1411 (mpt) REVERT: K 22 LEU cc_start: 0.3567 (OUTLIER) cc_final: 0.2903 (mp) REVERT: K 61 HIS cc_start: 0.2649 (m170) cc_final: 0.2145 (m170) REVERT: K 96 MET cc_start: 0.1032 (mmp) cc_final: -0.1199 (mmp) REVERT: L 22 LEU cc_start: 0.3574 (OUTLIER) cc_final: 0.2814 (mp) REVERT: L 44 LEU cc_start: -0.0107 (OUTLIER) cc_final: -0.1089 (mm) REVERT: L 61 HIS cc_start: 0.2677 (m170) cc_final: 0.2177 (m170) REVERT: M 22 LEU cc_start: 0.3542 (OUTLIER) cc_final: 0.2933 (mp) REVERT: M 44 LEU cc_start: -0.0109 (OUTLIER) cc_final: -0.1089 (mm) REVERT: M 61 HIS cc_start: 0.2679 (m170) cc_final: 0.2171 (m170) REVERT: M 134 LEU cc_start: -0.0303 (OUTLIER) cc_final: -0.0762 (mt) REVERT: N 22 LEU cc_start: 0.3556 (OUTLIER) cc_final: 0.2952 (mp) REVERT: N 44 LEU cc_start: -0.0094 (OUTLIER) cc_final: -0.1082 (mm) REVERT: N 61 HIS cc_start: 0.2696 (m170) cc_final: 0.2206 (m170) REVERT: N 96 MET cc_start: 0.0958 (mmp) cc_final: -0.1252 (mmp) REVERT: O 22 LEU cc_start: 0.3567 (OUTLIER) cc_final: 0.2813 (mp) REVERT: O 44 LEU cc_start: -0.0134 (OUTLIER) cc_final: -0.1087 (mm) REVERT: O 61 HIS cc_start: 0.2685 (m170) cc_final: 0.2175 (m170) REVERT: O 134 LEU cc_start: -0.0293 (OUTLIER) cc_final: -0.0745 (mt) REVERT: P 22 LEU cc_start: 0.3574 (OUTLIER) cc_final: 0.2905 (mp) REVERT: P 44 LEU cc_start: -0.0109 (OUTLIER) cc_final: -0.1112 (mm) REVERT: P 61 HIS cc_start: 0.2689 (m170) cc_final: 0.2184 (m170) REVERT: P 96 MET cc_start: 0.1008 (mmp) cc_final: -0.1248 (mmp) REVERT: P 134 LEU cc_start: -0.0305 (OUTLIER) cc_final: -0.0768 (mt) REVERT: Q 22 LEU cc_start: 0.3568 (OUTLIER) cc_final: 0.2811 (mp) REVERT: Q 44 LEU cc_start: -0.0115 (OUTLIER) cc_final: -0.1093 (mm) REVERT: Q 61 HIS cc_start: 0.2691 (m170) cc_final: 0.2184 (m170) REVERT: R 22 LEU cc_start: 0.3572 (OUTLIER) cc_final: 0.2809 (mp) REVERT: R 44 LEU cc_start: -0.0110 (OUTLIER) cc_final: -0.1092 (mm) REVERT: R 61 HIS cc_start: 0.2689 (m170) cc_final: 0.2182 (m170) REVERT: R 134 LEU cc_start: -0.0343 (OUTLIER) cc_final: -0.0797 (mt) REVERT: S 22 LEU cc_start: 0.3576 (OUTLIER) cc_final: 0.2815 (mp) REVERT: S 44 LEU cc_start: 0.0057 (OUTLIER) cc_final: -0.1183 (mm) REVERT: S 61 HIS cc_start: 0.2688 (m170) cc_final: 0.2182 (m170) REVERT: S 134 LEU cc_start: -0.0352 (OUTLIER) cc_final: -0.0814 (mt) REVERT: T 22 LEU cc_start: 0.3569 (OUTLIER) cc_final: 0.2923 (mp) REVERT: T 44 LEU cc_start: -0.0116 (OUTLIER) cc_final: -0.1086 (mm) REVERT: T 61 HIS cc_start: 0.2620 (m170) cc_final: 0.2071 (m170) REVERT: T 134 LEU cc_start: -0.0310 (OUTLIER) cc_final: -0.0785 (mt) REVERT: V 22 LEU cc_start: 0.3574 (OUTLIER) cc_final: 0.2912 (mp) REVERT: V 44 LEU cc_start: -0.0106 (OUTLIER) cc_final: -0.1104 (mm) REVERT: V 61 HIS cc_start: 0.2683 (m170) cc_final: 0.2180 (m170) REVERT: V 96 MET cc_start: 0.0998 (mmp) cc_final: -0.1230 (mmp) REVERT: V 134 LEU cc_start: -0.0298 (OUTLIER) cc_final: -0.0766 (mt) REVERT: W 22 LEU cc_start: 0.3585 (OUTLIER) cc_final: 0.2823 (mp) REVERT: W 44 LEU cc_start: -0.0126 (OUTLIER) cc_final: -0.1117 (mm) REVERT: W 61 HIS cc_start: 0.2678 (m170) cc_final: 0.2178 (m170) REVERT: W 96 MET cc_start: 0.1004 (mmp) cc_final: -0.1161 (mmp) REVERT: W 134 LEU cc_start: -0.0304 (OUTLIER) cc_final: -0.0738 (mt) REVERT: X 22 LEU cc_start: 0.3586 (OUTLIER) cc_final: 0.2928 (mp) REVERT: X 61 HIS cc_start: 0.2687 (m170) cc_final: 0.2176 (m170) REVERT: X 134 LEU cc_start: -0.0299 (OUTLIER) cc_final: -0.0746 (mt) outliers start: 151 outliers final: 28 residues processed: 329 average time/residue: 1.1721 time to fit residues: 478.2882 Evaluate side-chains 329 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 240 time to evaluate : 3.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 83 LYS Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 154 MET Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain J residue 134 LEU Chi-restraints excluded: chain J residue 154 MET Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 134 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 134 LEU Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 134 LEU Chi-restraints excluded: chain V residue 149 THR Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain W residue 149 THR Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 65 LEU Chi-restraints excluded: chain X residue 134 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 9.9990 chunk 279 optimal weight: 0.9990 chunk 192 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 177 optimal weight: 0.0980 chunk 249 optimal weight: 0.9990 chunk 372 optimal weight: 0.4980 chunk 394 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 353 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 135 ASN A 7 ASN B 7 ASN B 135 ASN C 7 ASN C 19 GLN D 7 ASN D 19 GLN E 7 ASN E 19 GLN F 7 ASN G 3 GLN G 7 ASN G 19 GLN H 7 ASN H 19 GLN I 7 ASN I 19 GLN J 3 GLN J 7 ASN J 19 GLN K 3 GLN K 7 ASN K 19 GLN L 7 ASN L 19 GLN M 19 GLN N 3 GLN N 7 ASN N 19 GLN O 7 ASN O 19 GLN P 19 GLN Q 7 ASN Q 19 GLN R 3 GLN R 7 ASN R 19 GLN S 7 ASN S 19 GLN T 7 ASN T 19 GLN V 7 ASN V 19 GLN W 3 GLN W 7 ASN W 19 GLN X 7 ASN X 19 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1128 moved from start: 0.4930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 33912 Z= 0.150 Angle : 0.547 8.823 45792 Z= 0.285 Chirality : 0.037 0.161 4896 Planarity : 0.003 0.033 6024 Dihedral : 4.505 19.314 4464 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 3.13 % Allowed : 7.27 % Favored : 89.60 % 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: 3.01 (0.13), residues: 4080 helix: 2.74 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : -0.94 (0.23), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP N 89 HIS 0.003 0.001 HIS X 169 PHE 0.010 0.001 PHE G 47 TYR 0.024 0.002 TYR I 164 ARG 0.002 0.000 ARG M 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 222 time to evaluate : 3.778 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: U 61 HIS cc_start: 0.2644 (m170) cc_final: 0.2083 (m170) REVERT: U 83 LYS cc_start: 0.1615 (OUTLIER) cc_final: 0.1335 (ptmm) REVERT: A 22 LEU cc_start: 0.2497 (OUTLIER) cc_final: 0.2291 (mt) REVERT: A 61 HIS cc_start: 0.2543 (m170) cc_final: 0.2050 (m90) REVERT: A 96 MET cc_start: 0.0600 (mmp) cc_final: -0.0957 (mmp) REVERT: A 134 LEU cc_start: -0.0561 (OUTLIER) cc_final: -0.0943 (mt) REVERT: B 44 LEU cc_start: -0.0417 (OUTLIER) cc_final: -0.0975 (mm) REVERT: B 61 HIS cc_start: 0.2623 (m170) cc_final: 0.2110 (m90) REVERT: C 22 LEU cc_start: 0.2618 (OUTLIER) cc_final: 0.2222 (mt) REVERT: C 44 LEU cc_start: -0.0415 (OUTLIER) cc_final: -0.0956 (mm) REVERT: C 96 MET cc_start: 0.0441 (mmp) cc_final: -0.0948 (mmp) REVERT: D 22 LEU cc_start: 0.2469 (OUTLIER) cc_final: 0.2248 (mt) REVERT: D 44 LEU cc_start: -0.0499 (OUTLIER) cc_final: -0.1044 (mm) REVERT: D 61 HIS cc_start: 0.2554 (m170) cc_final: 0.2044 (m170) REVERT: D 134 LEU cc_start: -0.0602 (OUTLIER) cc_final: -0.0987 (mt) REVERT: E 22 LEU cc_start: 0.2632 (OUTLIER) cc_final: 0.2271 (mt) REVERT: E 134 LEU cc_start: -0.0545 (OUTLIER) cc_final: -0.0956 (mt) REVERT: F 44 LEU cc_start: -0.0386 (OUTLIER) cc_final: -0.0958 (mm) REVERT: F 61 HIS cc_start: 0.2586 (m170) cc_final: 0.2047 (m170) REVERT: F 96 MET cc_start: 0.0481 (mmp) cc_final: -0.0983 (mmp) REVERT: F 134 LEU cc_start: -0.0605 (OUTLIER) cc_final: -0.0978 (mt) REVERT: G 22 LEU cc_start: 0.2616 (OUTLIER) cc_final: 0.2269 (mt) REVERT: G 44 LEU cc_start: -0.0262 (OUTLIER) cc_final: -0.0835 (mm) REVERT: G 61 HIS cc_start: 0.2587 (m170) cc_final: 0.2067 (m170) REVERT: G 96 MET cc_start: 0.0241 (mmp) cc_final: -0.1192 (mmp) REVERT: H 22 LEU cc_start: 0.2597 (OUTLIER) cc_final: 0.2298 (mt) REVERT: H 44 LEU cc_start: -0.0435 (OUTLIER) cc_final: -0.1068 (mm) REVERT: H 61 HIS cc_start: 0.2564 (m170) cc_final: 0.2048 (m170) REVERT: H 96 MET cc_start: 0.0269 (mmp) cc_final: -0.1165 (mmp) REVERT: H 134 LEU cc_start: -0.0597 (OUTLIER) cc_final: -0.0960 (mt) REVERT: I 22 LEU cc_start: 0.2601 (OUTLIER) cc_final: 0.2313 (mt) REVERT: I 44 LEU cc_start: -0.0280 (OUTLIER) cc_final: -0.0941 (mm) REVERT: I 61 HIS cc_start: 0.2569 (m170) cc_final: 