Starting phenix.real_space_refine (version: dev) on Sun Dec 18 15:48:49 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v66_31736/12_2022/7v66_31736.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v66_31736/12_2022/7v66_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_31736/12_2022/7v66_31736.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v66_31736/12_2022/7v66_31736.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v66_31736/12_2022/7v66_31736.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v66_31736/12_2022/7v66_31736.pdb" } resolution = 1.89 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 Convert atoms to be neutral 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 17.65, per 1000 atoms: 0.53 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: 13.92 Conformation dependent library (CDL) restraints added in 5.0 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: 0.85 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: 10.88 Time building geometry restraints manager: 14.96 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 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. 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: 2.480 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: 16.630 Check model and map are aligned: 0.540 Convert atoms to be neutral: 0.320 Process input model: 83.690 Find NCS groups from input model: 2.370 Set up NCS constraints: 0.300 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 117.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0515 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 : 1.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.91 % Favored : 98.04 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 *********************** 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 : 3.602 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 outliers start: 72 outliers final: 0 residues processed: 360 average time/residue: 1.0896 time to fit residues: 493.2685 Evaluate side-chains 240 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 3.785 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6361 ------------------------------------------------------------------------------- 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: 5.9990 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: 0.9990 chunk 123 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 238 optimal weight: 9.9990 chunk 370 optimal weight: 7.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 94 ASN U 108 GLN U 135 ASN U 150 ASN A 7 ASN A 19 GLN A 94 ASN A 108 GLN A 135 ASN A 150 ASN B 7 ASN B 10 GLN B 19 GLN B 94 ASN B 135 ASN B 150 ASN C 7 ASN C 19 GLN C 94 ASN C 108 GLN C 150 ASN ** D 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN D 94 ASN D 108 GLN D 150 ASN ** E 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN E 94 ASN E 108 GLN E 150 ASN F 7 ASN F 19 GLN F 94 ASN F 150 ASN ** G 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN G 94 ASN G 108 GLN G 150 ASN ** H 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN H 94 ASN H 108 GLN H 150 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN I 94 ASN I 108 GLN I 135 ASN I 150 ASN J 7 ASN J 19 GLN J 79 GLN J 94 ASN J 108 GLN J 150 ASN K 7 ASN K 19 GLN K 94 ASN K 108 GLN K 150 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN L 94 ASN L 108 GLN L 150 ASN ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN M 94 ASN M 108 GLN M 150 ASN N 7 ASN N 19 GLN N 94 ASN N 150 ASN ** O 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN O 94 ASN O 108 GLN O 150 ASN ** P 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN P 94 ASN P 108 GLN P 150 ASN ** Q 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN Q 94 ASN Q 108 GLN Q 150 ASN ** R 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 GLN R 94 ASN R 108 GLN R 135 ASN R 150 ASN S 7 ASN S 19 GLN S 94 ASN S 108 GLN S 150 ASN T 7 ASN T 19 GLN T 94 ASN T 108 GLN T 150 ASN ** V 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN V 94 ASN V 108 GLN V 150 ASN W 7 ASN W 19 GLN W 94 ASN W 108 GLN W 150 ASN ** X 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 GLN X 94 ASN X 108 GLN X 150 ASN Total number of N/Q/H flips: 110 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1019 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 33912 Z= 0.232 Angle : 0.663 9.344 45792 Z= 0.354 Chirality : 0.043 0.183 4896 Planarity : 0.004 0.025 6024 Dihedral : 4.785 21.074 4464 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.06 (0.13), residues: 4080 helix: 2.68 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : -0.85 (0.23), residues: 816 *********************** 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 303 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 204 time to evaluate : 3.686 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 outliers start: 99 outliers final: 14 residues processed: 269 average time/residue: 1.0235 time to fit residues: 353.3033 Evaluate side-chains 206 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 192 time to evaluate : 3.831 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 4 residues processed: 11 average time/residue: 0.4990 time to fit residues: 14.1263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 chunk 308 optimal weight: 0.8980 chunk 252 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 10.0000 chunk 400 optimal weight: 2.9990 chunk 330 optimal weight: 1.9990 chunk 368 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 297 optimal weight: 0.7980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 132 HIS U 135 ASN A 19 GLN A 135 ASN B 19 GLN B 108 GLN B 135 ASN D 7 ASN D 19 GLN E 3 GLN E 7 ASN E 19 GLN F 19 GLN F 108 GLN G 7 ASN G 19 GLN H 3 GLN H 7 ASN H 19 GLN I 3 GLN I 7 ASN I 19 GLN I 135 ASN K 19 GLN L 7 ASN L 19 GLN ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN N 108 GLN O 3 GLN O 7 ASN O 19 GLN P 7 ASN P 19 GLN Q 7 ASN R 7 ASN R 19 GLN R 135 ASN S 19 GLN V 7 ASN V 19 GLN W 19 GLN X 7 ASN Total number of N/Q/H flips: 43 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1220 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 33912 Z= 0.248 Angle : 0.685 8.129 45792 Z= 0.360 Chirality : 0.041 0.174 4896 Planarity : 0.004 0.031 6024 Dihedral : 4.975 21.341 4464 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 15.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 3.71 % 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: 2.58 (0.13), residues: 4080 helix: 2.43 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -1.08 (0.23), residues: 888 *********************** 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 347 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 218 time to evaluate : 4.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 129 outliers final: 49 residues processed: 267 average time/residue: 1.0261 time to fit residues: 350.2213 Evaluate side-chains 245 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 196 time to evaluate : 3.461 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 26 residues processed: 26 average time/residue: 0.5131 time to fit residues: 25.4224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 2.9990 chunk 192 optimal weight: 8.9990 chunk 41 optimal weight: 2.9990 chunk 177 optimal weight: 0.2980 chunk 249 optimal weight: 5.9990 chunk 372 optimal weight: 0.0040 chunk 394 optimal weight: 4.9990 chunk 194 optimal weight: 9.9990 chunk 353 optimal weight: 0.7980 chunk 106 optimal weight: 0.6980 overall best weight: 0.9594 ------------------------------------------------------------------------------- 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 A 19 GLN B 19 GLN C 19 GLN D 19 GLN E 3 GLN E 19 GLN F 19 GLN G 19 GLN H 3 GLN H 19 GLN I 3 GLN I 19 GLN J 19 GLN L 19 GLN ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN N 3 GLN N 19 GLN O 3 GLN O 19 GLN P 19 GLN Q 19 GLN R 3 GLN R 19 GLN S 19 GLN T 19 GLN V 19 GLN W 19 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1119 moved from start: 0.4445 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= 0.151 Angle : 0.537 11.184 45792 Z= 0.280 Chirality : 0.037 0.166 4896 Planarity : 0.003 0.035 6024 Dihedral : 4.435 20.518 4464 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 3.62 % 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: 3.59 (0.13), residues: 4080 helix: 3.12 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.63 (0.24), residues: 888 *********************** 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 342 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 216 time to evaluate : 3.614 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 outliers start: 126 outliers final: 48 residues processed: 266 average time/residue: 1.0422 time to fit residues: 355.1408 Evaluate side-chains 242 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 194 time to evaluate : 3.651 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 24 residues processed: 24 average time/residue: 0.4136 time to fit residues: 21.7847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 10.0000 chunk 223 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 293 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 chunk 336 optimal weight: 0.8980 chunk 272 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 201 optimal weight: 0.5980 chunk 353 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 overall best weight: 1.6582 ------------------------------------------------------------------------------- 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 19 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 137 GLN B 19 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 19 GLN ** N 70 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 19 GLN ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 GLN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 19 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 GLN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 19 GLN ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 GLN ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 132 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1279 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 33912 Z= 0.207 Angle : 0.636 11.835 45792 Z= 0.329 Chirality : 0.039 0.172 4896 Planarity : 0.004 0.037 6024 Dihedral : 4.565 18.957 4464 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer Outliers : 3.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.13), residues: 4080 helix: 2.76 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -0.97 (0.24), residues: 888 *********************** 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 293 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 175 time to evaluate : 4.160 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 outliers start: 118 outliers final: 54 residues processed: 242 average time/residue: 1.1333 time to fit residues: 346.1901 Evaluate side-chains 225 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 171 time to evaluate : 3.592 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 31 residues processed: 29 average time/residue: 0.6118 time to fit residues: 30.8658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 77 optimal weight: 8.9990 chunk 231 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 394 optimal weight: 0.8980 chunk 327 optimal weight: 5.9990 chunk 182 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- 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** U 137 GLN A 19 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 132 HIS B 19 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 132 HIS B 137 GLN C 19 GLN ** C 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 132 HIS C 137 GLN D 19 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 HIS D 137 GLN E 19 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS E 137 GLN F 19 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 132 HIS F 137 GLN G 19 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS G 137 GLN H 19 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 132 HIS H 137 GLN I 19 GLN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 132 HIS I 137 GLN J 19 GLN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 132 HIS J 137 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 132 HIS K 137 GLN L 19 GLN ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 