0.2049 (m170) REVERT: I 96 MET cc_start: 0.0566 (mmp) cc_final: -0.0968 (mmp) REVERT: I 134 LEU cc_start: -0.0583 (OUTLIER) cc_final: -0.0982 (mt) REVERT: J 22 LEU cc_start: 0.2594 (OUTLIER) cc_final: 0.2163 (mt) REVERT: J 44 LEU cc_start: -0.0421 (OUTLIER) cc_final: -0.1083 (mm) REVERT: J 61 HIS cc_start: 0.2557 (m170) cc_final: 0.2042 (m170) REVERT: J 96 MET cc_start: 0.0561 (mmp) cc_final: -0.0993 (mmp) REVERT: K 22 LEU cc_start: 0.2630 (OUTLIER) cc_final: 0.2248 (mt) REVERT: L 22 LEU cc_start: 0.2598 (OUTLIER) cc_final: 0.2305 (mt) REVERT: L 44 LEU cc_start: -0.0408 (OUTLIER) cc_final: -0.1000 (mm) REVERT: L 61 HIS cc_start: 0.2558 (m170) cc_final: 0.2043 (m170) REVERT: L 96 MET cc_start: 0.0238 (mmp) cc_final: -0.1180 (mmp) REVERT: L 134 LEU cc_start: -0.0596 (OUTLIER) cc_final: -0.0970 (mt) REVERT: M 22 LEU cc_start: 0.2666 (OUTLIER) cc_final: 0.2456 (mt) REVERT: M 44 LEU cc_start: -0.0390 (OUTLIER) cc_final: -0.0969 (mm) REVERT: M 61 HIS cc_start: 0.2562 (m170) cc_final: 0.2050 (m170) REVERT: M 96 MET cc_start: 0.0268 (mmp) cc_final: -0.1181 (mmp) REVERT: M 134 LEU cc_start: -0.0609 (OUTLIER) cc_final: -0.0944 (mt) REVERT: N 44 LEU cc_start: -0.0395 (OUTLIER) cc_final: -0.0971 (mm) REVERT: N 61 HIS cc_start: 0.2607 (m170) cc_final: 0.2095 (m170) REVERT: N 149 THR cc_start: 0.5244 (OUTLIER) cc_final: 0.4984 (t) REVERT: O 22 LEU cc_start: 0.2589 (OUTLIER) cc_final: 0.2287 (mt) REVERT: O 44 LEU cc_start: -0.0359 (OUTLIER) cc_final: -0.0914 (mm) REVERT: O 61 HIS cc_start: 0.2588 (m170) cc_final: 0.2075 (m170) REVERT: O 96 MET cc_start: 0.0266 (mmp) cc_final: -0.1167 (mmp) REVERT: O 134 LEU cc_start: -0.0602 (OUTLIER) cc_final: -0.0978 (mt) REVERT: P 22 LEU cc_start: 0.2600 (OUTLIER) cc_final: 0.2306 (mt) REVERT: P 44 LEU cc_start: -0.0416 (OUTLIER) cc_final: -0.0983 (mm) REVERT: P 61 HIS cc_start: 0.2555 (m170) cc_final: 0.2035 (m170) REVERT: P 96 MET cc_start: 0.0516 (mmp) cc_final: -0.0947 (mmp) REVERT: P 134 LEU cc_start: -0.0615 (OUTLIER) cc_final: -0.0973 (mt) REVERT: Q 22 LEU cc_start: 0.2590 (OUTLIER) cc_final: 0.2291 (mt) REVERT: Q 44 LEU cc_start: -0.0345 (OUTLIER) cc_final: -0.0934 (mm) REVERT: Q 61 HIS cc_start: 0.2589 (m170) cc_final: 0.2078 (m170) REVERT: Q 96 MET cc_start: 0.0252 (mmp) cc_final: -0.1183 (mmp) REVERT: R 22 LEU cc_start: 0.2581 (OUTLIER) cc_final: 0.2296 (mt) REVERT: R 44 LEU cc_start: -0.0384 (OUTLIER) cc_final: -0.0958 (mm) REVERT: R 61 HIS cc_start: 0.2556 (m170) cc_final: 0.2047 (m170) REVERT: R 96 MET cc_start: 0.0266 (mmp) cc_final: -0.1185 (mmp) REVERT: R 134 LEU cc_start: -0.0586 (OUTLIER) cc_final: -0.0966 (mt) REVERT: S 22 LEU cc_start: 0.2583 (OUTLIER) cc_final: 0.2288 (mt) REVERT: S 44 LEU cc_start: -0.0141 (OUTLIER) cc_final: -0.1057 (mm) REVERT: S 61 HIS cc_start: 0.2558 (m170) cc_final: 0.2031 (m170) REVERT: S 96 MET cc_start: 0.0266 (mmp) cc_final: -0.1172 (mmp) REVERT: S 134 LEU cc_start: -0.0594 (OUTLIER) cc_final: -0.0975 (mt) REVERT: T 22 LEU cc_start: 0.2642 (OUTLIER) cc_final: 0.2283 (mt) REVERT: T 44 LEU cc_start: -0.0427 (OUTLIER) cc_final: -0.1000 (mm) REVERT: T 96 MET cc_start: 0.0231 (mmp) cc_final: -0.1189 (mmp) REVERT: T 134 LEU cc_start: -0.0587 (OUTLIER) cc_final: -0.0998 (mt) REVERT: V 22 LEU cc_start: 0.2587 (OUTLIER) cc_final: 0.2294 (mt) REVERT: V 44 LEU cc_start: -0.0402 (OUTLIER) cc_final: -0.1011 (mm) REVERT: V 61 HIS cc_start: 0.2552 (m170) cc_final: 0.2047 (m170) REVERT: V 96 MET cc_start: 0.0561 (mmp) cc_final: -0.1017 (mmp) REVERT: V 134 LEU cc_start: -0.0576 (OUTLIER) cc_final: -0.0968 (mt) REVERT: W 22 LEU cc_start: 0.2599 (OUTLIER) cc_final: 0.2302 (mt) REVERT: W 44 LEU cc_start: -0.0446 (OUTLIER) cc_final: -0.1013 (mm) REVERT: W 61 HIS cc_start: 0.2556 (m170) cc_final: 0.2041 (m170) REVERT: W 134 LEU cc_start: -0.0585 (OUTLIER) cc_final: -0.0964 (mt) REVERT: W 149 THR cc_start: 0.5353 (OUTLIER) cc_final: 0.5136 (t) REVERT: X 22 LEU cc_start: 0.2595 (OUTLIER) cc_final: 0.2281 (mt) REVERT: X 61 HIS cc_start: 0.2559 (m170) cc_final: 0.2027 (m170) REVERT: X 96 MET cc_start: 0.0275 (mmp) cc_final: -0.1161 (mmp) REVERT: X 134 LEU cc_start: -0.0571 (OUTLIER) cc_final: -0.0952 (mt) outliers start: 109 outliers final: 5 residues processed: 295 average time/residue: 1.0981 time to fit residues: 409.8928 Evaluate side-chains 264 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 201 time to evaluate : 3.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 83 LYS Chi-restraints excluded: chain U residue 149 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 134 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 134 LEU Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 134 LEU Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 134 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 134 LEU Chi-restraints excluded: chain P residue 5 ARG Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 134 LEU Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 134 LEU Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 134 LEU Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain W residue 134 LEU Chi-restraints excluded: chain W residue 149 THR Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 134 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 4.9990 chunk 223 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 293 optimal weight: 0.8980 chunk 162 optimal weight: 9.9990 chunk 336 optimal weight: 6.9990 chunk 272 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 7.9990 chunk 353 optimal weight: 0.9990 chunk 99 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 19 GLN ** U 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 HIS ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 3 GLN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 3 GLN ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 7 ASN N 19 GLN ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 GLN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 19 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 3 GLN ** W 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 19 GLN ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 GLN ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1484 moved from start: 0.5862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 33912 Z= 0.303 Angle : 0.782 18.768 45792 Z= 0.418 Chirality : 0.044 0.249 4896 Planarity : 0.005 0.038 6024 Dihedral : 5.225 18.962 4464 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.84 % Allowed : 9.71 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.13), residues: 4080 helix: 1.48 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -1.71 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 89 HIS 0.009 0.002 HIS A 132 PHE 0.011 0.003 PHE X 51 TYR 0.028 0.003 TYR E 164 ARG 0.006 0.001 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 198 time to evaluate : 2.955 Fit side-chains REVERT: U 61 HIS cc_start: 0.2830 (m170) cc_final: 0.2258 (m170) REVERT: U 66 MET cc_start: 0.0723 (ttm) cc_final: 0.0380 (ptt) REVERT: U 96 MET cc_start: 0.1021 (mmp) cc_final: 0.0366 (mmm) REVERT: A 22 LEU cc_start: 0.3338 (OUTLIER) cc_final: 0.2866 (mp) REVERT: A 61 HIS cc_start: 0.2756 (m170) cc_final: 0.2224 (m170) REVERT: A 96 MET cc_start: 0.0913 (mmp) cc_final: -0.1264 (mmp) REVERT: A 134 LEU cc_start: -0.0315 (OUTLIER) cc_final: -0.0731 (mt) REVERT: B 44 LEU cc_start: -0.0206 (OUTLIER) cc_final: -0.1293 (mm) REVERT: B 61 HIS cc_start: 0.2865 (m170) cc_final: 0.2341 (m170) REVERT: B 66 MET cc_start: 0.0763 (ttm) cc_final: 0.0350 (ptp) REVERT: B 96 MET cc_start: 0.0922 (mmp) cc_final: -0.1134 (mmp) REVERT: B 134 LEU cc_start: -0.0183 (OUTLIER) cc_final: -0.0438 (mt) REVERT: C 22 LEU cc_start: 0.3248 (OUTLIER) cc_final: 0.2555 (mp) REVERT: C 44 LEU cc_start: -0.0182 (OUTLIER) cc_final: -0.1236 (mm) REVERT: C 61 HIS cc_start: 0.2929 (m170) cc_final: 0.2432 (m170) REVERT: C 96 MET cc_start: 0.0845 (mmp) cc_final: -0.0980 (mmp) REVERT: D 22 LEU cc_start: 0.3333 (OUTLIER) cc_final: 0.2890 (mp) REVERT: D 44 LEU cc_start: -0.0194 (OUTLIER) cc_final: -0.1244 (mm) REVERT: D 61 HIS cc_start: 0.2818 (m170) cc_final: 0.2307 (m90) REVERT: D 96 MET cc_start: 0.0815 (mmp) cc_final: -0.1319 (mmp) REVERT: E 22 LEU cc_start: 0.3211 (OUTLIER) cc_final: 0.2594 (mp) REVERT: E 61 HIS cc_start: 0.2898 (m170) cc_final: 0.2358 (m170) REVERT: E 71 GLN cc_start: 0.2083 (OUTLIER) cc_final: 0.1394 (pt0) REVERT: E 96 MET cc_start: 0.0872 (mmp) cc_final: -0.1004 (mmp) REVERT: E 154 MET cc_start: 0.2987 (mmt) cc_final: 0.2762 (mmt) REVERT: F 44 LEU cc_start: -0.0181 (OUTLIER) cc_final: -0.1242 (mm) REVERT: F 61 HIS cc_start: 0.2852 (m170) cc_final: 0.2316 (m170) REVERT: F 96 MET cc_start: 0.0846 (mmp) cc_final: -0.1008 (mmp) REVERT: G 22 LEU cc_start: 0.3372 (OUTLIER) cc_final: 0.2876 (mp) REVERT: G 44 LEU cc_start: -0.0060 (OUTLIER) cc_final: -0.1144 (mm) REVERT: G 61 HIS cc_start: 0.2817 (m170) cc_final: 0.2301 (m170) REVERT: G 66 MET cc_start: 0.0785 (ttm) cc_final: 0.0405 (ptp) REVERT: G 96 MET cc_start: 0.0828 (mmp) cc_final: -0.1530 (mmp) REVERT: H 22 LEU cc_start: 0.3350 (OUTLIER) cc_final: 0.2853 (mp) REVERT: H 44 LEU cc_start: -0.0228 (OUTLIER) cc_final: -0.1345 (mm) REVERT: H 61 HIS cc_start: 0.2842 (m170) cc_final: 0.2309 (m170) REVERT: H 96 MET cc_start: 0.0850 (mmp) cc_final: -0.1513 (mmp) REVERT: I 22 LEU cc_start: 0.3356 (OUTLIER) cc_final: 0.2865 (mp) REVERT: I 44 LEU cc_start: -0.0123 (OUTLIER) cc_final: -0.1231 (mm) REVERT: I 61 HIS cc_start: 0.2826 (m170) cc_final: 0.2303 (m90) REVERT: I 96 MET cc_start: 0.0903 (mmp) cc_final: -0.1358 (mmp) REVERT: J 22 LEU cc_start: 0.3364 (OUTLIER) cc_final: 0.2878 (mp) REVERT: J 44 LEU cc_start: -0.0219 (OUTLIER) cc_final: -0.1342 (mm) REVERT: J 61 HIS cc_start: 0.2827 (m170) cc_final: 0.2303 (m170) REVERT: J 66 MET cc_start: 0.0793 (ttm) cc_final: 0.0468 (ptt) REVERT: J 96 MET cc_start: 0.0864 (mmp) cc_final: -0.1302 (mmp) REVERT: K 22 LEU cc_start: 0.3204 (OUTLIER) cc_final: 0.2600 (mp) REVERT: K 61 HIS cc_start: 0.2911 (m170) cc_final: 0.2391 (m170) REVERT: K 96 MET cc_start: 0.0871 (mmp) cc_final: -0.1029 (mmp) REVERT: L 22 LEU cc_start: 0.3343 (OUTLIER) cc_final: 0.2857 (mp) REVERT: L 44 LEU cc_start: -0.0182 (OUTLIER) cc_final: -0.1290 (mm) REVERT: L 61 HIS cc_start: 0.2831 (m170) cc_final: 0.2308 (m170) REVERT: L 96 MET cc_start: 0.0845 (mmp) cc_final: -0.1537 (mmp) REVERT: M 22 LEU cc_start: 0.3402 (OUTLIER) cc_final: 0.2956 (mp) REVERT: M 44 LEU cc_start: -0.0178 (OUTLIER) cc_final: -0.1266 (mm) REVERT: M 61 HIS cc_start: 0.2840 (m170) cc_final: 0.2318 (m170) REVERT: M 66 MET cc_start: 0.0802 (ttm) cc_final: 0.0418 (ptp) REVERT: M 96 MET cc_start: 0.0844 (mmp) cc_final: -0.1512 (mmp) REVERT: N 22 LEU cc_start: 0.3191 (OUTLIER) cc_final: 0.2612 (mp) REVERT: N 44 LEU cc_start: -0.0193 (OUTLIER) cc_final: -0.1262 (mm) REVERT: N 61 HIS cc_start: 0.2855 (m170) cc_final: 0.2324 (m90) REVERT: N 66 MET cc_start: 0.0599 (ttm) cc_final: 0.0372 (ptp) REVERT: N 96 MET cc_start: 0.0858 (mmp) cc_final: -0.1234 (mmp) REVERT: O 22 LEU cc_start: 0.3338 (OUTLIER) cc_final: 0.2853 (mp) REVERT: O 44 LEU cc_start: -0.0141 (OUTLIER) cc_final: -0.1230 (mm) REVERT: O 61 HIS cc_start: 0.2845 (m170) cc_final: 0.2326 (m90) REVERT: O 96 MET cc_start: 0.0860 (mmp) cc_final: -0.1505 (mmp) REVERT: P 22 LEU cc_start: 0.3358 (OUTLIER) cc_final: 0.2855 (mp) REVERT: P 44 LEU cc_start: -0.0198 (OUTLIER) cc_final: -0.1275 (mm) REVERT: P 61 HIS cc_start: 0.2838 (m170) cc_final: 0.2310 (m170) REVERT: P 96 MET cc_start: 0.0846 (mmp) cc_final: -0.0981 (mmp) REVERT: Q 22 LEU cc_start: 0.3348 (OUTLIER) cc_final: 0.2859 (mp) REVERT: Q 44 LEU cc_start: -0.0212 (OUTLIER) cc_final: -0.1312 (mm) REVERT: Q 61 HIS cc_start: 0.2832 (m170) cc_final: 0.2315 (m90) REVERT: Q 96 MET cc_start: 0.0859 (mmp) cc_final: -0.1508 (mmp) REVERT: R 22 LEU cc_start: 0.3348 (OUTLIER) cc_final: 0.2848 (mp) REVERT: R 44 LEU cc_start: -0.0191 (OUTLIER) cc_final: -0.1252 (mm) REVERT: R 61 HIS cc_start: 0.2834 (m170) cc_final: 0.2309 (m170) REVERT: R 66 MET cc_start: 0.0799 (ttm) cc_final: 0.0403 (ptp) REVERT: R 96 MET cc_start: 0.0850 (mmp) cc_final: -0.1505 (mmp) REVERT: S 22 LEU cc_start: 0.3345 (OUTLIER) cc_final: 0.2854 (mp) REVERT: S 44 LEU cc_start: 0.0096 (OUTLIER) cc_final: -0.1134 (mm) REVERT: S 61 HIS cc_start: 0.2837 (m170) cc_final: 0.2311 (m170) REVERT: S 96 MET cc_start: 0.0850 (mmp) cc_final: -0.1513 (mmp) REVERT: T 22 LEU cc_start: 0.3188 (OUTLIER) cc_final: 0.2568 (mp) REVERT: T 44 LEU cc_start: -0.0186 (OUTLIER) cc_final: -0.1274 (mm) REVERT: T 61 HIS cc_start: 0.2833 (m170) cc_final: 0.2292 (m170) REVERT: T 71 GLN cc_start: 0.2068 (OUTLIER) cc_final: 0.1413 (pt0) REVERT: T 96 MET cc_start: 0.0842 (mmp) cc_final: -0.1531 (mmp) REVERT: T 134 LEU cc_start: -0.0441 (OUTLIER) cc_final: -0.0912 (mt) REVERT: V 22 LEU cc_start: 0.3347 (OUTLIER) cc_final: 0.2859 (mp) REVERT: V 44 LEU cc_start: -0.0191 (OUTLIER) cc_final: -0.1293 (mm) REVERT: V 61 HIS cc_start: 0.2830 (m170) cc_final: 0.2308 (m170) REVERT: V 96 MET cc_start: 0.0891 (mmp) cc_final: -0.1331 (mmp) REVERT: W 22 LEU cc_start: 0.3355 (OUTLIER) cc_final: 0.2845 (mp) REVERT: W 44 LEU cc_start: -0.0181 (OUTLIER) cc_final: -0.1262 (mm) REVERT: W 61 HIS cc_start: 0.2832 (m170) cc_final: 0.2303 (m170) REVERT: W 66 MET cc_start: 0.0760 (ttm) cc_final: 0.0459 (ptt) REVERT: W 96 MET cc_start: 0.0897 (mmp) cc_final: -0.1101 (mmp) REVERT: X 22 LEU cc_start: 0.3386 (OUTLIER) cc_final: 0.2900 (mp) REVERT: X 61 HIS cc_start: 0.2818 (m170) cc_final: 0.2283 (m170) REVERT: X 66 MET cc_start: 0.0770 (ttm) cc_final: 0.0366 (ptp) REVERT: X 96 MET cc_start: 0.0895 (mmp) cc_final: -0.1473 (mmp) outliers start: 99 outliers final: 35 residues processed: 288 average time/residue: 1.0178 time to fit residues: 373.8447 Evaluate side-chains 278 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 198 time to evaluate : 3.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 138 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 138 VAL Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 71 GLN Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 138 VAL Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 138 VAL Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 138 VAL Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 138 VAL Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain N residue 7 ASN Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 138 VAL Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain P residue 138 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 138 VAL Chi-restraints excluded: chain Q residue 154 MET Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 65 LEU Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 71 GLN Chi-restraints excluded: chain T residue 134 LEU Chi-restraints excluded: chain T residue 138 VAL Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 138 VAL Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 138 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 4.9990 chunk 355 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 231 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 394 optimal weight: 3.9990 chunk 327 optimal weight: 0.0970 chunk 182 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 207 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 135 ASN ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 19 GLN ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 3 GLN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 135 ASN ** S 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1340 moved from start: 0.5807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 33912 Z= 0.181 Angle : 0.590 9.964 45792 Z= 0.315 Chirality : 0.039 0.396 4896 Planarity : 0.003 0.039 6024 Dihedral : 4.630 20.432 4464 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.79 % Allowed : 10.23 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.13), residues: 4080 helix: 2.17 (0.08), residues: 3168 sheet: None (None), residues: 0 loop : -1.66 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 89 HIS 0.004 0.001 HIS C 124 PHE 0.012 0.002 PHE X 51 TYR 0.018 0.002 TYR U 164 ARG 0.003 0.000 ARG N 