132 HIS L 137 GLN ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 132 HIS M 137 GLN N 19 GLN ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 132 HIS N 137 GLN O 19 GLN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 132 HIS O 137 GLN P 19 GLN ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 132 HIS P 137 GLN Q 19 GLN ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 132 HIS Q 137 GLN R 3 GLN R 19 GLN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 132 HIS R 137 GLN S 19 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 132 HIS ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 137 GLN T 19 GLN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 132 HIS T 137 GLN V 19 GLN ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 132 HIS V 137 GLN W 19 GLN ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 132 HIS ** W 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 137 GLN X 19 GLN ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 GLN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1429 moved from start: 0.5688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 33912 Z= 0.256 Angle : 0.728 11.074 45792 Z= 0.381 Chirality : 0.042 0.176 4896 Planarity : 0.004 0.039 6024 Dihedral : 4.980 20.179 4464 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 20.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 2.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.13), residues: 4080 helix: 2.06 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -1.54 (0.22), residues: 888 *********************** 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 249 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 173 time to evaluate : 3.755 Fit side-chains revert: symmetry clash outliers start: 76 outliers final: 33 residues processed: 201 average time/residue: 1.2512 time to fit residues: 310.8235 Evaluate side-chains 204 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 171 time to evaluate : 3.599 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 12 residues processed: 21 average time/residue: 0.4052 time to fit residues: 19.0319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 224 optimal weight: 5.9990 chunk 288 optimal weight: 10.0000 chunk 223 optimal weight: 0.9980 chunk 332 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 393 optimal weight: 0.8980 chunk 246 optimal weight: 0.4980 chunk 239 optimal weight: 6.9990 chunk 181 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 19 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN D 19 GLN ** D 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN ** M 70 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 19 GLN ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 GLN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 19 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 GLN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 19 GLN ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1260 moved from start: 0.5539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 33912 Z= 0.155 Angle : 0.568 8.552 45792 Z= 0.290 Chirality : 0.037 0.161 4896 Planarity : 0.003 0.041 6024 Dihedral : 4.442 20.106 4464 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer Outliers : 1.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.13), residues: 4080 helix: 2.71 (0.08), residues: 3192 sheet: None (None), residues: 0 loop : -1.20 (0.22), residues: 888 *********************** 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 246 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 191 time to evaluate : 3.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 17 residues processed: 216 average time/residue: 1.2369 time to fit residues: 333.0214 Evaluate side-chains 206 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 189 time to evaluate : 3.682 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 5 average time/residue: 0.4175 time to fit residues: 8.9488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 chunk 234 optimal weight: 0.6980 chunk 118 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 250 optimal weight: 4.9990 chunk 267 optimal weight: 0.9990 chunk 194 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 309 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 19 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 19 GLN E 19 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN ** J 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 71 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 GLN ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 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 19 GLN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 19 GLN ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 71 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1527 moved from start: 0.6232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 33912 Z= 0.295 Angle : 0.782 11.069 45792 Z= 0.409 Chirality : 0.044 0.188 4896 Planarity : 0.005 0.043 6024 Dihedral : 5.092 19.924 4464 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 22.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.13), residues: 4080 helix: 1.71 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : -1.84 (0.22), residues: 888 *********************** 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 259 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 176 time to evaluate : 3.