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 180 time to evaluate : 3.429 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: U 61 HIS cc_start: 0.2860 (m170) cc_final: 0.2243 (m170) REVERT: U 66 MET cc_start: 0.0594 (ttm) cc_final: 0.0338 (ptt) REVERT: U 96 MET cc_start: 0.0869 (mmp) cc_final: 0.0375 (mmm) REVERT: A 22 LEU cc_start: 0.3014 (OUTLIER) cc_final: 0.2547 (mp) REVERT: A 61 HIS cc_start: 0.2764 (m170) cc_final: 0.2243 (m90) REVERT: A 96 MET cc_start: 0.0712 (mmp) cc_final: -0.1115 (mmp) REVERT: A 134 LEU cc_start: -0.0385 (OUTLIER) cc_final: -0.0670 (mt) REVERT: B 44 LEU cc_start: -0.0412 (OUTLIER) cc_final: -0.1088 (mm) REVERT: B 61 HIS cc_start: 0.2853 (m170) cc_final: 0.2309 (m90) REVERT: B 66 MET cc_start: 0.0562 (ttm) cc_final: 0.0251 (ptp) REVERT: B 96 MET cc_start: 0.0724 (mmp) cc_final: -0.1267 (mmp) REVERT: C 22 LEU cc_start: 0.2931 (OUTLIER) cc_final: 0.2453 (mp) REVERT: C 44 LEU cc_start: -0.0373 (OUTLIER) cc_final: -0.1009 (mm) REVERT: C 61 HIS cc_start: 0.2914 (m170) cc_final: 0.2256 (m90) REVERT: D 22 LEU cc_start: 0.2939 (OUTLIER) cc_final: 0.2564 (mp) REVERT: D 44 LEU cc_start: -0.0390 (OUTLIER) cc_final: -0.1086 (mm) REVERT: D 61 HIS cc_start: 0.2857 (m170) cc_final: 0.2233 (m170) REVERT: E 22 LEU cc_start: 0.2961 (OUTLIER) cc_final: 0.2457 (mp) REVERT: E 134 LEU cc_start: -0.0464 (OUTLIER) cc_final: -0.0702 (mp) REVERT: F 44 LEU cc_start: -0.0354 (OUTLIER) cc_final: -0.1041 (mm) REVERT: F 61 HIS cc_start: 0.2855 (m170) cc_final: 0.2279 (m90) REVERT: G 22 LEU cc_start: 0.3016 (OUTLIER) cc_final: 0.2511 (mp) REVERT: G 44 LEU cc_start: -0.0173 (OUTLIER) cc_final: -0.0939 (mm) REVERT: G 61 HIS cc_start: 0.2858 (m170) cc_final: 0.2257 (m90) REVERT: G 96 MET cc_start: 0.0636 (mmp) cc_final: -0.1474 (mmp) REVERT: H 22 LEU cc_start: 0.3034 (OUTLIER) cc_final: 0.2547 (mp) REVERT: H 44 LEU cc_start: -0.0280 (OUTLIER) cc_final: -0.1059 (mm) REVERT: H 61 HIS cc_start: 0.2858 (m170) cc_final: 0.2308 (m90) REVERT: H 96 MET cc_start: 0.0664 (mmp) cc_final: -0.1452 (mmp) REVERT: I 22 LEU cc_start: 0.3041 (OUTLIER) cc_final: 0.2523 (mp) REVERT: I 44 LEU cc_start: -0.0190 (OUTLIER) cc_final: -0.0992 (mm) REVERT: I 61 HIS cc_start: 0.2836 (m170) cc_final: 0.2289 (m90) REVERT: I 96 MET cc_start: 0.0736 (mmp) cc_final: -0.1337 (mmp) REVERT: I 134 LEU cc_start: -0.0500 (OUTLIER) cc_final: -0.0858 (mt) REVERT: J 22 LEU cc_start: 0.3003 (OUTLIER) cc_final: 0.2489 (mt) REVERT: J 44 LEU cc_start: -0.0292 (OUTLIER) cc_final: -0.1052 (mm) REVERT: J 61 HIS cc_start: 0.2871 (m170) cc_final: 0.2237 (m90) REVERT: J 66 MET cc_start: 0.0689 (ttm) cc_final: 0.0460 (ptt) REVERT: J 96 MET cc_start: 0.0695 (mmp) cc_final: -0.1137 (mmp) REVERT: K 22 LEU cc_start: 0.2867 (OUTLIER) cc_final: 0.2380 (mp) REVERT: K 61 HIS cc_start: 0.2878 (m170) cc_final: 0.2213 (m170) REVERT: K 96 MET cc_start: 0.0722 (mmp) cc_final: -0.1094 (mmp) REVERT: L 22 LEU cc_start: 0.3026 (OUTLIER) cc_final: 0.2548 (mp) REVERT: L 44 LEU cc_start: -0.0373 (OUTLIER) cc_final: -0.1059 (mm) REVERT: L 61 HIS cc_start: 0.2857 (m170) cc_final: 0.2308 (m90) REVERT: L 96 MET cc_start: 0.0675 (mmp) cc_final: -0.1444 (mmp) REVERT: M 22 LEU cc_start: 0.3062 (OUTLIER) cc_final: 0.2584 (mp) REVERT: M 44 LEU cc_start: -0.0304 (OUTLIER) cc_final: -0.0983 (mm) REVERT: M 61 HIS cc_start: 0.2889 (m170) cc_final: 0.2252 (m170) REVERT: M 66 MET cc_start: 0.0675 (ttm) cc_final: 0.0397 (ptp) REVERT: M 96 MET cc_start: 0.0668 (mmp) cc_final: -0.1463 (mmp) REVERT: N 44 LEU cc_start: -0.0362 (OUTLIER) cc_final: -0.1001 (mm) REVERT: N 61 HIS cc_start: 0.2861 (m170) cc_final: 0.2301 (m90) REVERT: N 96 MET cc_start: 0.0651 (mmp) cc_final: -0.1143 (mmp) REVERT: O 22 LEU cc_start: 0.3016 (OUTLIER) cc_final: 0.2563 (mp) REVERT: O 44 LEU cc_start: -0.0352 (OUTLIER) cc_final: -0.1109 (mm) REVERT: O 61 HIS cc_start: 0.2851 (m170) cc_final: 0.2307 (m90) REVERT: O 96 MET cc_start: 0.0676 (mmp) cc_final: -0.1448 (mmp) REVERT: P 22 LEU cc_start: 0.3044 (OUTLIER) cc_final: 0.2540 (mp) REVERT: P 44 LEU cc_start: -0.0419 (OUTLIER) cc_final: -0.1072 (mm) REVERT: P 61 HIS cc_start: 0.2847 (m170) cc_final: 0.2286 (m90) REVERT: Q 22 LEU cc_start: 0.3024 (OUTLIER) cc_final: 0.2559 (mp) REVERT: Q 44 LEU cc_start: -0.0337 (OUTLIER) cc_final: -0.1074 (mm) REVERT: Q 61 HIS cc_start: 0.2831 (m170) cc_final: 0.2299 (m90) REVERT: Q 96 MET cc_start: 0.0679 (mmp) cc_final: -0.1459 (mmp) REVERT: R 22 LEU cc_start: 0.3004 (OUTLIER) cc_final: 0.2505 (mp) REVERT: R 44 LEU cc_start: -0.0359 (OUTLIER) cc_final: -0.1034 (mm) REVERT: R 61 HIS cc_start: 0.2820 (m170) cc_final: 0.2289 (m90) REVERT: R 66 MET cc_start: 0.0674 (ttm) cc_final: 0.0432 (ptt) REVERT: R 96 MET cc_start: 0.0659 (mmp) cc_final: -0.1484 (mmp) REVERT: S 22 LEU cc_start: 0.3009 (OUTLIER) cc_final: 0.2542 (mp) REVERT: S 44 LEU cc_start: -0.0108 (OUTLIER) cc_final: -0.1108 (mm) REVERT: S 61 HIS cc_start: 0.2828 (m170) cc_final: 0.2300 (m90) REVERT: S 96 MET cc_start: 0.0670 (mmp) cc_final: -0.1458 (mmp) REVERT: T 22 LEU cc_start: 0.2964 (OUTLIER) cc_final: 0.2430 (mp) REVERT: T 44 LEU cc_start: -0.0415 (OUTLIER) cc_final: -0.1082 (mm) REVERT: T 61 HIS cc_start: 0.2883 (m170) cc_final: 0.2201 (m170) REVERT: T 96 MET cc_start: 0.0663 (mmp) cc_final: -0.1452 (mmp) REVERT: T 134 LEU cc_start: -0.0508 (OUTLIER) cc_final: -0.0751 (mp) REVERT: V 22 LEU cc_start: 0.3023 (OUTLIER) cc_final: 0.2553 (mp) REVERT: V 44 LEU cc_start: -0.0279 (OUTLIER) cc_final: -0.1000 (mm) REVERT: V 61 HIS cc_start: 0.2836 (m170) cc_final: 0.2285 (m90) REVERT: V 96 MET cc_start: 0.0759 (mmp) cc_final: -0.1144 (mmp) REVERT: W 22 LEU cc_start: 0.3022 (OUTLIER) cc_final: 0.2533 (mp) REVERT: W 44 LEU cc_start: -0.0395 (OUTLIER) cc_final: -0.1061 (mm) REVERT: W 61 HIS cc_start: 0.2824 (m170) cc_final: 0.2283 (m90) REVERT: W 66 MET cc_start: 0.0640 (ttm) cc_final: 0.0425 (ptt) REVERT: X 22 LEU cc_start: 0.3024 (OUTLIER) cc_final: 0.2545 (mp) REVERT: X 61 HIS cc_start: 0.2874 (m170) cc_final: 0.2222 (m170) REVERT: X 66 MET cc_start: 0.0607 (ttm) cc_final: 0.0377 (ptt) REVERT: X 96 MET cc_start: 0.0684 (mmp) cc_final: -0.1459 (mmp) outliers start: 97 outliers final: 22 residues processed: 266 average time/residue: 1.0333 time to fit residues: 349.5887 Evaluate side-chains 238 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 173 time to evaluate : 3.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 83 LYS Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 154 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 65 LEU Chi-restraints excluded: chain I residue 134 LEU Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain J residue 65 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 65 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 154 MET Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 65 LEU Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 154 MET Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 134 LEU Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain X residue 22 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 9.9990 chunk 44 optimal weight: 4.9990 chunk 224 optimal weight: 3.9990 chunk 288 optimal weight: 6.9990 chunk 223 optimal weight: 0.9990 chunk 332 optimal weight: 0.8980 chunk 220 optimal weight: 4.9990 chunk 393 optimal weight: 2.9990 chunk 246 optimal weight: 3.9990 chunk 239 optimal weight: 0.9980 chunk 181 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1372 moved from start: 0.6057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33912 Z= 0.184 Angle : 0.610 8.754 45792 Z= 0.321 Chirality : 0.039 0.294 4896 Planarity : 0.003 0.041 6024 Dihedral : 4.554 20.319 4464 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.53 % Allowed : 12.16 % Favored : 85.32 % 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: 2.32 (0.13), residues: 4080 helix: 2.37 (0.09), residues: 3168 sheet: None (None), residues: 0 loop : -1.61 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 89 HIS 0.004 0.001 HIS O 169 PHE 0.012 0.002 PHE X 51 TYR 0.020 0.002 TYR U 164 ARG 0.003 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 171 time to evaluate : 3.711 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: U 61 HIS cc_start: 0.2859 (m170) cc_final: 0.2240 (m170) REVERT: U 66 MET cc_start: 0.0560 (ttm) cc_final: 0.0351 (ptt) REVERT: U 96 MET cc_start: 0.0847 (mmp) cc_final: 0.0405 (mmm) REVERT: A 22 LEU cc_start: 0.2993 (OUTLIER) cc_final: 0.2561 (mt) REVERT: A 61 HIS cc_start: 0.2825 (m170) cc_final: 0.2298 (m90) REVERT: A 66 MET cc_start: 0.2116 (OUTLIER) cc_final: 0.0624 (tpp) REVERT: A 96 MET cc_start: 0.0714 (mmp) cc_final: -0.1109 (mmp) REVERT: B 44 LEU cc_start: -0.0307 (OUTLIER) cc_final: -0.0991 (mm) REVERT: B 61 HIS cc_start: 0.2875 (m170) cc_final: 0.2296 (m90) REVERT: B 66 MET cc_start: 0.0495 (ttm) cc_final: 0.0260 (ptp) REVERT: B 96 MET cc_start: 0.0696 (mmp) cc_final: -0.1323 (mmp) REVERT: B 149 THR cc_start: 0.5628 (OUTLIER) cc_final: 0.5071 (p) REVERT: C 22 LEU cc_start: 0.2998 (OUTLIER) cc_final: 0.2518 (mp) REVERT: C 44 LEU cc_start: -0.0385 (OUTLIER) cc_final: -0.1000 (mm) REVERT: C 61 HIS cc_start: 0.2983 (m170) cc_final: 0.2348 (m90) REVERT: D 22 LEU cc_start: 0.2886 (OUTLIER) cc_final: 0.2528 (mp) REVERT: D 44 LEU cc_start: -0.0436 (OUTLIER) cc_final: -0.1089 (mm) REVERT: D 61 HIS cc_start: 0.2926 (m170) cc_final: 0.2324 (m90) REVERT: E 22 LEU cc_start: 0.2961 (OUTLIER) cc_final: 0.2476 (mp) REVERT: E 61 HIS cc_start: 0.2951 (m170) cc_final: 0.2290 (m90) REVERT: F 44 LEU cc_start: -0.0273 (OUTLIER) cc_final: -0.0932 (mm) REVERT: F 61 HIS cc_start: 0.2844 (m170) cc_final: 0.2295 (m90) REVERT: F 66 MET cc_start: 0.2053 (OUTLIER) cc_final: 0.0641 (tpp) REVERT: F 96 MET cc_start: 0.0666 (mmp) cc_final: -0.1079 (mmp) REVERT: G 22 LEU cc_start: 0.2972 (OUTLIER) cc_final: 0.2439 (mp) REVERT: G 44 LEU cc_start: -0.0162 (OUTLIER) cc_final: -0.0975 (mm) REVERT: G 61 HIS cc_start: 0.2932 (m170) cc_final: 0.2322 (m90) REVERT: G 96 MET cc_start: 0.0617 (mmp) cc_final: -0.1471 (mmp) REVERT: H 22 LEU cc_start: 0.3033 (OUTLIER) cc_final: 0.2563 (mp) REVERT: H 44 LEU cc_start: -0.0252 (OUTLIER) cc_final: -0.1056 (mm) REVERT: H 61 HIS cc_start: 0.2885 (m170) cc_final: 0.2320 (m90) REVERT: H 96 MET cc_start: 0.0699 (mmp) cc_final: -0.1348 (mmp) REVERT: I 22 LEU cc_start: 0.3051 (OUTLIER) cc_final: 0.2588 (mp) REVERT: I 44 LEU cc_start: -0.0213 (OUTLIER) cc_final: -0.1006 (mm) REVERT: I 61 HIS cc_start: 0.2889 (m170) cc_final: 0.2360 (m90) REVERT: I 66 MET cc_start: 0.2091 (OUTLIER) cc_final: 0.0635 (tpp) REVERT: I 96 MET cc_start: 0.0688 (mmp) cc_final: -0.1177 (mmp) REVERT: J 22 LEU cc_start: 0.2855 (OUTLIER) cc_final: 0.2392 (mp) REVERT: J 44 LEU cc_start: -0.0335 (OUTLIER) cc_final: -0.1098 (mm) REVERT: J 61 HIS cc_start: 0.2932 (m170) cc_final: 0.2319 (m90) REVERT: J 96 MET cc_start: 0.0755 (mmp) cc_final: -0.1326 (mmp) REVERT: K 22 LEU cc_start: 0.2965 (OUTLIER) cc_final: 0.2463 (mp) REVERT: K 61 HIS cc_start: 0.2936 (m170) cc_final: 0.2327 (m90) REVERT: K 96 MET cc_start: 0.0707 (mmp) cc_final: -0.1092 (mmp) REVERT: L 22 LEU cc_start: 0.3024 (OUTLIER) cc_final: 0.2559 (mp) REVERT: L 44 LEU cc_start: -0.0268 (OUTLIER) cc_final: -0.1004 (mm) REVERT: L 61 HIS cc_start: 0.2879 (m170) cc_final: 0.2318 (m90) REVERT: L 96 MET cc_start: 0.0695 (mmp) cc_final: -0.1426 (mmp) REVERT: M 22 LEU cc_start: 0.2950 (OUTLIER) cc_final: 0.2559 (mp) REVERT: M 44 LEU cc_start: -0.0246 (OUTLIER) cc_final: -0.0941 (mm) REVERT: M 61 HIS cc_start: 0.2927 (m170) cc_final: 0.2303 (m90) REVERT: M 96 MET cc_start: 0.0669 (mmp) cc_final: -0.1433 (mmp) REVERT: N 44 LEU cc_start: -0.0353 (OUTLIER) cc_final: -0.0927 (mm) REVERT: N 61 HIS cc_start: 0.2914 (m170) cc_final: 0.2250 (m170) REVERT: O 22 LEU cc_start: 0.3037 (OUTLIER) cc_final: 0.2549 (mp) REVERT: O 44 LEU cc_start: -0.0358 (OUTLIER) cc_final: -0.1114 (mm) REVERT: O 61 HIS cc_start: 0.2878 (m170) cc_final: 0.2327 (m90) REVERT: O 96 MET cc_start: 0.0693 (mmp) cc_final: -0.1407 (mmp) REVERT: P 22 LEU cc_start: 0.3054 (OUTLIER) cc_final: 0.2636 (mp) REVERT: P 44 LEU cc_start: -0.0309 (OUTLIER) cc_final: -0.0958 (mm) REVERT: P 61 HIS cc_start: 0.2858 (m170) cc_final: 0.2335 (m90) REVERT: P 66 MET cc_start: 0.2081 (OUTLIER) cc_final: 0.0610 (tpp) REVERT: P 96 MET cc_start: 0.0623 (mmp) cc_final: -0.1022 (mmp) REVERT: Q 22 LEU cc_start: 0.3038 (OUTLIER) cc_final: 0.2580 (mp) REVERT: Q 44 LEU cc_start: -0.0284 (OUTLIER) cc_final: -0.1043 (mm) REVERT: Q 61 HIS cc_start: 0.2884 (m170) cc_final: 0.2328 (m90) REVERT: Q 96 MET cc_start: 0.0713 (mmp) cc_final: -0.1395 (mmp) REVERT: R 22 LEU cc_start: 0.3029 (OUTLIER) cc_final: 0.2572 (mp) REVERT: R 44 LEU cc_start: -0.0273 (OUTLIER) cc_final: -0.1001 (mm) REVERT: R 61 HIS cc_start: 0.2865 (m170) cc_final: 0.2299 (m90) REVERT: R 96 MET cc_start: 0.0691 (mmp) cc_final: -0.1445 (mmp) REVERT: S 22 LEU cc_start: 0.3030 (OUTLIER) cc_final: 0.2561 (mp) REVERT: S 44 LEU cc_start: -0.0074 (OUTLIER) cc_final: -0.1072 (mm) REVERT: S 61 HIS cc_start: 0.2868 (m170) cc_final: 0.2323 (m90) REVERT: S 96 MET cc_start: 0.0694 (mmp) cc_final: -0.1426 (mmp) REVERT: T 22 LEU cc_start: 0.3002 (OUTLIER) cc_final: 0.2431 (mp) REVERT: T 44 LEU cc_start: -0.0321 (OUTLIER) cc_final: -0.1002 (mm) REVERT: T 61 HIS cc_start: 0.2951 (m170) cc_final: 0.2286 (m170) REVERT: T 96 MET cc_start: 0.0652 (mmp) cc_final: -0.1428 (mmp) REVERT: T 134 LEU cc_start: -0.0442 (OUTLIER) cc_final: -0.0662 (mp) REVERT: V 22 LEU cc_start: 0.3029 (OUTLIER) cc_final: 0.2568 (mp) REVERT: V 44 LEU cc_start: -0.0238 (OUTLIER) cc_final: -0.0988 (mm) REVERT: V 61 HIS cc_start: 0.2857 (m170) cc_final: 0.2264 (m90) REVERT: V 96 MET cc_start: 0.0721 (mmp) cc_final: -0.1349 (mmp) REVERT: W 22 LEU cc_start: 0.3039 (OUTLIER) cc_final: 0.2586 (mp) REVERT: W 44 LEU cc_start: -0.0274 (OUTLIER) cc_final: -0.0997 (mm) REVERT: W 61 HIS cc_start: 0.2864 (m170) cc_final: 0.2292 (m90) REVERT: X 22 LEU cc_start: 0.2815 (OUTLIER) cc_final: 0.2358 (mp) REVERT: X 96 MET cc_start: 0.0639 (mmp) cc_final: -0.1231 (mmp) outliers start: 88 outliers final: 19 residues processed: 235 average time/residue: 1.0835 time to fit residues: 323.6256 Evaluate side-chains 216 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 152 time to evaluate : 3.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 83 LYS Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 154 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 66 MET Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 154 MET Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 154 MET Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 134 LEU Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain X residue 22 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 chunk 77 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 250 optimal weight: 0.8980 chunk 267 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 309 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 19 GLN ** U 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1449 moved from start: 0.6378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33912 Z= 0.215 Angle : 0.667 9.905 45792 Z= 0.350 Chirality : 0.041 0.445 4896 Planarity : 0.003 0.042 6024 Dihedral : 4.701 20.473 4464 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.61 % Allowed : 12.84 % Favored : 84.54 % 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: 2.10 (0.13), residues: 4080 helix: 2.21 (0.09), residues: 3144 sheet: None (None), residues: 0 loop : -1.60 (0.21), residues: 936 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 89 HIS 0.005 0.001 HIS H 169 PHE 0.014 0.002 PHE X 51 TYR 0.028 0.002 TYR Q 35 ARG 0.003 0.000 ARG J 152 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 182 time to evaluate : 3.690 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: U 61 HIS cc_start: 0.2887 (m170) cc_final: 0.2230 (m170) REVERT: U 96 MET cc_start: 0.0880 (mmp) cc_final: 0.0467 (mmm) REVERT: A 22 LEU cc_start: 0.3029 (OUTLIER) cc_final: 0.2510 (mp) REVERT: A 66 MET cc_start: 0.2085 (OUTLIER) cc_final: 0.0519 (tpp) REVERT: A 96 MET cc_start: 0.0724 (mmp) cc_final: -0.1140 (mmp) REVERT: A 154 MET cc_start: 0.1957 (mmt) cc_final: 