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 83 outliers final: 39 residues processed: 209 average time/residue: 1.2273 time to fit residues: 319.1942 Evaluate side-chains 215 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 176 time to evaluate : 3.580 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 13 residues processed: 26 average time/residue: 0.7416 time to fit residues: 32.1119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 10.0000 chunk 376 optimal weight: 3.9990 chunk 343 optimal weight: 4.9990 chunk 366 optimal weight: 8.9990 chunk 220 optimal weight: 0.5980 chunk 159 optimal weight: 7.9990 chunk 287 optimal weight: 0.0070 chunk 112 optimal weight: 1.9990 chunk 331 optimal weight: 0.6980 chunk 346 optimal weight: 2.9990 chunk 365 optimal weight: 2.9990 overall best weight: 1.2602 ------------------------------------------------------------------------------- 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 19 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN D 19 GLN E 19 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 19 GLN ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN J 71 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 71 GLN ** N 70 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 19 GLN ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 GLN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 19 GLN ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 GLN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 19 GLN ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 71 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1372 moved from start: 0.6145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 33912 Z= 0.194 Angle : 0.644 9.801 45792 Z= 0.332 Chirality : 0.039 0.167 4896 Planarity : 0.003 0.045 6024 Dihedral : 4.644 20.153 4464 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer Outliers : 1.98 % 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: 2.00 (0.13), residues: 4080 helix: 2.10 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : -1.65 (0.22), residues: 888 *********************** 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 252 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 183 time to evaluate : 3.663 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 69 outliers final: 35 residues processed: 196 average time/residue: 1.3248 time to fit residues: 320.7556 Evaluate side-chains 208 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 173 time to evaluate : 3.683 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 10 residues processed: 25 average time/residue: 1.3365 time to fit residues: 45.6934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 5.9990 chunk 387 optimal weight: 4.9990 chunk 236 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 269 optimal weight: 2.9990 chunk 406 optimal weight: 0.0270 chunk 374 optimal weight: 4.9990 chunk 323 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 250 optimal weight: 0.9990 chunk 198 optimal weight: 5.9990 overall best weight: 1.1642 ------------------------------------------------------------------------------- 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 19 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN E 19 GLN ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 19 GLN ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 19 GLN ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 GLN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN ** V 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1365 moved from start: 0.6283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 33912 Z= 0.190 Angle : 0.652 11.042 45792 Z= 0.333 Chirality : 0.039 0.166 4896 Planarity : 0.003 0.045 6024 Dihedral : 4.624 19.590 4464 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.13), residues: 4080 helix: 2.25 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : -1.58 (0.22), residues: 888 ********************** 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 243 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 194 time to evaluate : 3.928 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 outliers start: 49 outliers final: 27 residues processed: 206 average time/residue: 1.2610 time to fit residues: 321.0305 Evaluate side-chains 206 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 179 time to evaluate : 3.915 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 11 residues processed: 16 average time/residue: 1.1451 time to fit residues: 28.2175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 10.0000 chunk 344 optimal weight: 2.9990 chunk 99 optimal weight: 0.7980 chunk 298 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 324 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 chunk 332 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 59 optimal weight: 0.5980 overall best weight: 2.0584 ------------------------------------------------------------------------------- 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 19 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 19 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 GLN D 19 GLN ** E 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 19 GLN ** F 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 19 GLN ** G 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 19 GLN ** L 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 19 GLN ** M 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN ** O 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 19 GLN ** Q 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 19 GLN ** R 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 19 GLN ** T 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 19 GLN ** V 70 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** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4845 r_free = 0.4845 target = 0.287364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.280003 restraints weight = 249332.378| |-----------------------------------------------------------------------------| r_work (start): 0.4732 rms_B_bonded: 3.88 r_work: 0.4490 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.4490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1462 moved from start: 0.6633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 33912 Z= 0.250 Angle : 0.746 13.581 45792 Z= 0.385 Chirality : 0.042 0.173 4896 Planarity : 0.004 0.045 6024 Dihedral : 4.934 19.368 4464 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 22.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer Outliers : 1.55 % 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: 1.68 (0.13), residues: 4080 helix: 1.88 (0.09), residues: 3192 sheet: None (None), residues: 0 loop : -1.81 (0.22), residues: 888 =============================================================================== Job complete usr+sys time: 7573.10 seconds wall clock time: 137 minutes 28.47 seconds (8248.47 seconds total)