0.0786 (mpp) REVERT: B 44 LEU cc_start: -0.0225 (OUTLIER) cc_final: -0.1001 (mm) REVERT: B 61 HIS cc_start: 0.2970 (m170) cc_final: 0.2412 (m90) REVERT: B 96 MET cc_start: 0.0710 (mmp) cc_final: -0.1132 (mmp) REVERT: C 22 LEU cc_start: 0.3163 (OUTLIER) cc_final: 0.2672 (mp) REVERT: C 44 LEU cc_start: -0.0329 (OUTLIER) cc_final: -0.0987 (mm) REVERT: C 61 HIS cc_start: 0.3046 (m170) cc_final: 0.2430 (m90) REVERT: D 22 LEU cc_start: 0.3098 (OUTLIER) cc_final: 0.2687 (mp) REVERT: D 44 LEU cc_start: -0.0405 (OUTLIER) cc_final: -0.1098 (mm) REVERT: E 22 LEU cc_start: 0.3132 (OUTLIER) cc_final: 0.2573 (mp) REVERT: E 61 HIS cc_start: 0.3009 (m170) cc_final: 0.2415 (m90) REVERT: E 96 MET cc_start: 0.0718 (mmp) cc_final: -0.1098 (mmp) REVERT: E 134 LEU cc_start: -0.0317 (OUTLIER) cc_final: -0.0665 (mp) REVERT: F 44 LEU cc_start: -0.0201 (OUTLIER) cc_final: -0.1034 (mm) REVERT: F 61 HIS cc_start: 0.2905 (m170) cc_final: 0.2380 (m90) REVERT: F 66 MET cc_start: 0.2107 (OUTLIER) cc_final: 0.0503 (tpp) REVERT: G 22 LEU cc_start: 0.3075 (OUTLIER) cc_final: 0.2588 (mp) REVERT: G 44 LEU cc_start: -0.0158 (OUTLIER) cc_final: -0.1050 (mm) REVERT: G 61 HIS cc_start: 0.3001 (m170) cc_final: 0.2336 (m90) REVERT: G 66 MET cc_start: 0.2231 (OUTLIER) cc_final: 0.0785 (tpp) REVERT: G 96 MET cc_start: 0.0704 (mmp) cc_final: -0.1363 (mmp) REVERT: H 22 LEU cc_start: 0.3166 (OUTLIER) cc_final: 0.2694 (mp) REVERT: H 44 LEU cc_start: -0.0241 (OUTLIER) cc_final: -0.1118 (mm) REVERT: H 96 MET cc_start: 0.0709 (mmp) cc_final: -0.1377 (mmp) REVERT: I 22 LEU cc_start: 0.3153 (OUTLIER) cc_final: 0.2722 (mp) REVERT: I 44 LEU cc_start: -0.0151 (OUTLIER) cc_final: -0.1062 (mm) REVERT: I 66 MET cc_start: 0.2238 (OUTLIER) cc_final: 0.0553 (tpp) REVERT: I 96 MET cc_start: 0.0776 (mmp) cc_final: -0.1213 (mmp) REVERT: J 22 LEU cc_start: 0.3094 (OUTLIER) cc_final: 0.2492 (mp) REVERT: J 44 LEU cc_start: -0.0304 (OUTLIER) cc_final: -0.1170 (mm) REVERT: J 96 MET cc_start: 0.0723 (mmp) cc_final: -0.1290 (mmp) REVERT: K 22 LEU cc_start: 0.3146 (OUTLIER) cc_final: 0.2626 (mp) REVERT: K 61 HIS cc_start: 0.2969 (m170) cc_final: 0.2344 (m90) REVERT: K 66 MET cc_start: 0.2028 (OUTLIER) cc_final: 0.0472 (tpp) REVERT: K 96 MET cc_start: 0.0735 (mmp) cc_final: -0.1074 (mmp) REVERT: L 22 LEU cc_start: 0.3153 (OUTLIER) cc_final: 0.2687 (mp) REVERT: L 33 MET cc_start: 0.1098 (mtt) cc_final: 0.0530 (mtt) REVERT: L 44 LEU cc_start: -0.0216 (OUTLIER) cc_final: -0.1019 (mm) REVERT: L 96 MET cc_start: 0.0730 (mmp) cc_final: -0.1345 (mmp) REVERT: M 22 LEU cc_start: 0.3128 (OUTLIER) cc_final: 0.2609 (mp) REVERT: M 44 LEU cc_start: -0.0186 (OUTLIER) cc_final: -0.0974 (mm) REVERT: M 96 MET cc_start: 0.0725 (mmp) cc_final: -0.1376 (mmp) REVERT: N 44 LEU cc_start: -0.0340 (OUTLIER) cc_final: -0.0995 (mm) REVERT: N 96 MET cc_start: 0.0360 (mmp) cc_final: -0.1027 (mmp) REVERT: O 22 LEU cc_start: 0.3173 (OUTLIER) cc_final: 0.2921 (mp) REVERT: O 44 LEU cc_start: -0.0273 (OUTLIER) cc_final: -0.1114 (mm) REVERT: O 96 MET cc_start: 0.0725 (mmp) cc_final: -0.1365 (mmp) REVERT: P 22 LEU cc_start: 0.3177 (OUTLIER) cc_final: 0.2758 (mp) REVERT: P 44 LEU cc_start: -0.0241 (OUTLIER) cc_final: -0.1033 (mm) REVERT: P 61 HIS cc_start: 0.2913 (m170) cc_final: 0.2399 (m90) REVERT: P 66 MET cc_start: 0.2267 (OUTLIER) cc_final: 0.0519 (tpp) REVERT: Q 22 LEU cc_start: 0.3167 (OUTLIER) cc_final: 0.2923 (mp) REVERT: Q 44 LEU cc_start: -0.0220 (OUTLIER) cc_final: -0.1052 (mm) REVERT: Q 96 MET cc_start: 0.0696 (mmp) cc_final: -0.1403 (mmp) REVERT: R 22 LEU cc_start: 0.3175 (OUTLIER) cc_final: 0.2695 (mp) REVERT: R 33 MET cc_start: 0.1068 (mtt) cc_final: 0.0496 (mtt) REVERT: R 44 LEU cc_start: -0.0239 (OUTLIER) cc_final: -0.1020 (mm) REVERT: R 61 HIS cc_start: 0.2977 (m170) cc_final: 0.2421 (m90) REVERT: R 96 MET cc_start: 0.0700 (mmp) cc_final: -0.1383 (mmp) REVERT: R 154 MET cc_start: 0.2337 (mmt) cc_final: 0.1146 (mpp) REVERT: S 22 LEU cc_start: 0.3142 (OUTLIER) cc_final: 0.2650 (mp) REVERT: S 44 LEU cc_start: 0.0052 (OUTLIER) cc_final: -0.1036 (mm) REVERT: S 61 HIS cc_start: 0.2944 (m170) cc_final: 0.2402 (m90) REVERT: S 66 MET cc_start: 0.2127 (OUTLIER) cc_final: 0.0608 (tpp) REVERT: S 96 MET cc_start: 0.0654 (mmp) cc_final: -0.1406 (mmp) REVERT: T 22 LEU cc_start: 0.3055 (OUTLIER) cc_final: 0.2542 (mp) REVERT: T 44 LEU cc_start: -0.0302 (OUTLIER) cc_final: -0.1058 (mm) REVERT: T 61 HIS cc_start: 0.2959 (m170) cc_final: 0.2368 (m90) REVERT: T 66 MET cc_start: 0.1976 (tpp) cc_final: 0.0817 (tpp) REVERT: T 71 GLN cc_start: 0.1837 (OUTLIER) cc_final: 0.1333 (mp10) REVERT: T 96 MET cc_start: 0.0685 (mmp) cc_final: -0.1400 (mmp) REVERT: T 154 MET cc_start: 0.2947 (mmt) cc_final: 0.2317 (mmt) REVERT: V 22 LEU cc_start: 0.3168 (OUTLIER) cc_final: 0.2712 (mp) REVERT: V 44 LEU cc_start: -0.0213 (OUTLIER) cc_final: -0.1018 (mm) REVERT: V 61 HIS cc_start: 0.2935 (m170) cc_final: 0.2409 (m90) REVERT: V 96 MET cc_start: 0.0816 (mmp) cc_final: -0.1249 (mmp) REVERT: W 22 LEU cc_start: 0.3194 (OUTLIER) cc_final: 0.2710 (mp) REVERT: W 44 LEU cc_start: -0.0273 (OUTLIER) cc_final: -0.1009 (mm) REVERT: W 61 HIS cc_start: 0.2978 (m170) cc_final: 0.2428 (m90) REVERT: W 96 MET cc_start: 0.0693 (mmp) cc_final: -0.1122 (mmp) REVERT: X 22 LEU cc_start: 0.3199 (OUTLIER) cc_final: 0.2561 (mp) REVERT: X 61 HIS cc_start: 0.3023 (m170) cc_final: 0.2375 (m90) REVERT: X 96 MET cc_start: 0.0712 (mmp) cc_final: -0.1353 (mmp) REVERT: X 134 LEU cc_start: -0.0422 (OUTLIER) cc_final: -0.0770 (mp) outliers start: 91 outliers final: 21 residues processed: 246 average time/residue: 1.0560 time to fit residues: 331.6845 Evaluate side-chains 248 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 178 time to evaluate : 3.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 83 LYS Chi-restraints excluded: chain U residue 149 THR Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain A residue 66 MET Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 134 LEU Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 154 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 66 MET Chi-restraints excluded: chain I residue 138 VAL Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 66 MET Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 154 MET Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 154 MET Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain S residue 138 VAL Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 71 GLN Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain W residue 138 VAL Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 134 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 2.9990 chunk 376 optimal weight: 5.9990 chunk 343 optimal weight: 1.9990 chunk 366 optimal weight: 0.9980 chunk 220 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 287 optimal weight: 0.9990 chunk 112 optimal weight: 0.9980 chunk 331 optimal weight: 0.9990 chunk 346 optimal weight: 7.9990 chunk 365 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 ASN ** S 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 7 ASN ** T 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1346 moved from start: 0.6372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33912 Z= 0.168 Angle : 0.602 10.379 45792 Z= 0.311 Chirality : 0.040 0.431 4896 Planarity : 0.003 0.045 6024 Dihedral : 4.424 20.573 4464 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 2.10 % Allowed : 13.13 % Favored : 84.77 % 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: 2.52 (0.13), residues: 4080 helix: 2.47 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : -1.49 (0.22), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 89 HIS 0.005 0.001 HIS V 124 PHE 0.011 0.001 PHE E 51 TYR 0.021 0.002 TYR Q 35 ARG 0.004 0.000 ARG I 152 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 177 time to evaluate : 3.647 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: U 61 HIS cc_start: 0.2871 (m170) cc_final: 0.2176 (m170) REVERT: U 96 MET cc_start: 0.0693 (mmp) cc_final: -0.1287 (mmp) REVERT: U 154 MET cc_start: 0.2305 (mmm) cc_final: 0.0937 (mtm) REVERT: A 22 LEU cc_start: 0.2698 (OUTLIER) cc_final: 0.2407 (mp) REVERT: A 61 HIS cc_start: 0.2911 (m170) cc_final: 0.2369 (m90) REVERT: A 154 MET cc_start: 0.1729 (mmt) cc_final: 0.1050 (mpp) REVERT: B 44 LEU cc_start: -0.0390 (OUTLIER) cc_final: -0.0899 (mm) REVERT: B 61 HIS cc_start: 0.2922 (m170) cc_final: 0.2293 (m90) REVERT: C 22 LEU cc_start: 0.2821 (OUTLIER) cc_final: 0.2566 (mp) REVERT: C 44 LEU cc_start: -0.0423 (OUTLIER) cc_final: -0.0849 (mm) REVERT: C 61 HIS cc_start: 0.2990 (m170) cc_final: 0.2341 (m90) REVERT: C 96 MET cc_start: -0.0053 (mmp) cc_final: -0.0349 (mmm) REVERT: C 154 MET cc_start: 0.2787 (mmt) cc_final: 0.1825 (mmt) REVERT: D 22 LEU cc_start: 0.2597 (OUTLIER) cc_final: 0.2386 (mp) REVERT: D 33 MET cc_start: 0.0308 (mtt) cc_final: -0.0134 (mtp) REVERT: D 44 LEU cc_start: -0.0560 (OUTLIER) cc_final: -0.0967 (mm) REVERT: D 61 HIS cc_start: 0.2944 (m170) cc_final: 0.2317 (m90) REVERT: E 22 LEU cc_start: 0.2810 (OUTLIER) cc_final: 0.2497 (mp) REVERT: E 61 HIS cc_start: 0.2988 (m170) cc_final: 0.2337 (m90) REVERT: E 134 LEU cc_start: -0.0366 (OUTLIER) cc_final: -0.0583 (mp) REVERT: F 44 LEU cc_start: -0.0283 (OUTLIER) cc_final: -0.0863 (mm) REVERT: F 61 HIS cc_start: 0.2909 (m170) cc_final: 0.2319 (m90) REVERT: F 66 MET cc_start: 0.2028 (OUTLIER) cc_final: 0.0536 (tpp) REVERT: F 96 MET cc_start: 0.0336 (mmp) cc_final: -0.1034 (mmp) REVERT: G 22 LEU cc_start: 0.2763 (OUTLIER) cc_final: 0.2428 (mp) REVERT: G 44 LEU cc_start: -0.0202 (OUTLIER) cc_final: -0.0886 (mm) REVERT: G 61 HIS cc_start: 0.2949 (m170) cc_final: 0.2335 (m90) REVERT: G 66 MET cc_start: 0.2204 (OUTLIER) cc_final: 0.0644 (tpp) REVERT: G 96 MET cc_start: 0.0539 (mmp) cc_final: -0.1241 (mmp) REVERT: H 22 LEU cc_start: 0.2811 (OUTLIER) cc_final: 0.2526 (mp) REVERT: H 44 LEU cc_start: -0.0286 (OUTLIER) cc_final: -0.0966 (mm) REVERT: H 61 HIS cc_start: 0.2914 (m170) cc_final: 0.2360 (m90) REVERT: H 96 MET cc_start: 0.0541 (mmp) cc_final: -0.1243 (mmp) REVERT: I 22 LEU cc_start: 0.2823 (OUTLIER) cc_final: 0.2549 (mp) REVERT: I 44 LEU cc_start: -0.0272 (OUTLIER) cc_final: -0.1039 (mm) REVERT: I 66 MET cc_start: 0.2196 (OUTLIER) cc_final: 0.0530 (tpp) REVERT: J 22 LEU cc_start: 0.2782 (OUTLIER) cc_final: 0.2395 (mp) REVERT: J 44 LEU cc_start: -0.0373 (OUTLIER) cc_final: -0.1045 (mm) REVERT: J 61 HIS cc_start: 0.2953 (m170) cc_final: 0.2304 (m90) REVERT: K 22 LEU cc_start: 0.2775 (OUTLIER) cc_final: 0.2453 (mp) REVERT: K 61 HIS cc_start: 0.2963 (m170) cc_final: 0.2303 (m90) REVERT: L 22 LEU cc_start: 0.2801 (OUTLIER) cc_final: 0.2516 (mp) REVERT: L 44 LEU cc_start: -0.0310 (OUTLIER) cc_final: -0.0904 (mm) REVERT: L 61 HIS cc_start: 0.2926 (m170) cc_final: 0.2376 (m90) REVERT: L 96 MET cc_start: 0.0561 (mmp) cc_final: -0.1222 (mmp) REVERT: M 22 LEU cc_start: 0.2788 (OUTLIER) cc_final: 0.2576 (mp) REVERT: M 44 LEU cc_start: -0.0282 (OUTLIER) cc_final: -0.0835 (mm) REVERT: M 66 MET cc_start: 0.2085 (OUTLIER) cc_final: 0.0777 (tpp) REVERT: M 96 MET cc_start: 0.0470 (mmp) cc_final: -0.1244 (mmp) REVERT: N 22 LEU cc_start: 0.2707 (OUTLIER) cc_final: 0.2480 (mp) REVERT: N 44 LEU cc_start: -0.0545 (OUTLIER) cc_final: -0.0901 (mm) REVERT: N 96 MET cc_start: 0.0352 (mmp) cc_final: -0.0929 (mmp) REVERT: O 22 LEU cc_start: 0.2816 (OUTLIER) cc_final: 0.2546 (mp) REVERT: O 44 LEU cc_start: -0.0359 (OUTLIER) cc_final: -0.0992 (mm) REVERT: O 61 HIS cc_start: 0.2923 (m170) cc_final: 0.2382 (m90) REVERT: O 96 MET cc_start: 0.0525 (mmp) cc_final: -0.1242 (mmp) REVERT: P 44 LEU cc_start: -0.0368 (OUTLIER) cc_final: -0.0913 (mm) REVERT: P 66 MET cc_start: 0.2163 (OUTLIER) cc_final: 0.0576 (tpp) REVERT: P 96 MET cc_start: 0.0222 (mmp) cc_final: -0.1019 (mmp) REVERT: Q 22 LEU cc_start: 0.2818 (OUTLIER) cc_final: 0.2547 (mp) REVERT: Q 44 LEU cc_start: -0.0308 (OUTLIER) cc_final: -0.0941 (mm) REVERT: Q 61 HIS cc_start: 0.2913 (m170) cc_final: 0.2377 (m90) REVERT: Q 96 MET cc_start: 0.0557 (mmp) cc_final: -0.1243 (mmp) REVERT: R 22 LEU cc_start: 0.2798 (OUTLIER) cc_final: 0.2491 (mt) REVERT: R 44 LEU cc_start: -0.0308 (OUTLIER) cc_final: -0.0861 (mm) REVERT: R 61 HIS cc_start: 0.2848 (m170) cc_final: 0.2310 (m90) REVERT: R 96 MET cc_start: 0.0539 (mmp) cc_final: -0.1277 (mmp) REVERT: S 22 LEU cc_start: 0.2769 (OUTLIER) cc_final: 0.2525 (mp) REVERT: S 44 LEU cc_start: -0.0075 (OUTLIER) cc_final: -0.1035 (mm) REVERT: S 61 HIS cc_start: 0.2894 (m170) cc_final: 0.2333 (m90) REVERT: S 66 MET cc_start: 0.2056 (OUTLIER) cc_final: 0.0363 (tpp) REVERT: S 96 MET cc_start: 0.0498 (mmp) cc_final: -0.1246 (mmp) REVERT: T 22 LEU cc_start: 0.2850 (OUTLIER) cc_final: 0.2513 (mp) REVERT: T 44 LEU cc_start: -0.0358 (OUTLIER) cc_final: -0.0884 (mm) REVERT: T 61 HIS cc_start: 0.2946 (m170) cc_final: 0.2322 (m90) REVERT: T 66 MET cc_start: 0.1863 (OUTLIER) cc_final: 0.0337 (ttm) REVERT: T 96 MET cc_start: 0.0510 (mmp) cc_final: -0.1263 (mmp) REVERT: V 22 LEU cc_start: 0.2799 (OUTLIER) cc_final: 0.2516 (mp) REVERT: V 44 LEU cc_start: -0.0270 (OUTLIER) cc_final: -0.0844 (mm) REVERT: V 61 HIS cc_start: 0.2877 (m170) cc_final: 0.2328 (m90) REVERT: W 22 LEU cc_start: 0.2806 (OUTLIER) cc_final: 0.2493 (mt) REVERT: W 44 LEU cc_start: -0.0348 (OUTLIER) cc_final: -0.0870 (mm) REVERT: W 61 HIS cc_start: 0.2841 (m170) cc_final: 0.2309 (m90) REVERT: X 22 LEU cc_start: 0.2858 (OUTLIER) cc_final: 0.2504 (mp) REVERT: X 61 HIS cc_start: 0.3069 (m170) cc_final: 0.2366 (m170) REVERT: X 96 MET cc_start: 0.0378 (mmp) cc_final: -0.1176 (mmp) REVERT: X 134 LEU cc_start: -0.0496 (OUTLIER) cc_final: -0.0766 (mp) outliers start: 73 outliers final: 15 residues processed: 229 average time/residue: 1.1502 time to fit residues: 331.0389 Evaluate side-chains 221 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 158 time to evaluate : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 83 LYS Chi-restraints excluded: chain A residue 22 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 22 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain D residue 22 LEU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 154 MET Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 66 MET Chi-restraints excluded: chain G residue 22 LEU Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 66 MET Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 154 MET Chi-restraints excluded: chain I residue 22 LEU Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain I residue 66 MET Chi-restraints excluded: chain J residue 22 LEU Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain L residue 22 LEU Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain M residue 22 LEU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain M residue 66 MET Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 44 LEU Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain O residue 22 LEU Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 154 MET Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain P residue 66 MET Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 154 MET Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain S residue 22 LEU Chi-restraints excluded: chain S residue 33 MET Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain S residue 66 MET Chi-restraints excluded: chain T residue 22 LEU Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain T residue 66 MET Chi-restraints excluded: chain V residue 22 LEU Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 134 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 0.9980 chunk 387 optimal weight: 0.6980 chunk 236 optimal weight: 0.0040 chunk 183 optimal weight: 0.7980 chunk 269 optimal weight: 0.6980 chunk 406 optimal weight: 0.0170 chunk 374 optimal weight: 10.0000 chunk 323 optimal weight: 0.0670 chunk 33 optimal weight: 0.9980 chunk 250 optimal weight: 1.9990 chunk 198 optimal weight: 0.2980 overall best weight: 0.2168 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 ASN C 7 ASN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN E 7 ASN ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 7 ASN G 7 ASN H 7 ASN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 ASN J 7 ASN K 7 ASN ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 7 ASN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN Q 7 ASN ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 ASN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 ASN T 7 ASN ** T 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 7 ASN ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 7 ASN ** X 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1159 moved from start: 0.6327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 33912 Z= 0.168 Angle : 0.590 9.984 45792 Z= 0.301 Chirality : 0.038 0.313 4896 Planarity : 0.002 0.043 6024 Dihedral : 4.166 20.075 4464 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.55 % Allowed : 13.91 % Favored : 84.54 % 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: 3.30 (0.13), residues: 4080 helix: 3.01 (0.09), residues: 3168 sheet: None (None), residues: 0 loop : -1.01 (0.23), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 89 HIS 0.004 0.001 HIS B 124 PHE 0.011 0.001 PHE S 47 TYR 0.022 0.001 TYR J 35 ARG 0.002 0.000 ARG M 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 208 time to evaluate : 3.408 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: U 96 MET cc_start: 0.0469 (mmp) cc_final: -0.0436 (ptp) REVERT: U 154 MET cc_start: 0.2195 (mmm) cc_final: 0.0879 (mtm) REVERT: A 66 MET cc_start: 0.1960 (tpp) cc_final: 0.0756 (tpp) REVERT: B 44 LEU cc_start: -0.0720 (OUTLIER) cc_final: -0.0944 (mm) REVERT: B 96 MET cc_start: -0.0031 (mmp) cc_final: -0.0951 (mmp) REVERT: C 31 LEU cc_start: 0.2150 (tp) cc_final: 0.1901 (mm) REVERT: C 154 MET cc_start: 0.2545 (mmt) cc_final: 0.1826 (mmt) REVERT: D 66 MET cc_start: 0.2040 (tpp) cc_final: 0.0853 (tpp) REVERT: E 66 MET cc_start: 0.1485 (tpp) cc_final: 0.0511 (ttm) REVERT: F 19 GLN cc_start: 0.2219 (tp-100) cc_final: 0.1936 (mm-40) REVERT: F 44 LEU cc_start: -0.0507 (OUTLIER) cc_final: -0.0771 (mm) REVERT: G 44 LEU cc_start: -0.0423 (OUTLIER) cc_final: -0.0950 (mm) REVERT: G 66 MET cc_start: 0.2158 (tpp) cc_final: 0.1865 (tpp) REVERT: G 129 ILE cc_start: 0.3659 (mp) cc_final: 0.3072 (mp) REVERT: G 154 MET cc_start: 0.2209 (OUTLIER) cc_final: 0.1528 (mmt) REVERT: H 44 LEU cc_start: -0.0541 (OUTLIER) cc_final: -0.1026 (mm) REVERT: I 44 LEU cc_start: -0.0409 (OUTLIER) cc_final: -0.0911 (mm) REVERT: J 44 LEU cc_start: -0.0623 (OUTLIER) cc_final: -0.1016 (mm) REVERT: L 44 LEU cc_start: -0.0618 (OUTLIER) cc_final: -0.0872 (mm) REVERT: L 154 MET cc_start: 0.2380 (mmt) cc_final: 0.0800 (mmt) REVERT: M 44 LEU cc_start: -0.0644 (OUTLIER) cc_final: -0.0877 (mm) REVERT: N 66 MET cc_start: 0.2005 (tpp) cc_final: 0.0684 (tpp) REVERT: N 96 MET cc_start: 0.0100 (mmp) cc_final: -0.0908 (mmp) REVERT: O 31 LEU cc_start: 0.2323 (tp) cc_final: 0.2076 (mm) REVERT: O 44 LEU cc_start: -0.0625 (OUTLIER) cc_final: -0.0938 (mm) REVERT: P 44 LEU cc_start: -0.0629 (OUTLIER) cc_final: -0.0882 (mm) REVERT: Q 31 LEU cc_start: 0.2318 (tp) cc_final: 0.2081 (mm) REVERT: Q 44 LEU cc_start: -0.0571 (OUTLIER) cc_final: -0.0880 (mm) REVERT: R 44 LEU cc_start: -0.0622 (OUTLIER) cc_final: -0.0862 (mm) REVERT: S 44 LEU cc_start: -0.0523 (OUTLIER) cc_final: -0.1091 (mm) REVERT: T 44 LEU cc_start: -0.0679 (OUTLIER) cc_final: -0.0898 (mm) REVERT: T 66 MET cc_start: 0.1867 (tpp) cc_final: 0.0808 (tpp) REVERT: T 129 ILE cc_start: 0.3476 (mp) cc_final: 0.2913 (mp) REVERT: V 44 LEU cc_start: -0.0587 (OUTLIER) cc_final: -0.0845 (mm) REVERT: W 44 LEU cc_start: -0.0644 (OUTLIER) cc_final: -0.0888 (mm) REVERT: X 66 MET cc_start: 0.1644 (tpp) cc_final: 0.0594 (ttm) outliers start: 54 outliers final: 30 residues processed: 250 average time/residue: 1.0682 time to fit residues: 338.9503 Evaluate side-chains 247 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 200 time to evaluate : 3.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 83 LYS Chi-restraints excluded: chain B residue 7 ASN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain C residue 7 ASN Chi-restraints excluded: chain D residue 7 ASN Chi-restraints excluded: chain E residue 7 ASN Chi-restraints excluded: chain F residue 7 ASN Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain G residue 7 ASN Chi-restraints excluded: chain G residue 44 LEU Chi-restraints excluded: chain G residue 154 MET Chi-restraints excluded: chain H residue 7 ASN Chi-restraints excluded: chain H residue 44 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 154 MET Chi-restraints excluded: chain I residue 7 ASN Chi-restraints excluded: chain I residue 44 LEU Chi-restraints excluded: chain J residue 7 ASN Chi-restraints excluded: chain J residue 44 LEU Chi-restraints excluded: chain L residue 7 ASN Chi-restraints excluded: chain L residue 44 LEU Chi-restraints excluded: chain L residue 65 LEU Chi-restraints excluded: chain M residue 44 LEU Chi-restraints excluded: chain N residue 149 THR Chi-restraints excluded: chain O residue 7 ASN Chi-restraints excluded: chain O residue 44 LEU Chi-restraints excluded: chain O residue 65 LEU Chi-restraints excluded: chain O residue 154 MET Chi-restraints excluded: chain P residue 44 LEU Chi-restraints excluded: chain Q residue 7 ASN Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 65 LEU Chi-restraints excluded: chain Q residue 154 MET Chi-restraints excluded: chain R residue 7 ASN Chi-restraints excluded: chain R residue 44 LEU Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain S residue 7 ASN Chi-restraints excluded: chain S residue 33 MET Chi-restraints excluded: chain S residue 44 LEU Chi-restraints excluded: chain T residue 7 ASN Chi-restraints excluded: chain T residue 44 LEU Chi-restraints excluded: chain V residue 44 LEU Chi-restraints excluded: chain W residue 7 ASN Chi-restraints excluded: chain W residue 44 LEU Chi-restraints excluded: chain W residue 65 LEU Chi-restraints excluded: chain X residue 7 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 0.0170 chunk 344 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 298 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 324 optimal weight: 9.9990 chunk 135 optimal weight: 0.9980 chunk 332 optimal weight: 6.9990 chunk 41 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** U 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 ASN ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 7 ASN E 7 ASN ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 7 ASN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 ASN J 7 ASN ** K 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 7 ASN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 7 ASN ** T 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 7 ASN ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 7 ASN ** X 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4779 r_free = 0.4779 target = 0.278973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4715 r_free = 0.4715 target = 0.271608 restraints weight = 242328.579| |-----------------------------------------------------------------------------| r_work (start): 0.4667 rms_B_bonded: 3.88 r_work: 0.4401 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.4401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1165 moved from start: 0.6344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.193 33912 Z= 0.411 Angle : 1.419 59.200 45792 Z= 0.882 Chirality : 0.044 0.638 4896 Planarity : 0.008 0.197 6024 Dihedral : 4.192 19.825 4464 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.58 % Allowed : 13.97 % Favored : 84.45 % Cbeta Deviations : 0.20 % 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: 3.25 (0.13), residues: 4080 helix: 3.01 (0.09), residues: 3168 sheet: None (None), residues: 0 loop : -1.18 (0.22), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP V 89 HIS 0.005 0.001 HIS K 114 PHE 0.050 0.001 PHE K 51 TYR 0.065 0.002 TYR J 164 ARG 0.002 0.000 ARG E 39 =============================================================================== Job complete usr+sys time: 8155.50 seconds wall clock time: 147 minutes 42.26 seconds (8862.26 seconds total)